Progress 09/01/16 to 08/31/23
Outputs
Target Audience:The audience for the web site being developed for this project includes all members of the scientific and breeding communities interested in phenotypic information important for crop production and improvement. Results are shared with stakeholders at international, national, regional and local grower and industry meetings and at field days. Carrot is a crop that the general public is familiar with, so to better communicate with the general public, approx. 40 selected diverse carrots were grown and managed annually by undergraduate students at land grant universities including those in California, North Carolina, Washington and Wisconsin. This diversity garden approach is being the basis of interactive science outreach programs for K-12 students, undergraduate students, educational, and consumer groups in those states focusing on breeding, genetic diversity and nutrition. These diverse carrots are available to any field-based STEM and agricultural education institution. The FARM SMART program at the University of California Desert Research and Extension Center developed an agricultural literacy component that incorporates agriculture (in particular an expanded awareness of carrots and other vegetables) in presentations to school (K-12) and community (adult) outreach programs in carrot nutrition and production. Markers and sequence information for traits phenotyped are available to stakeholders through conferences, web-accessible databases, and publications. Genomic tools were demonstrated at workshops including hands-on training with presentations/webinars/videos developed to demonstrate approaches to marker discovery and marker assisted selection for breeders. The process of discovering plants with desirable carrot phenotypes was described to the scientific and breeding communities in publications, webinars, and at meetings to instruct them on critical aspects of both the phenotype screening process as well as best procedures to utilize breeding pools developed by this project, and to initiate the development of breeding pools on their own. On-farm testing was used to engage growers in participating in the evaluation of breeding pools, and for them to provide critical feedback to project scientists about the on-farm level performance of early-generation breeding stocks. Quality assessments of breeding pools by chefs and consumers also both inform those stakeholders about germplasm under development from this project, as well as provide feedback to project scientists about the progress achieved by this project in carrot improvement at the consumer level. Nutritional quality evaluations were presented at horticulture, nutritional science, and grower meetings and in scientific and popular publications. Student and general public outreach staff and scientists involved in the project receive and dispense information from on-farm and consumer stakeholder testing. Information on economic impacts of carrot traits is being presented at agricultural economics and agribusiness meetings and in scientific publications. Cost and return results and consumer demand results were presented to industry stakeholders in reports, websites and other media based tools. Issues briefs and short information bulletins are developed to inform carrot industry stakeholders on important opportunities about new varieties, and the general public were extensively used this information. Changes/Problems:Some data collection and outreach activities were delayed or omitted due to COVID restrictions. What opportunities for training and professional development has the project provided?Activities included grow-out of diverse carrot breeding stocks which are being distributed to stakeholders and general public contacts for project promotion and as educational materials. Stakeholder training for database use was initiated through communication with stakeholders seeking information on project results and discussions virtually at grower meetings. As part of the education activities, undergraduate students, graduate students and post-doctorates were trained in vegetable breeding, crop and seed production, disease protection and diagnosis, drought tolerance, stand establishment and bolting, genomic analysis and database development and econometrics of food demand as they participate in research projects critical to the project achieving the research goals. We also presented practical economic findings to undergraduate and graduate classes. FARM SMART Carrot Activities during the project included field production of colored carrots, field tours, and extensive exposure to elementary high school and college students, and members of the general public visiting and touring the Desert Research and Extension Center (DREC) near El Centro, CA. These activities included: Year 1 2016/2017 FARM SMART Carrot Activities, September 2016: California Ag in the Classroom Conference, Sacramento, CA. Led a carrot themed "Taste of California" table at the annual Ag in the Classroom conference dinner; introducing California educators from across the state to the colored carrot research taking place at the University of California, Desert Research and Extension Center. The dinner included a display on colored carrots, information on current research from Dr. Simon, information on the history of carrots, packets of carrot seeds to take back to their classrooms, colored carrot tastings, and lesson plan development specifically related to the research. Lesson plans included an emphasis on carrots and carrot diversity, and health benefits of disease-preventive pigments that give plants their distinctive colors. Participants left with a better understanding of the history of carrots and methods to incorporate carrots into their varying grade levels and educational institutions. Conference attendance was over 300 educators. In January-February, 2017: FARM SMART Winter Visitor Program - Provided field tours to close to 1000 participants from across the United States and Canada and included hands-on activities such as carrot harvesting, carrot recipe demonstration, and carrot sampling. FARM SMART was able to introduce the research and history of the colored carrots, offer harvesting of colored and traditional carrots, and provide nutritional values of the different colored carrots. Participants were also introduced to carrot harvesting methods and carrot production facts for Imperial County and California. In March-April, 2017: FARM SMART K-12 Field Trips - Provided carrot education through outreach to over 7500 participants in our K-12 field trip program. Students who attended a FARM SMART program from March to April had the opportunity to learn what carrots need to grow, the history of colored carrots, the nutritional value, as well as an opportunity to harvest their own traditional and organic carrots. Teachers were also given resources to further enrich their lesson plans to include carrots. In April-May, 2017: Imperial Valley College Ag Students - Provided carrot research information and introduced colored carrots to over 30 visiting community college agriculture students. Students had the opportunity to harvest traditional and colored carrots from the FARM SMART garden and experiment with colored carrot recipes. Year 2 FARM SMART Carrot Activities continued those initiated in year 1 of the project including field production of colored carrots, field tours, and extensive exposure to elementary high school and college students, and members of the general public visiting and touring the Desert Research and Extension Center near El Centro, CA. Year 3 FARM SMART Carrot Activities continued those initiated in years 1-2 of the project including field production of colored carrots, field tours, and extensive exposure to elementary high school and college students, and members of the general public visiting and touring the Desert Research and Extension Center near El Centro, CA. Year 4 FARM SMART Carrot Activities continued those initiated in previous years of the project including field production of colored carrots, field tours, and extensive exposure to elementary high school and college students, and members of the general public visiting and touring the Desert Research and Extension Center near El Centro, CA. In addition to these activities at DREC, a short Carrot Research Video is being developed. Since the coronavirus (COVID-19) pandemic and quarantine began, it has been important to add more video content to the program of services offered to local educators, students and our community. Tracking of video content access has indicate the ability to reach a wider audience and reach beyond the local community. In a remote world, video allows us to meet, to educated and to provide services. The recorded short video gives an overview of colored carrot research at Desert REC. The video is still in the editing stage, but includes viewing the variety of colored carrots, observing the harvest, and sorting process of colored carrots for research and gives nutritional content information. Distribution of the short video includes social media sites, DREC website and linked to Farm Smart newsletter. We expect to distribute this video digitally to local teachers as well as show the video during field tours where we cover carrot research at Desert REC. In Davis, CA, the project allowed Student Farm undergraduate interns, volunteers and student employees to participate in carrot production in Student Farm Market Garden and Ecological Garden teaching areas. This numbers 50-60 students each academic quarter. Students involved in our undergraduate courses PLS 193 and PLS 49 also learn about how carrots are grown and have the opportunity to harvest and consume fresh product. This numbers roughly 25-30 students per quarter. In addition during spring quarter we hosted 2000 school children and roughly 200 chaperones on this site before COVID curtailed student visits. Roughly half of those students and their chaperones learn about and/or harvest and eat carrots during their educational activities. How have the results been disseminated to communities of interest?Educational events and conference presentations included: First PAG Workshop on Apiaceae; January, 2020: Simon, P.W. S.L. Ellison, D.Senalik. 2020. Trait Identification and Genomic Database Development for Carrot (Daucus carota) Improvement. XXVII Plant & Animal Genome, January 13, 2020, San Diego, California, USA. Iorizzo, M., H. Bostan, S.L. Ellison, D. Senalik, P.W. Simon. J.Curaba. 2020. Improved Hybrid de novo Genome Assembly, Gene Prediction and Annotation of Carrot (Daucus carota). XXVII Plant & Animal Genome, January 13, 2020, San Diego, California, USA. S.L. Ellison, Simon, P.W., D. Senalik. 2020. Genome-Wide Association Analysis of Carotenoids in Carrot. XXVII Plant & Animal Genome, January 13, 2020, San Diego, California, USA Van Deynze, A.. Hill, TA, Garcia-Llanos, A., Roberts, P., Mathews, W. Ellison, S., Senalik, D., Loarca, J. and Simon, P. 2020. Characterization of the Tendency for Bolting among Carrot Germplasm Accessions. XXVII Plant & Animal Genome, January 13, 2020, San Diego, California, USA. Macko-Podgorni, A., K. Stelmach, K. Kwolek, D. Grzebelus. 2020. Abundance and Insertional Polymorphism of Carrot Mites and Demography of Daucus carota. XXVII Plant & Animal Genome, January 13, 2020, San Diego, California, USA. 2nd Apiaceae Workshop at PAG Jan. 17, 2022, San Diego, California, USA Iorizzo, M. et al. Development of a genetic framework to regulate anthocyanin accumulation in carrot for improving its application in the food colorant industry Coe, K. et al. The influence of the Or gene on carotenoid accumulation in orange carrots Macko-Podgorni, A. et al. Diverse and Mobile - Eccdna-Based Identification of Carrot Low-Copy LTR Retrotransposons Active in Callus Cultures Meyer, C. et al. An efficient system for producing transgene-free gene edited carrot plants Brainard, S. et al. Dissecting the genetic basis of root shape in carrot with digital imaging Van Deynze, A. Genomic analysis of bolting in carrot Other educational events and conference presentations throughout the duration of the project: March 19, 2017, SCRI Advisory Panel meeting, Bakersfield, CA March 20, 2017, SCRI poster and oral presentations, International Carrot Conference, Bakersfield, CA August 30, 2017, SCRI PD meeting, Traverse City, MI January 13-17, 2018, poster presentation at Plant and Animal Genome Meeting, San Diego June 11, 2018, oral presentation (S. Tanumihardjo), FASEB Retinoids Conference, Steamboat Springs, CO June 19, 2018, oral presentation (S. Tanumihardjo), Gordon Research Conference on Carotenoids, Newry, ME July 31 - August 3, 2018, poster presentation (P. Simon) at ASHS, Washington, DC August 21-23 2018, poster and oral presentation (M. Iorizzo) oral presentation of population structure and potential core collection strategies (S. Ellison), poster (P. Simon) International Carrot Conference, Madison WI. September 20, 2018, oral presentations at International Apiaceae Meeting (P. Simon, M. Iorizzo, S. Ellison), September 19-22, 2018, Krakow, Poland January 12-16, 2019, poster presentation (K. Coe) at Plant and Animal Genome Meeting, San Diego February 18, 2019, Dept. Genetics Seminar series, (M. Iorizzo) NCSU Raleigh, NC March 12, 2019, oral presentations (P Roberts; P Simon; L. DuToit), California Carrot Symposium, Bakersfield, CA; hosted by California Fresh Carrot Advisory Board for carrot researchers, producers and processors. June 3-6, 2019, oral presentation (P. Simon) at CROPS, Huntsville, AL June 11, 2019, oral presentation (H. Bostan) at PHHI Seminar Series, RCCC-NCRC Kannapolis, NC July 22-25, 2019, oral presentation (P. Simon) at ASHS, Las Vegas, NV Van Deynze, A. 2020. Seed Biotechnology Center update. California Seed Association annual meeting. March 6, 2020, Carlsbad, CA. Nov. 20-21, 2019, oral presentation (L. du Toit). Carrot cavity spot. Pacific Northwest Vegetable Assoc. Annual Convention & Trade Show, Kennewick, WA. (200 people) February 24, 2020, oral presentation (H. Lee; R. Goldstein; D. A. Sumner), at UC Davis, CA; a seminar for undergraduates August 10, 2020, oral presentation (H. Lee; R. Goldstein; D. A. Sumner), 2020 Virtual Meeting, Agricultural & Applied Economics Association. February 18, 2021, Demand for Food Attributes during COVID-19: Evidence from a Large Sample of US Carrot Buyers. Agricultural Economics Workshop. Agricultural and Resource Economics, University of California, Davis, CA August 20-21, 2021, Demand for Organic, Convenience Foods: A Large Online Survey from U.S. Carrot Buyers during COVID-19. the 10th Congress of the Asian Association of Environmental and Resource Economics, Asian Association of Environmental and Resource Economics, Seoul, South Korea August 2021, oral presentation (Loarca, Jenyne) on "Identifying Phenotype and Genetic Markers in Diverse Carrot Germplasm (Daucus carota subsp. sativus) To Deliver Improved Stand Establishment to Growers". Invited Speaker, Midwest Population Genetics Conference, UW Madison September 2021, oral presentation (Loarca, Jenyne) on "Leveraging a Carrot Diversity Panel: Identification of Phenotypes and Genetic Markers to Deliver Improved Stand Establishment to Growers". Invited Speaker, JF Crow Institute Seminar Series, UW Madison October 2021 oral presentation (Loarca, Jenyne) on "Genome-Wide Association Analysis with a Carrot Diversity Panel". Plant Genetics Undergraduate Course, University of California Davis December 2021, oral presentation (Loarca, Jenyne) on "Why Genetic Diversity Matters in Science - A Case Study with 700 Carrot Cultivars" Participatory Learning And Teaching Organization (PLATO): UW Madison Division of Continuing Studie. March 20-21, 2021, oral presentation (L.J. duToit) Screening carrot germplasm for resistance to cavity spot and bacterial blight. Research presentation update at Carrot Research Symposium, CA Fresh Carrot Advisory Board, virtual because of COVID-19. (59 people) ?Stakeholder events included: March 19, 2017, SCRI Advisory Panel meeting, Bakersfield, CA March 20. 2018, SCRI Advisory Panel meeting, Bakersfield, CA Feb. 27- March 1, 2019, carrot harvest, PI collection demonstration and breeding pool development and March 5, hybrid trials (P. Simon, M. Colley, J. Sidhu, A. Van Deynze) at Desert Research and Extension Center, El Centro, CA March 12, 2019, SCRI Advisory Panel meeting, Bakersfield, CA October 8, 2019, carrot harvest and nematode evaluation (P. Roberts, P. Simon) at University of California Kearney Agricultural Center, Parlier, CA Various dates, in vitro cavity spot inoculation protocol evaluation (L. du Toit) at Washington State University Mount Vernon, WA; carrot phenotyping for carotenoids, flavor, root shape and top size; breeding pool development (P. Simon, S. Ellison) at the USDA, ARS Department of Horticulture, University of Wisconsin, Madison, WI March 4 - 13, 2020, carrot harvest, PI collection evaluation and breeding pool development; and March 10 hybrid trials (P. Simon, M. Colley, J. Sidhu) at Desert Research and Extension Center, El Centro, CA January to March 2020, FARM SMART delivered carrot info/curriculum and harvested carrots (876 participants including kids, youth and adults). We also reached 15 teachers with carrot information and seed distribution. January, 2021 - Stakeholder advisory panel zoom meetings were held to report project progress and seek input March 22, 2021, oral presentations (P Roberts; P Simon; L. DuToit), California Carrot Symposium (Virtual), Bakersfield, CA; hosted by California Fresh Carrot Advisory Board for carrot researchers, producers and processors. October, 2021 - A survey was sent to stakeholders to gather additional input from them on current and future project direction including input on traits, databases, and approaches for delivering data and germplasm to stakeholders What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Carrots are a high-value crop worth $750M to US growers and the largest crop source of vitamin A in the US diet. Approx. 86% of the carrot production area and 94% of crop value is in fresh market carrots, with 85% of fresh market carrots grown in CA. WA and WI are the largest producers of carrots for processing. Nation-wide expansion of small-scale local vegetable markets has increased carrot production, and this trend contributes to the growing organic market share of the US production, estimated at 14%. Conventional and organic growers, processers, and seed industry breeders and their marker lab scientists were surveyed in 2014 and convened in 2015 to identify top traits deemed important for improving productivity, expanding product development, and strengthening economic viability. Based on this stakeholder input, this project addresses the critical needs of the carrot industry, to identify novel sources of genes for carrot improvement in future carrot breeding. We are identifying genes for improved resistance to diseases and pests, reliable crop production and tolerance to environmental stress, and enhanced consumer quality. To complement this gene discovery, we are developing a carrot database to provide breeders and other researchers with a platform to deliver information for carrot breeders to tap into the breadth of carrot genetic diversity; and establish a science-based foundation for long-term carrot improvement. Nutritional profiles and consumer attitudes toward carrots are being developed, the economic value of new breeding traits is being measured, and students are being educated. These new gene sources will be used in future breeding efforts to develop crop germplasm that requires less pesticide use and increased farm value; novel, high-value carrot products; and improved flavor and nutritional value for consumers. Long-term impacts are expected to increase crop consumption, benefit the environment and human health, and develop crop improvement strategies applicable to other crops. Project Objectives and Annual Progress: 1 Phenotype diverse carrot germplasm and breeding stocks to discover and describe previously uncharacterized variation for important traits. Variation in key traits identified by stakeholders was phenotyped in a carrot germplasm collection that includes 694 diverse open-pollinated carrots from the USDA-NPGS and 70 public inbreds, referred to as the "PI collection". Screening to identify M. incognita nematode resistant entries was completed and several lines were confirmed to be resistant to M. javanica, M. arenaria and M. hapla. At the cavity spot (Pythium violoae and P. sulcatum) field nursery site established at WSU in 2019, a subset of 57 PI lines was evaluated, of which 2 had less severe cavity spot symptoms than Purple Haze, the resistant check, and 4 had symptoms more severe than Purple Haze but less severe than Propeel, the next more resistant commercial cultivar. In WI, ~39 PIs were confirmed to have superior Alternaria leaf blight resistance. Bolting was evaluated in summer and winter crops where ~30% of PIs bolted at time of harvest, with high concordance between lines across locations and years. Inheritance is complex with epistasis and genotype x environment interaction. Drought tolerance field and greenhouse phenotype data collected at UCRiverside were analyzed and prepared for GWAS, and a subset of most tolerant lines was increased for continue testing. Three years of data have been taken on early establishment, height, and final stand establishment on the PI collection in WI. An association analysis has been conducted and a manuscript has been prepared. Mapping populations were created and F2 families were phenotyped for linkage mapping of stand establishment. Four years of data on the PI collection has been taken on harsh flavor and sweetness, carotenoids, anthocyanins, total dissolved solids, sugars, ionomic profile, and root shape. Data for all traits are being used for GWAS analysis. The carotenoid study has been published, the total dissolved solids has been published in thesis form and the others are in preparation for publication. 2 - Develop an expanded carrot genomic database for breeders to catalogue genomic and phenotypic variation and track genes underlying important traits: We developed an improved genome assembly, gene annotation of carrot DH1. The new assembly v3, covers 440 Mb, all assembled into 9 chromosomes, with a contig N50 >6Mb. Compared with the previous assembly (v2), the v3 assembly include about 11% (54 Mb) new sequences, >21% (>100 Mb) extra sequence anchored to chromosome level, representing >189 fold increase in contig N50. In total, 36,216 genes were predicted, with >4,000 new gene models as compared to the previous gene prediction. Also, initiated efforts to sequence the genome of a white and dark purple genotypes using PacBio HiFi technology. Data from several QTL, transcriptome, gene annotation and functional analysis studies targeting anthocyanin genetics and genes in carrot, and anchored all these QTLs and genes to the v2 and v3 genomes. These allowed identification of novel candidate genes controlling carotenoids, anthocyanin biosynthesis in carrot root and petiole, and genes associated with carrot domestication and improvement. 3 - Initiate development and evaluation of breeding pools from diverse germplasm and breeding stocks, and detailed quality analysis: Roots with elite nematode, Alternaria and cavity spot resistance, drought tolerance, low-bolting incidence, large tops, vigorous stand establishment, excellent flavor, improved nutritional value and unique color were advanced to develop breeding pools. To advance studies on bioefficacy evaluation of carrot nutritional quality, two gerbil and one chicken nutrition evaluation studies were completed. Carrot was found to be effective in improving animal nutrition in these studies. 4 - Evaluate the economic impacts of new carrot traits on grower practices and costs, and consumer decisions: Large U.S. surveys (about 400,000 consumer responses) of self-reported carrot buyers were conducted to estimate expressed willingness to pay for carrot traits from 2019 to 20210. Specifically, we compared expressed willingness to pay for organic baby carrots, conventional baby carrots, organic full-sized carrots, and conventional full-sized carrots. Consumers' median willingness to pay is about $0.7 per pound for the organic trait. The results are robust across multiple surveys conducted from 2019 to 2021. The results document that consumers are willing to pay for observable and claimed trait differences when selecting carrot products. The willingness to pay for traits did not differ across rounds of the survey from before the pandemic and as the pandemic evolved.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Shelby L. Ellison, Claire H. Luby, Keo E. Corak, Kevin M. Coe, Douglas Senalik, Massimo Iorizzo, Irwin L. Goldman, Philipp W. Simon and Julie C. Dawson
GENETICS Early online October 23, 2018; https://doi.org/10.1534/genetics.118.301299
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Iorizzo M., Cavagnaro P.F., Bostan H., Zhao Y., Zhang J. and Simon PW. 2018. A cluster of MYB transcription factors regulates anthocyanin biosynthesis in carrot (Daucus carota L.) root and petiole. Frontier in Plant Science, 9:1927
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Titcomb, T., M. Kaeppler, J. Shannon, P.W. Simon, and S. Tanumihardjo. 2019. Carrot leaves maintain liver vitamin A concentrations in Mongolian gerbils regardless of the alpha- to beta-carotene ratio when beta-carotene equivalents are equalized. J. Nutrit. 149:951-958.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Titcomb T.J., M.S. Kaeppler, M.E. Cook, P.W. Simon, S.A. Tanumihardjo. 2019.Carrot leaves improve color and xanthophyll content of egg yolk in laying hens but are not as effective as commercially available marigold fortificant. Poult. Sci.; doi: 10.3382/ps/pez257.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Sheftel , J., M. Sowa, L. Mourao, L.T. Zou�, C.R. Davis, P.W. Simon, and S.A. Tanumihardjo. 2019. Total adipose retinol concentrations are correlated with total liver retinol concentrations in male Mongolian gerbils, but only partially explained by chylomicron deposition assessed with total ?-retinol. Curr. Dev. Nutr. 3:nzy096.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Bannoud F., Ellison S., Paolinelli M., Horejsi T., Senalik D., Fanzone M., Iorizzo M., Simon P. (2019) Dissecting the genetic control of root and leaf tissue-specific anthocyanin pigmentation in carrot (Daucus carota L.) Theor Appl Genet 132: 2485
- Type:
Book Chapters
Status:
Published
Year Published:
2019
Citation:
Simon P.W., Geoffriau E., Ellison S., Iorizzo M. 2019. Carrot Carotenoid Genetics and Genomics. In: Simon P., Iorizzo M., Grzebelus D., Baranski R. (eds) The Carrot Genome. Compendium of Plant Genomes. Springer International Publishing
- Type:
Book Chapters
Status:
Published
Year Published:
2019
Citation:
Ellison, S. 2019. Carrot Domestication. In: Simon P., Iorizzo M., Grzebelus D., Baranski R. (eds) The Carrot Genome. Compendium of Plant Genomes. Springer International Publishing.
- Type:
Book Chapters
Status:
Published
Year Published:
2019
Citation:
Iorizzo M., Ellison S., Pottorff M., Cavagnaro P.F. 2019. Carrot Molecular Genetics and Mapping. In: Simon P., Iorizzo M., Grzebelus D., Baranski R. (eds) The Carrot Genome. Compendium of Plant Genomes. Springer International Publishing.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Iorizzo M., Curaba J., Pottorff M., Ferruzzi G.M., Simon. P. and Cavagnaro P. 2020. Carrot anthocyanins genetics and genomics: status and perspectives to improve its application for the food colorant industry. Genes, 11: 906
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Curaba J., Bostan H., Cavagnaro P., Senalik D., Mengist M.F., Zhao Y., Simon P. and M. Iorizzo. 2020. Identification of an SCPL gene Controlling Anthocyanin Acylation in Carrot (Daucus carota L.) Root. Frontiers in Plant Science, 10:1770
- Type:
Book Chapters
Status:
Published
Year Published:
2019
Citation:
Cavagnaro P.F., and Iorizzo M. 2019. Carrot Anthocyanin Diversity, Genetics and Genomics. In: Simon P., Iorizzo M., Grzebelus D., Baranski R. (eds) The Carrot Genome. Compendium of Plant Genomes. Springer International Publishing.
- Type:
Book Chapters
Status:
Published
Year Published:
2019
Citation:
Iorizzo M., Macko-Podg�rni A., Senalik D., Van Deynze A., and Simon P.W. 2019. The Carrot Nuclear Genome and Comparative Analysis. In: Simon P., Iorizzo M., Grzebelus D., Baranski R. (eds) The Carrot Genome. Compendium of Plant Genomes. Springer International Publishing.
- Type:
Book Chapters
Status:
Published
Year Published:
2019
Citation:
Bostan H., Senalik D., Simon PW, and Iorizzo M. 2019. Carrot Genetics, Omics and Breeding Toolbox. In: Simon P., Iorizzo M., Grzebelus D., Baranski R. (eds) The Carrot Genome. Compendium of Plant Genomes. Springer International Publishing.
- Type:
Books
Status:
Published
Year Published:
2019
Citation:
Simon P., Iorizzo M., Grzebelus D., Baranski R. (eds) The Carrot Genome. Compendium of Plant Genomes. Springer International Publishing.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Iorizzo M., M. Pottorff, H. Bostan, S.L. Ellison, P.F. Cavagnaro, D. Senalik, D.M. Spooner and P.W. Simon. 2019. Recent advance in carrot genomics. ISHS Acta Horticulturae 1264: Proceedings of the II International Symposium on Carrot and Other Apiaceae. 10.17660/ActaHortic.2019.1264.9
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Cavagnaro P.F., F. Bannoud, M. Iorizzo, D. Senalik, S.L. Ellison and P.W. Simon. 2019. Carrot anthocyanins: nutrition, diversity and genetics. ISHS Acta Horticulturae 1264: International Symposium on Carrot and Other Apiaceae. 10.17660/ActaHortic.2019.1264.11
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Sowa, M., L. Mourao, J. Sheftel, M. Kaeppler, G. Simons, C. Davis, P.W. Simon, S. Tanumihardjo. Overlapping Vitamin A Interventions with Provitamin A Carotenoids and Preformed Vitamin A Fortificant Cause High Liver Retinol Stores in Male Mongolian Gerbils. Journal of Nutrition 150: 29122923. 2020. https://doi.org/10.1093/jn/nxaa142
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
du Toit, L., and Derie, M. 2020. Spot-on research. Establishing a carrot cavity spot nursery at Washington State University. Carrot Country, Spring 2020:4-9.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2020
Citation:
Su Liu, 2020. Improved Hybrid de novo Genome Assembly, Resistance Gene Prediction and Annotation of Carrot (Daucus carota). MS thesis. North Carolina State University, Raleigh.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2020
Citation:
Coe. Kevin. 2020. Genetic analysis of domestication and carotenoid accumulation in carrot (Daucus carota L.) and the polyploidization of switchgrass (Panicum virgatum L.). Ph.D thesis. University of Wisconsin-Madison
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2020
Citation:
Yildiz, Gunay. 2020. Genome Wide Association Analysis of Free Sugars in the Storage Roots of a Diverse Collection of Carrot (Daucus carota L.). MS thesis. University of Wisconsin-Madison.
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Bannoud F., Carvajal S., Ellison S., D. Senalik, Talquenca S.G., Iorizzo M., Simon P. and P.F. Cavagnaro. 2021. Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in carrot root phloem. Genes 2021, 12, 1464.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Iorizzo M., Mengit M.F., Bostan H., Curaba J., M. Pottorff. From genome to genes and DNA markers to improve agronomic performance and quality of fruit and vegetables crops. Genetyka Aplikacyjna Ro?lin XXI, September 22-24, 2021, Warsaw, Poland
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Iorizzo M. Development of a genetic framework to improve the efficiency of bioactive stability and delivery from carrot and blueberry. Webinar: Current status of Phyomediomics and Nutriomics. Organized by the Korean Academy of Science and Technology (KAST), December 15, 2020.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Rolling WR, Senalik D, Iorizzo M, Ellison S, Van Deynze A, Simon PW. CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota). Database (Oxford). 2022 Sep 7; 2022:baac079. doi: 10.1093/database/baac079. PMID: 36069936; PMCID: PMC9450951.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Coe, K., Bostan, H., Rolling, W., Turner-Hissong, S., Macko-Podgorni, A., Senalik, D., Liu, S., Seth, R., Curaba, J., Mengist, M.F., Grzebelus, D., Van Deynze, A., Dawson, J., Ellison, S., Simon, P. W., Iorizzo, M. (2023) Population genomics identifies genetic signatures of carrot domestication and improvement and uncovers the origin of high-carotenoid orange carrots. Nature Plants (2023). https://doi.org/10.1038/s41477-023-01526-6
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Sumner, Daniel A. 2021. "Impact of COVID-19 and the Lockdowns on Labor-Intensive Produce Markets, with Implication for Hired Farm Labor" Choices. Quarter 3. Available online: https://www.choicesmagazine.org/choices-magazine/theme-articles/agricultural-market-response-to-covid-19/impact-of-covid-19-and-the-lockdowns-on-labor-intensive-produce-markets-with-implication-for-hired-farm-labor
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Coe, K., S. Ellison, D. Senalik, J. Dawson, P.W. Simon. The influence of the Or and Carotene Hydroxylase genes on carotenoid accumulation in orange carrots [Daucus carota (L.)]. Theor. Applied Genet. 134: 3351-62. 2021. DOI: 10.1007/s00122-021-03901-3
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2021
Citation:
Loarca, Jenyne. 2021. Identifying Phenotypes and Markers in Diverse Cultivated Carrot Germplasm (Daucus carota) to Deliver Improved Stand Establishment to Growers. PhD thesis. University of Wisconsin-Madison.
|
Progress 09/01/21 to 08/31/22
Outputs
Target Audience:The audience for this project includes all members of the scientific and breeding communities interested in phenotypic information important for the carrot crop production and improvement. Results are shared with stakeholders at international, national, regional and local grower and industry meetings and at field days. Markers and sequence information for traits phenotyped are available to stakeholders through conferences, web-accessible databases, and publications.The audience for this project includes all members of the scientific and breeding communities interested in phenotypic information important for the carrot crop production and improvement. Results are shared with stakeholders at international, national, regional and local grower and industry meetings and at field days. Markers and sequence information for traits phenotyped are available to stakeholders through conferences, web-accessible databases, and publications. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Diverse carrot breeding stocks were distributed to stakeholders and general public contacts for project promotion and as educational materials. How have the results been disseminated to communities of interest?2nd Apiaceae Workshop at PAG Jan. 17, 2022, San Diego, California, USA Iorizzo, M. et al. Development of a genetic framework to regulate anthocyanin accumulation in carrot for improving its application in the food colorant industry Coe, K. et al. The influence of the Or gene on carotenoid accumulation in orange carrots Macko-Podgorni, A. et al. Diverse and Mobile - Eccdna-Based Identification of Carrot Low-Copy LTR Retrotransposons Active in Callus Cultures Meyer, C. et al. An efficient system for producing transgene-free gene edited carrot plants Brainard, S. et al. Dissecting the genetic basis of root shape in carrot with digital imaging Van Deynze, A. Genomic analysis of bolting in carrot What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Carrots are a high-value crop worth $750M to US growers and the largest crop source of vitamin A in the US diet. Approx. 86% of the carrot production area and 94% of crop value is in fresh market carrots, with 85% of fresh market carrots grown in CA. WA and WI are the largest producers of carrots for processing. Nation-wide expansion of small-scale local vegetable markets has increased carrot production, and this trend contributes to the growing organic market share of the US production, estimated at 14%. Conventional and organic growers, processers, and seed industry breeders and their marker lab scientists were surveyed in 2014 and convened in 2015 to identify top traits deemed important for improving productivity, expanding product development, and strengthening economic viability. Based on this stakeholder input, this project addresses the critical needs of the carrot industry, to identify novel sources of genes for carrot improvement in future carrot breeding. We are identifying genes for improved resistance to diseases and pests, reliable crop production and tolerance to environmental stress, and enhanced consumer quality. To complement this gene discovery, we are developing a carrot database to provide breeders and other researchers with a platform to deliver information for carrot breeders to tap into the breadth of carrot genetic diversity; and establish a science-based foundation for long-term carrot improvement. Nutritional profiles and consumer attitudes toward carrots are being developed, the economic value of new breeding traits is being measured, and students are being educated. These new gene sources will be used in future breeding efforts to develop crop germplasm that requires less pesticide use and increased farm value; novel, high-value carrot products; and improved flavor and nutritional value for consumers. Long-term impacts are expected to increase crop consumption, benefit the environment and human health, and develop crop improvement strategies applicable to other crops. Project Objectives and Annual Progress: 1- Mapping populations for nematode, cavity spot, and Alternaria leaf blight resistance; stand establishment, early bolting. and drought tolerance; flavor, color and nutritional pigment composition were advanced. 2- The CarrotOmics database was published.. 3- Breeding pool populations were advanced and bioefficacy evaluations of carrot nutritional quality were completed 4 - Evaluation the economic impacts of new carrot traits on grower practices and costs, and consumer decisions were completed.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Rolling WR, Senalik D, Iorizzo M, Ellison S, Van Deynze A, Simon PW. CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota). Database (Oxford). 2022 Sep 7; 2022:baac079. doi: 10.1093/database/baac079. PMID: 36069936; PMCID: PMC9450951.
|
Progress 09/01/16 to 12/28/21
Outputs
Target Audience:The audience for the web site being developed for this project includes all members of the scientific and breeding communities interested in phenotypic information important for crop production and improvement. Results are shared with stakeholders at international, national, regional and local grower and industry meetings and at field days. Carrot is a crop that the general public is familiar with, so to better communicate with the general public, approx. 40 selected diverse carrots were grown and managed annually by undergraduate students at land grant universities including those in California, North Carolina, Washington and Wisconsin. This diversity garden approach is being the basis of interactive science outreach programs for K-12 students, undergraduate students, educational, and consumer groups in those states focusing on breeding, genetic diversity and nutrition. These diverse carrots are available to any field-based STEM and agricultural education institution. The FARM SMART program at the University of California Desert Research and Extension Center developed an agricultural literacy component that incorporates agriculture (in particular an expanded awareness of carrots and other vegetables) in presentations to school (K-12) and community (adult) outreach programs in carrot nutrition and production. Markers and sequence information for traits phenotyped are available to stakeholders through conferences, web-accessible databases, and publications. Genomic tools were demonstrated at workshops including hands-on training with presentations/webinars/videos developed to demonstrate approaches to marker discovery and marker assisted selection for breeders. The process of discovering plants with desirable carrot phenotypes was described to the scientific and breeding communities in publications, webinars, and at meetings to instruct them on critical aspects of both the phenotype screening process as well as best procedures to utilize breeding pools developed by this project, and to initiate the development of breeding pools on their own. On-farm testing was used to engage growers in participating in the evaluation of breeding pools, and for them to provide critical feedback to project scientists about the on-farm level performance of early-generation breeding stocks. Quality assessments of breeding pools by chefs and consumers also both inform those stakeholders about germplasm under development from this project, as well as provide feedback to project scientists about the progress achieved by this project in carrot improvement at the consumer level. Nutritional quality evaluations were presented at horticulture, nutritional science, and grower meetings and in scientific and popular publications. Student and general public outreach staff and scientists involved in the project receive and dispense information from on-farm and consumer stakeholder testing. Information on economic impacts of carrot traits is being presented at agricultural economics and agribusiness meetings and in scientific publications. Cost and return results and consumer demand results were presented to industry stakeholders in reports, websites and other media based tools. Issues briefs and short information bulletins are developed to inform carrot industry stakeholders on important opportunities about new varieties, and the general public were extensively used this information. Changes/Problems:Some data collection and outreach activities were delayed or omitted due to COVID restrictions. What opportunities for training and professional development has the project provided?Activities included grow-out of diverse carrot breeding stocks which are being distributed to stakeholders and general public contacts for project promotion and as educational materials. Stakeholder training for database use was initiated through communication with stakeholders seeking information on project results and discussions virtually at grower meetings. As part of the education activities, undergraduate students, graduate students and post-doctorates were trained in vegetable breeding, crop and seed production, disease protection and diagnosis, drought tolerance, stand establishment and bolting, genomic analysis and database development and econometrics of food demand as they participate in research projects critical to the project achieving the research goals. We also presented practical economic findings to undergraduate and graduate classes. FARM SMART Carrot Activities during the project included field production of colored carrots, field tours, and extensive exposure to elementary high school and college students, and members of the general public visiting and touring the Desert Research and Extension Center (DREC) near El Centro, CA. These activities included: Year 1 2016/2017 FARM SMART Carrot Activities, September 2016: California Ag in the Classroom Conference, Sacramento, CA. Led a carrot themed "Taste of California" table at the annual Ag in the Classroom conference dinner; introducing California educators from across the state to the colored carrot research taking place at the University of California, Desert Research and Extension Center. The dinner included a display on colored carrots, information on current research from Dr. Simon, information on the history of carrots, packets of carrot seeds to take back to their classrooms, colored carrot tastings, and lesson plan development specifically related to the research. Lesson plans included an emphasis on carrots and carrot diversity, and health benefits of disease-preventive pigments that give plants their distinctive colors. Participants left with a better understanding of the history of carrots and methods to incorporate carrots into their varying grade levels and educational institutions. Conference attendance was over 300 educators. In January-February, 2017: FARM SMART Winter Visitor Program - Provided field tours to close to 1000 participants from across the United States and Canada and included hands-on activities such as carrot harvesting, carrot recipe demonstration, and carrot sampling. FARM SMART was able to introduce the research and history of the colored carrots, offer harvesting of colored and traditional carrots, and provide nutritional values of the different colored carrots. Participants were also introduced to carrot harvesting methods and carrot production facts for Imperial County and California. In March-April, 2017: FARM SMART K-12 Field Trips - Provided carrot education through outreach to over 7500 participants in our K-12 field trip program. Students who attended a FARM SMART program from March to April had the opportunity to learn what carrots need to grow, the history of colored carrots, the nutritional value, as well as an opportunity to harvest their own traditional and organic carrots. Teachers were also given resources to further enrich their lesson plans to include carrots. In April-May, 2017: Imperial Valley College Ag Students - Provided carrot research information and introduced colored carrots to over 30 visiting community college agriculture students. Students had the opportunity to harvest traditional and colored carrots from the FARM SMART garden and experiment with colored carrot recipes. Year 2 FARM SMART Carrot Activities continued those initiated in year 1 of the project including field production of colored carrots, field tours, and extensive exposure to elementary high school and college students, and members of the general public visiting and touring the Desert Research and Extension Center near El Centro, CA. Year 3 FARM SMART Carrot Activities continued those initiated in years 1-2 of the project including field production of colored carrots, field tours, and extensive exposure to elementary high school and college students, and members of the general public visiting and touring the Desert Research and Extension Center near El Centro, CA. Year 4 FARM SMART Carrot Activities continued those initiated in previous years of the project including field production of colored carrots, field tours, and extensive exposure to elementary high school and college students, and members of the general public visiting and touring the Desert Research and Extension Center near El Centro, CA. In addition to these activities at DREC, a short Carrot Research Video is being developed. Since the coronavirus (COVID-19) pandemic and quarantine began, it has been important to add more video content to the program of services offered to local educators, students and our community. Tracking of video content access has indicate the ability to reach a wider audience and reach beyond the local community. In a remote world, video allows us to meet, to educated and to provide services. The recorded short video gives an overview of colored carrot research at Desert REC. The video is still in the editing stage, but includes viewing the variety of colored carrots, observing the harvest, and sorting process of colored carrots for research and gives nutritional content information. Distribution of the short video includes social media sites, DREC website and linked to Farm Smart newsletter. We expect to distribute this video digitally to local teachers as well as show the video during field tours where we cover carrot research at Desert REC. In Davis, CA, the project allowed Student Farm undergraduate interns, volunteers and student employees to participate in carrot production in Student Farm Market Garden and Ecological Garden teaching areas. This numbers 50-60 students each academic quarter. Students involved in our undergraduate courses PLS 193 and PLS 49 also learn about how carrots are grown and have the opportunity to harvest and consume fresh product. This numbers roughly 25-30 students per quarter. In addition during spring quarter we hosted 2000 school children and roughly 200 chaperones on this site before COVID curtailed student visits. Roughly half of those students and their chaperones learn about and/or harvest and eat carrots during their educational activities. How have the results been disseminated to communities of interest?Educational events and conference presentations included: First PAG Workshop on Apiaceae; January, 2020: Simon, P.W. S.L. Ellison, D.Senalik. 2020. Trait Identification and Genomic Database Development for Carrot (Daucus carota) Improvement. XXVII Plant & Animal Genome, January 13, 2020, San Diego, California, USA. Iorizzo, M., H. Bostan, S.L. Ellison, D. Senalik, P.W. Simon. J.Curaba. 2020. Improved Hybrid de novo Genome Assembly, Gene Prediction and Annotation of Carrot (Daucus carota). XXVII Plant & Animal Genome, January 13, 2020, San Diego, California, USA. S.L. Ellison, Simon, P.W., D. Senalik. 2020. Genome-Wide Association Analysis of Carotenoids in Carrot. XXVII Plant & Animal Genome, January 13, 2020, San Diego, California, USA Van Deynze, A.. Hill, TA, Garcia-Llanos, A., Roberts, P., Mathews, W. Ellison, S., Senalik, D., Loarca, J. and Simon, P. 2020. Characterization of the Tendency for Bolting among Carrot Germplasm Accessions. XXVII Plant & Animal Genome, January 13, 2020, San Diego, California, USA. Macko-Podgorni, A., K. Stelmach, K. Kwolek, D. Grzebelus. 2020. Abundance and Insertional Polymorphism of Carrot Mites and Demography of Daucus carota. XXVII Plant & Animal Genome, January 13, 2020, San Diego, California, USA. Other educational events and conference presentations throughout the duration of the project: March 19, 2017, SCRI Advisory Panel meeting, Bakersfield, CA March 20, 2017, SCRI poster and oral presentations, International Carrot Conference, Bakersfield, CA August 30, 2017, SCRI PD meeting, Traverse City, MI January 13-17, 2018, poster presentation at Plant and Animal Genome Meeting, San Diego June 11, 2018, oral presentation (S. Tanumihardjo), FASEB Retinoids Conference, Steamboat Springs, CO June 19, 2018, oral presentation (S. Tanumihardjo), Gordon Research Conference on Carotenoids, Newry, ME July 31 - August 3, 2018, poster presentation (P. Simon) at ASHS, Washington, DC August 21-23 2018, poster and oral presentation (M. Iorizzo) oral presentation of population structure and potential core collection strategies (S. Ellison), poster (P. Simon) International Carrot Conference, Madison WI. September 20, 2018, oral presentations at International Apiaceae Meeting (P. Simon, M. Iorizzo, S. Ellison), September 19-22, 2018, Krakow, Poland January 12-16, 2019, poster presentation (K. Coe) at Plant and Animal Genome Meeting, San Diego February 18, 2019, Dept. Genetics Seminar series, (M. Iorizzo) NCSU Raleigh, NC March 12, 2019, oral presentations (P Roberts; P Simon; L. DuToit), California Carrot Symposium, Bakersfield, CA; hosted by California Fresh Carrot Advisory Board for carrot researchers, producers and processors. June 3-6, 2019, oral presentation (P. Simon) at CROPS, Huntsville, AL June 11, 2019, oral presentation (H. Bostan) at PHHI Seminar Series, RCCC-NCRC Kannapolis, NC July 22-25, 2019, oral presentation (P. Simon) at ASHS, Las Vegas, NV Van Deynze, A. 2020. Seed Biotechnology Center update. California Seed Association annual meeting. March 6, 2020, Carlsbad, CA. Nov. 20-21, 2019, oral presentation (L. du Toit). Carrot cavity spot. Pacific Northwest Vegetable Assoc. Annual Convention & Trade Show, Kennewick, WA. (200 people) February 24, 2020, oral presentation (H. Lee; R. Goldstein; D. A. Sumner), at UC Davis, CA; a seminar for undergraduates August 10, 2020, oral presentation (H. Lee; R. Goldstein; D. A. Sumner), 2020 Virtual Meeting, Agricultural & Applied Economics Association. February 18, 2021, Demand for Food Attributes during COVID-19: Evidence from a Large Sample of US Carrot Buyers. Agricultural Economics Workshop. Agricultural and Resource Economics, University of California, Davis, CA August 20-21, 2021, Demand for Organic, Convenience Foods: A Large Online Survey from U.S. Carrot Buyers during COVID-19. the 10th Congress of the Asian Association of Environmental and Resource Economics, Asian Association of Environmental and Resource Economics, Seoul, South Korea August 2021, oral presentation (Loarca, Jenyne) on "Identifying Phenotype and Genetic Markers in Diverse Carrot Germplasm (Daucus carota subsp. sativus) To Deliver Improved Stand Establishment to Growers". Invited Speaker, Midwest Population Genetics Conference, UW Madison September 2021, oral presentation (Loarca, Jenyne) on "Leveraging a Carrot Diversity Panel: Identification of Phenotypes and Genetic Markers to Deliver Improved Stand Establishment to Growers". Invited Speaker, JF Crow Institute Seminar Series, UW Madison October 2021 oral presentation (Loarca, Jenyne) on "Genome-Wide Association Analysis with a Carrot Diversity Panel". Plant Genetics Undergraduate Course, University of California Davis December 2021, oral presentation (Loarca, Jenyne) on "Why Genetic Diversity Matters in Science - A Case Study with 700 Carrot Cultivars" Participatory Learning And Teaching Organization (PLATO): UW Madison Division of Continuing Studie. March 20-21, 2021, oral presentation (L.J. duToit) Screening carrot germplasm for resistance to cavity spot and bacterial blight. Research presentation update at Carrot Research Symposium, CA Fresh Carrot Advisory Board, virtual because of COVID-19. (59 people) Poster presentations Loarca, Jenyne, Dawson, Julie. and Simon, Philipp. "LeveragingDiverse Carrot Germplasm: Identification of Phenotypes and Genetic Markers to Deliver Improved Stand Establishment to Growers". Midwest Women in Science Conference, University of Chicago - September 2021. Loarca, Jenyne, Dawson, Julie. and Simon, Philipp. "LeveragingDiverse Carrot Germplasm to Deliver Improved Stand Establishment to Growers" UW Madison Plant Sciences Symposium. November 2021. Loarca, Jenyne. "Why Genetic Diversity Matters: A Study of 700 Carrot Tops". UW Madison Plant Sciences Symposium. November 2021. Lightning talk competitor. Stakeholder events included: March 19, 2017, SCRI Advisory Panel meeting, Bakersfield, CA March 20. 2018, SCRI Advisory Panel meeting, Bakersfield, CA Feb. 27- March 1, 2019, carrot harvest, PI collection demonstration and breeding pool development and March 5, hybrid trials (P. Simon, M. Colley, J. Sidhu, A. Van Deynze) at Desert Research and Extension Center, El Centro, CA March 12, 2019, SCRI Advisory Panel meeting, Bakersfield, CA October 8, 2019, carrot harvest and nematode evaluation (P. Roberts, P. Simon) at University of California Kearney Agricultural Center, Parlier, CA Various dates, in vitro cavity spot inoculation protocol evaluation (L. du Toit) at Washington State University Mount Vernon, WA; carrot phenotyping for carotenoids, flavor, root shape and top size; breeding pool development (P. Simon, S. Ellison) at the USDA, ARS Department of Horticulture, University of Wisconsin, Madison, WI March 4 - 13, 2020, carrot harvest, PI collection evaluation and breeding pool development; and March 10 hybrid trials (P. Simon, M. Colley, J. Sidhu) at Desert Research and Extension Center, El Centro, CA January to March 2020, FARM SMART delivered carrot info/curriculum and harvested carrots (876 participants including kids, youth and adults). We also reached 15 teachers with carrot information and seed distribution. January, 2021 - Stakeholder advisory panel zoom meetings were held to report project progress and seek input March 22, 2021, oral presentations (P Roberts; P Simon; L. DuToit), California Carrot Symposium (Virtual), Bakersfield, CA; hosted by California Fresh Carrot Advisory Board for carrot researchers, producers and processors. October, 2021 - A survey was sent to stakeholders to gather additional input from them on current and future project direction including input on traits, databases, and approaches for delivering data and germplasm to stakeholders What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Carrots are a high-value crop worth $750M to US growers and the largest crop source of vitamin A in the US diet. Approx. 86% of the carrot production area and 94% of crop value is in fresh market carrots, with 85% of fresh market carrots grown in CA. WA and WI are the largest producers of carrots for processing. Nation-wide expansion of small-scale local vegetable markets has increased carrot production, and this trend contributes to the growing organic market share of the US production, estimated at 14%. Conventional and organic growers, processers, and seed industry breeders and their marker lab scientists were surveyed in 2014 and convened in 2015 to identify top traits deemed important for improving productivity, expanding product development, and strengthening economic viability. Based on this stakeholder input, this project addresses the critical needs of the carrot industry, to identify novel sources of genes for carrot improvement in future carrot breeding. We are identifying genes for improved resistance to diseases and pests, reliable crop production and tolerance to environmental stress, and enhanced consumer quality. To complement this gene discovery, we are developing a carrot database to provide breeders and other researchers with a platform to deliver information for carrot breeders to tap into the breadth of carrot genetic diversity; and establish a science-based foundation for long-term carrot improvement. Nutritional profiles and consumer attitudes toward carrots are being developed, the economic value of new breeding traits is being measured, and students are being educated. These new gene sources will be used in future breeding efforts to develop crop germplasm that requires less pesticide use and increased farm value; novel, high-value carrot products; and improved flavor and nutritional value for consumers. Long-term impacts are expected to increase crop consumption, benefit the environment and human health, and develop crop improvement strategies applicable to other crops. Project Objectives and Annual Progress: 1 Phenotype diverse carrot germplasm and breeding stocks to discover and describe previously uncharacterized variation for important traits. Variation in key traits identified by stakeholders was phenotyped in a carrot germplasm collection that includes 694 diverse open-pollinated carrots from the USDA-NPGS and 70 public inbreds, referred to as the "PI collection". Screening to identify M. incognita nematode resistant entries was completed and several lines were confirmed to be resistant to M. javanica, M. arenaria and M. hapla. At the cavity spot (Pythium violoae and P. sulcatum) field nursery site established at WSU in 2019, a subset of 57 PI lines was evaluated, of which 2 had less severe cavity spot symptoms than Purple Haze, the resistant check, and 4 had symptoms more severe than Purple Haze but less severe than Propeel, the next more resistant commercial cultivar. In WI, ~39 PIs were confirmed to have superior Alternaria leaf blight resistance. Bolting was evaluated in summer and winter crops where ~30% of PIs bolted at time of harvest, with high concordance between lines across locations and years. Inheritance is complex with epistasis and genotype x environment interaction. Drought tolerance field and greenhouse phenotype data collected at UCRiverside were analyzed and prepared for GWAS, and a subset of most tolerant lines was increased for continue testing. Three years of data have been taken on early establishment, height, and final stand establishment on the PI collection in WI. An association analysis has been conducted and a manuscript has been prepared. Mapping populations were created and F2 families were phenotyped for linkage mapping of stand establishment. Four years of data on the PI collection has been taken on harsh flavor and sweetness, carotenoids, anthocyanins, total dissolved solids, sugars, ionomic profile, and root shape. Data for all traits are being used for GWAS analysis. The carotenoid study has been published, the total dissolved solids has been published in thesis form and the others are in preparation for publication. 2 - Develop an expanded carrot genomic database for breeders to catalogue genomic and phenotypic variation and track genes underlying important traits: We developed an improved genome assembly, gene annotation of carrot DH1. The new assembly v3, covers 440 Mb, all assembled into 9 chromosomes, with a contig N50 >6Mb. Compared with the previous assembly (v2), the v3 assembly include about 11% (54 Mb) new sequences, >21% (>100 Mb) extra sequence anchored to chromosome level, representing >189 fold increase in contig N50. In total, 36,216 genes were predicted, with >4,000 new gene models as compared to the previous gene prediction. Also, initiated efforts to sequence the genome of a white and dark purple genotypes using PacBio HiFi technology. Data from several QTL, transcriptome, gene annotation and functional analysis studies targeting anthocyanin genetics and genes in carrot, and anchored all these QTLs and genes to the v2 and v3 genomes. These allowed identification of novel candidate genes controlling carotenoids, anthocyanin biosynthesis in carrot root and petiole, and genes associated with carrot domestication and improvement. 3 - Initiate development and evaluation of breeding pools from diverse germplasm and breeding stocks, and detailed quality analysis: Roots with elite nematode, Alternaria and cavity spot resistance, drought tolerance, low-bolting incidence, large tops, vigorous stand establishment, excellent flavor, improved nutritional value and unique color were advanced to develop breeding pools. To advance studies on bioefficacy evaluation of carrot nutritional quality, two gerbil and one chicken nutrition evaluation studies were completed. Carrot was found to be effective in improving animal nutrition in these studies. 4 - Evaluate the economic impacts of new carrot traits on grower practices and costs, and consumer decisions: Large U.S. surveys (about 400,000 consumer responses) of self-reported carrot buyers were conducted to estimate expressed willingness to pay for carrot traits from 2019 to 20210. Specifically, we compared expressed willingness to pay for organic baby carrots, conventional baby carrots, organic full-sized carrots, and conventional full-sized carrots. Consumers' median willingness to pay is about $0.7 per pound for the organic trait. The results are robust across multiple surveys conducted from 2019 to 2021. The results document that consumers are willing to pay for observable and claimed trait differences when selecting carrot products. The willingness to pay for traits did not differ across rounds of the survey from before the pandemic and as the pandemic evolved.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Shelby L. Ellison, Claire H. Luby, Keo E. Corak, Kevin M. Coe, Douglas Senalik, Massimo Iorizzo, Irwin L. Goldman, Philipp W. Simon and Julie C. Dawson
GENETICS Early online October 23, 2018; https://doi.org/10.1534/genetics.118.301299
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Iorizzo M., Cavagnaro P.F., Bostan H., Zhao Y., Zhang J. and Simon PW. 2018. A cluster of MYB transcription factors regulates anthocyanin biosynthesis in carrot (Daucus carota L.) root and petiole. Frontier in Plant Science, 9:1927
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Titcomb, T., M. Kaeppler, J. Shannon, P.W. Simon, and S. Tanumihardjo. 2019. Carrot leaves maintain liver vitamin A concentrations in Mongolian gerbils regardless of the alpha- to beta-carotene ratio when beta-carotene equivalents are equalized. J. Nutrit. 149:951-958.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Titcomb T.J., M.S. Kaeppler, M.E. Cook, P.W. Simon, S.A. Tanumihardjo. 2019.Carrot leaves improve color and xanthophyll content of egg yolk in laying hens but are not as effective as commercially available marigold fortificant. Poult. Sci.; doi: 10.3382/ps/pez257.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Sheftel , J., M. Sowa, L. Mourao, L.T. Zou�, C.R. Davis, P.W. Simon, and S.A. Tanumihardjo. 2019. Total adipose retinol concentrations are correlated with total liver retinol concentrations in male Mongolian gerbils, but only partially explained by chylomicron deposition assessed with total ?-retinol. Curr. Dev. Nutr. 3:nzy096.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Bannoud F., Ellison S., Paolinelli M., Horejsi T., Senalik D., Fanzone M., Iorizzo M., Simon P. (2019) Dissecting the genetic control of root and leaf tissue-specific anthocyanin pigmentation in carrot (Daucus carota L.) Theor Appl Genet 132: 2485
- Type:
Book Chapters
Status:
Published
Year Published:
2019
Citation:
Simon P.W., Geoffriau E., Ellison S., Iorizzo M. 2019. Carrot Carotenoid Genetics and Genomics. In: Simon P., Iorizzo M., Grzebelus D., Baranski R. (eds) The Carrot Genome. Compendium of Plant Genomes. Springer International Publishing
- Type:
Book Chapters
Status:
Published
Year Published:
2019
Citation:
Ellison, S. 2019. Carrot Domestication. In: Simon P., Iorizzo M., Grzebelus D., Baranski R. (eds) The Carrot Genome. Compendium of Plant Genomes. Springer International Publishing.
- Type:
Book Chapters
Status:
Published
Year Published:
2019
Citation:
Iorizzo M., Ellison S., Pottorff M., Cavagnaro P.F. 2019. Carrot Molecular Genetics and Mapping. In: Simon P., Iorizzo M., Grzebelus D., Baranski R. (eds) The Carrot Genome. Compendium of Plant Genomes. Springer International Publishing.
- Type:
Book Chapters
Status:
Published
Year Published:
2019
Citation:
Cavagnaro P.F., and Iorizzo M. 2019. Carrot Anthocyanin Diversity, Genetics and Genomics. In: Simon P., Iorizzo M., Grzebelus D., Baranski R. (eds) The Carrot Genome. Compendium of Plant Genomes. Springer International Publishing.
- Type:
Book Chapters
Status:
Published
Year Published:
2019
Citation:
Iorizzo M., Macko-Podg�rni A., Senalik D., Van Deynze A., and Simon P.W. 2019. The Carrot Nuclear Genome and Comparative Analysis. In: Simon P., Iorizzo M., Grzebelus D., Baranski R. (eds) The Carrot Genome. Compendium of Plant Genomes. Springer International Publishing.
- Type:
Book Chapters
Status:
Published
Year Published:
2019
Citation:
Bostan H., Senalik D., Simon PW, and Iorizzo M. 2019. Carrot Genetics, Omics and Breeding Toolbox. In: Simon P., Iorizzo M., Grzebelus D., Baranski R. (eds) The Carrot Genome. Compendium of Plant Genomes. Springer International Publishing.
- Type:
Books
Status:
Published
Year Published:
2019
Citation:
Simon P., Iorizzo M., Grzebelus D., Baranski R. (eds) The Carrot Genome. Compendium of Plant Genomes. Springer International Publishing.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Iorizzo M., Curaba J., Pottorff M., Ferruzzi G.M., Simon. P. and Cavagnaro P. 2020. Carrot anthocyanins genetics and genomics: status and perspectives to improve its application for the food colorant industry. Genes, 11: 906
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Curaba J., Bostan H., Cavagnaro P., Senalik D., Mengist M.F., Zhao Y., Simon P. and M. Iorizzo. 2020. Identification of an SCPL gene Controlling Anthocyanin Acylation in Carrot (Daucus carota L.) Root. Frontiers in Plant Science, 10:1770
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Iorizzo M., M. Pottorff, H. Bostan, S.L. Ellison, P.F. Cavagnaro, D. Senalik, D.M. Spooner and P.W. Simon. 2019. Recent advance in carrot genomics. ISHS Acta Horticulturae 1264: Proceedings of the II International Symposium on Carrot and Other Apiaceae. 10.17660/ActaHortic.2019.1264.9
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Cavagnaro P.F., F. Bannoud, M. Iorizzo, D. Senalik, S.L. Ellison and P.W. Simon. 2019. Carrot anthocyanins: nutrition, diversity and genetics. ISHS Acta Horticulturae 1264: International Symposium on Carrot and Other Apiaceae. 10.17660/ActaHortic.2019.1264.11
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2020
Citation:
Su Liu, 2020. Improved Hybrid de novo Genome Assembly, Resistance Gene Prediction and Annotation of Carrot (Daucus carota). MS thesis. North Carolina State University, Raleigh.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2020
Citation:
Coe. Kevin. 2020. Genetic analysis of domestication and carotenoid accumulation in carrot (Daucus carota L.) and the polyploidization of switchgrass (Panicum virgatum L.). Ph.D thesis. University of Wisconsin-Madison
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2020
Citation:
Yildiz, Gunay. 2020. Genome Wide Association Analysis of Free Sugars in the Storage Roots of a Diverse Collection of Carrot (Daucus carota L.). MS thesis. University of Wisconsin-Madison.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Sowa, M., L. Mourao, J. Sheftel, M. Kaeppler, G. Simons, C. Davis, P.W. Simon, S. Tanumihardjo. Overlapping Vitamin A Interventions with Provitamin A Carotenoids and Preformed Vitamin A Fortificant Cause High Liver Retinol Stores in Male Mongolian Gerbils. Journal of Nutrition 150: 29122923. 2020. https://doi.org/10.1093/jn/nxaa142
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
du Toit, L., and Derie, M. 2020. Spot-on research. Establishing a carrot cavity spot nursery at Washington State University. Carrot Country, Spring 2020:4-9.
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Bannoud F., Carvajal S., Ellison S., D. Senalik, Talquenca S.G., Iorizzo M., Simon P. and P.F. Cavagnaro. 2021. Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in carrot root phloem. Genes 2021, 12, 1464.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Iorizzo M., Mengit M.F., Bostan H., Curaba J., M. Pottorff. From genome to genes and DNA markers to improve agronomic performance and quality of fruit and vegetables crops. Genetyka Aplikacyjna Ro?lin XXI, September 22-24, 2021, Warsaw, Poland
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Iorizzo M. Development of a genetic framework to improve the efficiency of bioactive stability and delivery from carrot and blueberry. Webinar: Current status of Phyomediomics and Nutriomics. Organized by the Korean Academy of Science and Technology (KAST), December 15, 2020.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Sumner, Daniel A. 2021. "Impact of COVID-19 and the Lockdowns on Labor-Intensive Produce Markets, with Implication for Hired Farm Labor" Choices. Quarter 3. Available online: https://www.choicesmagazine.org/choices-magazine/theme-articles/agricultural-market-response-to-covid-19/impact-of-covid-19-and-the-lockdowns-on-labor-intensive-produce-markets-with-implication-for-hired-farm-labor
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Coe, K., S. Ellison, D. Senalik, J. Dawson, P.W. Simon. The influence of the Or and Carotene Hydroxylase genes on carotenoid accumulation in orange carrots [Daucus carota (L.)]. Theor. Applied Genet. 134: 3351-62. 2021. DOI: 10.1007/s00122-021-03901-3
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2021
Citation:
Loarca, Jenyne. 2021. Identifying Phenotypes and Markers in Diverse Cultivated Carrot Germplasm (Daucus carota) to Deliver Improved Stand Establishment to Growers. PhD thesis. University of Wisconsin-Madison.
|
Progress 09/01/20 to 08/31/21
Outputs
Target Audience:The audience for the web site being developed for this project includes all members of the scientific and breeding communities interested in phenotypic information important for crop production and improvement. Results are shared with stakeholders at international, national, regional and local grower and industry meetings and at field days. Carrot is a crop that the general public is familiar with, so to better communicate with the general public, approx. 40 selected diverse carrots were grown and managed annually by undergraduate students at land grant universities including those in California, North Carolina, Washington and Wisconsin. This diversity garden approach is being the basis of interactive science outreach programs for K-12 students, undergraduate students, educational, and consumer groups in those states focusing on breeding, genetic diversity and nutrition. These diverse carrots are available to any field-based STEM and agricultural education institution. The FARM SMART program at the University of California Desert Research and Extension Center developed an agricultural literacy component that incorporates agriculture (in particular an expanded awareness of carrots and other vegetables) in presentations to school (K-12) and community (adult) outreach programs in carrot nutrition and production. Markers and sequence information for traits phenotyped are available to stakeholders through conferences, web-accessible databases, and publications. Genomic tools were demonstrated at workshops including hands-on training with presentations/webinars/videos developed to demonstrate approaches to marker discovery and marker assisted selection for breeders. The process of discovering plants with desirable carrot phenotypes was described to the scientific and breeding communities in publications, webinars, and at meetings to instruct them on critical aspects of both the phenotype screening process as well as best procedures to utilize breeding pools developed by this project, and to initiate the development of breeding pools on their own. On-farm testing was used to engage growers in participating in the evaluation of breeding pools, and for them to provide critical feedback to project scientists about the on-farm level performance of early-generation breeding stocks. Quality assessments of breeding pools by chefs and consumers also both inform those stakeholders about germplasm under development from this project, as well as provide feedback to project scientists about the progress achieved by this project in carrot improvement at the consumer level. Nutritional quality evaluations were presented at horticulture, nutritional science, and grower meetings and in scientific and popular publications. Student and general public outreach staff and scientists involved in the project receive and dispense information from on-farm and consumer stakeholder testing. Information on economic impacts of carrot traits is being presented at agricultural economics and agribusiness meetings and in scientific publications. Cost and return results and consumer demand results were presented to industry stakeholders in reports, websites and other media based tools. Issues briefs and short information bulletins are developed to inform carrot industry stakeholders on important opportunities about new varieties, and the general public were extensively used this information. Changes/Problems:Some data collection and outreach activities were delayed or omitted due to Covid restrictions What opportunities for training and professional development has the project provided?Year 5 activities included grow-out of diverse carrot breeding stocks which are being distributed to stakeholders and general public contacts for project promotion and as educational materials. Stakeholder training for database use was initiated through communication with stakeholders seeking information on project results and discussions virtually at grower meetings. As part of the education activities, undergraduate students, graduate students and post-doctorates were trained in vegetable breeding, crop and seed production, disease protection and diagnosis, drought tolerance, stand establishment and bolting, genomic analysis and database development and econometrics of food demand as they participate in research projects critical to the project achieving the research goals. We also presented practical economic findings to undergraduate and graduate classes. Year 5 FARM SMART Carrot Activities continued those initiated in years 1-2 of the project including field production of colored carrots, field tours, and extensive exposure to elementary high school and college students, and members of the general public visiting and touring the Desert Research and Extension Center near El Centro, CA. In addition to this, a short Carrot Research Video is being developed. Since the coronavirus (COVID-19) pandemic and quarantine began, it has been important to add more video content to the program of services offered to local educators, students and our community. Tracking of video content access has indicate the ability to reach a wider audience and reach beyond the local community. In a remote world, video allows us to meet, to educated and to provide services. The recorded short video gives an overview of colored carrot research at Desert REC. The video is still in the editing stage, but includes viewing the variety of colored carrots, observing the harvest, and sorting process of colored carrots for research and gives nutritional content information. Distribution of the short video includes social media sites, DREC website and linked to Farm Smart newsletter. We expect to distribute this video digitally to local teachers as well as show the video during field tours where we cover carrot research at Desert REC. How have the results been disseminated to communities of interest?Educational events and conference presentations delivered in 2021included: Demand for Organic, Convenience Foods: A Large Online Survey from U.S. Carrot Buyers during COVID-19. the 10th Congress of the Asian Association of Environmental and Resource Economics, Asian Association of Environmental and Resource Economics, Seoul, South Korea, August 20-21, 2021. Demand for Food Attributes during COVID-19: Evidence from a Large Sample of US Carrot Buyers. Agricultural Economics Workshop. Agricultural and Resource Economics, University of California, Davis, California, February 18, 2021. Loarca, Jenyne. "Identifying Phenotype and Genetic Markers in Diverse Carrot Germplasm (Daucus carota subsp. sativus) To Deliver Improved Stand Establishment to Growers". Invited Speaker, Midwest Population Genetics Conference, UW Madison. August 2021. Loarca, Jenyne. "Leveraging a Carrot Diversity Panel: Identification of Phenotypes and Genetic Markers to Deliver Improved Stand Establishment to Growers". Invited Speaker, JF Crow Institute Seminar Series, UW Madison, September 2021. Loarca, Jenyne. "Genome-Wide Association Analysis with a Carrot Diversity Panel". Plant Genetics Undergraduate Course, University of California Davis. October 2021. Loarca, Jenyne. "Why Genetic Diversity Matters in Science - A Case Study with 700 Carrot Cultivars" Participatory Learning And Teaching Organization (PLATO): UW Madison Division of Continuing Studies. December 2021. du Toit, L.J. Screening carrot germplasm for resistance to cavity spot and bacterial blight. Research presentation update at Carrot Research Symposium, CA Fresh Carrot Advisory Board, 22 Mar. 2021, virtual because of COVID-19. (59 people) Due to COVID-19 PAG 2021 was not organized, and as a result the Apiaceae workshop was not organized. To ensure continuation of this workshop at PAG, the 2022 Apiaceae workshop has already been scheduled and is being organized by PD and Co-PI. Poster presentations Loarca, Jenyne, Dawson, Julie. and Simon, Philipp. "LeveragingDiverse Carrot Germplasm: Identification of Phenotypes and Genetic Markers to Deliver Improved Stand Establishment to Growers". Midwest Women in Science Conference, University of Chicago - September 2021. Loarca, Jenyne, Dawson, Julie. and Simon, Philipp. "LeveragingDiverse Carrot Germplasm to Deliver Improved Stand Establishment to Growers" UW Madison Plant Sciences Symposium. November 2021. Loarca, Jenyne. "Why Genetic Diversity Matters: A Study of 700 Carrot Tops". UW Madison Plant Sciences Symposium. November 2021. Lightning talk competitor. Stakeholder events included: March 22, 2021, oral presentations (P Roberts; P Simon; L. DuToit), California Carrot Symposium (Virtual), Bakersfield, CA; hosted by California Fresh Carrot Advisory Board for carrot researchers, producers and processors. What do you plan to do during the next reporting period to accomplish the goals?Since this was the final year of the project, there are no more reporting periods. However, additional research, outreach, and publication of results initiated in this project will be continued. These include: Publish and release the carrot v3 assembly and release of the CarrotOmics database. A subset of field evaluations and research activities, and database development described for Year 5 is being re-tested from selected germplasm entries with more desirable performance to confirm previous results.This will include evaluation of 340 PIs in DREC for sugar, flavor and pigment phenotyping, additional Alternaria and nematode tolerance testing, and additional development of mapping populations for Mendelian genetic analysis. In addition, breeding pool seed will be advanced and initial evaluations traits will again be trialed and evaluated. GWAS analysis will be published on flavor, top size, alternaria and nematode resistance, stand establishment, bolting and water-stress (drought) tolerance. Addition of resequencing and GBS data and images to the CarrotOmics database will proceed. A stakeholder zoom meeting was held January, 2021 to report project progress and to gather additional input from them on current and future project direction. Individual zoom or phone conference calls will again be held in spring of 2022 with individual carrot production and processing industry companies and stakeholder groups, and with seed companies with carrot breeding programs to obtain more detailed input on traits of importance and types of publically available information this project can provide that is most useful for them. The CarrotOmics database will be discussed in detail. We did additional consumer acceptance on-line surveys, assess shipment data during the pandemic relative to prior years and have initiated and made progress on the cost of production studies with current best practices and exploring innovations. The 2021 WSU Carrot Cavity Spot Nursery planted in May 2021 was harvested and the roots rated for cavity spot in October-November 2021, with results presented at the CA Carrot Symposium in March 2022. Roots selected from lines with the least severe symptoms were shipped to WI for crossing by Simon's program to continue selecting for cavity spot resistance.
Impacts
What was accomplished under these goals?
Carrots are a high-value crop worth $750M to US growers and the largest crop source of vitamin A in the US diet. Approx. 86% of the carrot production area and 94% of crop value is in fresh market carrots, with 85% of fresh market carrots grown in CA. WA and WI are the largest producers of carrots for processing. Nation-wide expansion of small-scale local vegetable markets has increased carrot production, and this trend contributes to the growing organic market share of the US production, estimated at 14%. Conventional and organic growers, processers, and seed industry breeders and their marker lab scientists were surveyed in 2014 and convened in 2015 to identify top traits deemed important for improving productivity, expanding product development, and strengthening economic viability. Based on this stakeholder input, this project addresses the critical needs of the carrot industry, to identify novel sources of genes for carrot improvement in future carrot breeding. We are identifying genes for improved resistance to diseases and pests, reliable crop production and tolerance to environmental stress, and enhanced consumer quality. To complement this gene discovery, we are developing a carrot database to provide breeders and other researchers with a platform to deliver information for carrot breeders to tap into the breadth of carrot genetic diversity; and establish a science-based foundation for long-term carrot improvement. Nutritional profiles and consumer attitudes toward carrots are being developed, the economic value of new breeding traits is being measured, and students are being educated. These new gene sources will be used in future breeding efforts to develop crop germplasm that requires less pesticide use and increased farm value; novel, high-value carrot products; and improved flavor and nutritional value for consumers. Longterm impacts are expected to increase crop consumption, benefit the environment and human health, and develop crop improvement strategies applicable to other crops. Project Objectives and Annual Progress: 1 Phenotype diverse carrot germplasm and breeding stocks to discover and describe previously uncharacterized variation for important traits. Variation in key traits identified by stakeholders was phenotyped in a carrot germplasm collection that includes 694 diverse open-pollinated carrots from the USDA-NPGS and 70 public inbreds, referred to as the "PI collection". In year 5 final screening screening of M. incognita nematode resistant entries identified in previous years was completed in field and greenhouse tests; among these, some lines were confirmed to be resistant to M. javanica, M. arenaria and M. hapla. Segregating progeny phenotype and GBS-genotype data were used to map five new nematode resistance traits At the cavity spot (Pythium violoae and P. sulcatum) field nursery site established at WSU in 2019, a subset of 57 PI lines was evaluated, of which 2 had less severe cavity spot symptoms than Purple Haze, the resistant check, and 4 had symptoms more severe than Purple Haze but less severe than Propeel, the next more resistance commercial cultivar. In WI, ~39 PIs were confirmed to have superior Alternaria leaf blight resistance. Drought tolerance field and greenhouse phenotype data collected at UCR were analyzed for correlations and prepared for GWAS, and a subset of most tolerant lines were increased for further testing. Three years of data have been taken on early establishment, height, and final stand establishment on the PI collection in WI. An association analysis has been conducted and a manuscript has been prepared for submission by the end of the year. Mapping populations were created and F2 families were phenotyped for linkage mapping of stand establishment. These populations had insufficient phenotypic segregation for stand establishment for successful mapping of the trait, but did help to refine methods of phenotyping stand establishment which were used to identify accessions with more stable phenotypes to create better mapping populations. Four years of data on the PI collection has been taken on harsh flavor and sweetness, carotenoids, anthocyanins, total dissolved solids, sugars, ionomic profile, and root shape. Data for all traits are being used for GWAS analysis. The carotenoid study has been published (Coe et al, see products), the total dissolved solids has been published in thesis form (Yildiz, see products) and the others are in preparation for publication. 2 - Develop an expanded carrot genomic database for breeders to catalogue genomic and phenotypic variation and track genes underlying important traits Developed an improved genome assembly, gene annotation of carrot DH1. The new assembly v3, covers 440 Mb, all assembled into 9 chromosomes, with a contig N50 >6Mb. Compared with the previous assembly (v2), the v3 assembly include about 11% (54 Mb) new sequences, >21% (>100 Mb) extra sequence anchored to chromosome level, representing >189 fold increase in contig N50. In total, 36,216 genes were predicted, with >4,000 new gene models as compared to the previous gene prediction. Also, initiated efforts to sequence the genome of a white and dark purple genotypes using PacBio HiFi technology. Data from several QTL, transcriptome, gene annotation and functional analysis studies targeting anthocyanin genetics and genes in carrot, and anchored all these QTLs and genes to the v2 and v3 genomes. These allowed identification of novel candidate genes controlling carotenoids, anthocyanin biosynthesis in carrot root and petiole, and genes associated with carrot domestication and improvement. In addition, to compare genotypes, DNA form a bulked sample of 25 seeds for each PI was extracted and sequenced using GBS. Initial analysis analyses indicate that at least two populations representing western and eastern carrots exist. 3 - Initiate development and evaluation of breeding pools from diverse germplasm and breeding stocks, and detailed quality analysis: Roots with elite nematode and Alternaria resistance, low-bolting incidence, large tops, vigorous stand establishment, excellent flavor, and unique color were advanced to develop breeding pools. 4 - Evaluate the economic impacts of new carrot traits on grower practices and costs, and consumer decisions: Large U.S. surveys (about 400,000 consumer responses) of self-reported carrot buyers were conducted to estimate expressed willingness to pay for carrot traits from 2019 to 20210. Specifically, we compared expressed willingness to pay for organic baby carrots, conventional baby carrots, organic full-sized carrots, and conventional full-sized carrots. Consumers' median willingness to pay is about $0.7 per pound for the organic trait. The results are robust across multiple surveys conducted from 2019 to 2021. The results document that consumers are willing to pay for observable and claimed trait differences when selecting carrot products. The willingness to pay for traits did not differ across rounds of the survey from before the pandemic and as the pandemic evolved.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Bannoud F., Carvajal S., Ellison S., D. Senalik, Talquenca S.G., Iorizzo M., Simon P. and P.F. Cavagnaro. 2021. Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in carrot root phloem. Genes 2021, 12, 1464.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Iorizzo M., Mengit M.F., Bostan H., Curaba J., M. Pottorff. From genome to genes and DNA markers to improve agronomic performance and quality of fruit and vegetables crops. Genetyka Aplikacyjna Ro?lin XXI, September 22-24, 2021, Warsaw, Poland
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Iorizzo M. Development of a genetic framework to improve the efficiency of bioactive stability and delivery from carrot and blueberry. Webinar: Current status of Phyomediomics and Nutriomics. Organized by the Korean Academy of Science and Technology (KAST), December 15, 2020.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Sumner, Daniel A. 2021. "Impact of COVID-19 and the Lockdowns on Labor-Intensive Produce Markets, with Implication for Hired Farm Labor" Choices. Quarter 3. Available online: https://www.choicesmagazine.org/choices-magazine/theme-articles/agricultural-market-response-to-covid-19/impact-of-covid-19-and-the-lockdowns-on-labor-intensive-produce-markets-with-implication-for-hired-farm-labor
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Coe, K., S. Ellison, D. Senalik, J. Dawson, P.W. Simon. The influence of the Or and Carotene Hydroxylase genes on carotenoid accumulation in orange carrots [Daucus carota (L.)]. Theor. Applied Genet. 134: 3351-62. 2021. DOI: 10.1007/s00122-021-03901-3
- Type:
Theses/Dissertations
Status:
Under Review
Year Published:
2021
Citation:
Loarca, Jenyne. 2021. Identifying Phenotypes and Markers in Diverse Cultivated Carrot Germplasm (Daucus carota) to Deliver Improved Stand Establishment to Growers. PhD thesis. University of Wisconsin-Madison.
|
Progress 09/01/19 to 08/31/20
Outputs
Target Audience:The audience for the web site being developed for this project includes all members of the scientific and breeding communities interested in phenotypic information important for crop production and improvement. Results are shared with stakeholders at international, national, regional and local grower and industry meetings and at field days. Carrot is a crop that the general public is familiar with, so to better communicate with the general public, approx. 40 selected diverse carrots are being grown and managed annually by undergraduate students at land grant universities including those in California, North Carolina, Washington and Wisconsin. This diversity garden approach is being the basis of interactive science outreach programs for K-12 students, undergraduate students, educational, and consumer groups in those states focusing on breeding, genetic diversity and nutrition. These diverse carrots are available to any field-based STEM and agricultural education institution. The FARM SMART program at the University of California Desert Research and Extension Center is developing an agricultural literacy component that incorporates agriculture (in particular an expanded awareness of carrots and other vegetables) in presentations to school (K-12) and community (adult) outreach programs in carrot nutrition and production. Markers and sequence information for traits phenotyped are available to stakeholders through conferences, web-accessible databases, and publications. Genomic tools are being demonstrated at workshops including hands-on training with presentations/webinars/videos developed to demonstrate approaches to marker discovery and marker assisted selection for breeders. The process of discovering plants with desirable carrot phenotypes are being described to the scientific and breeding communities in publications, webinars, and at meetings to instruct them on critical aspects of both the phenotype screening process as well as best procedures to utilize breeding pools developed by this project, and to initiate the development of breeding pools on their own. On-farm testing is being used to engage growers in participating in the evaluation of breeding pools, and for them to provide critical feedback to project scientists about the on-farm level performance of early-generation breeding stocks. Quality assessments of breeding pools by chefs and consumers also both inform those stakeholders about germplasm under development from this project, as well as provide feedback to project scientists about the progress achieved by this project in carrot improvement at the consumer level. Nutritional quality evaluations are being presented at horticulture, nutritional science, and grower meetings and in scientific and popular publications. Student and general public outreach staff and scientists involved in the project receive and dispense information from on-farm and consumer stakeholder testing. Information on economic impacts of carrot traits is being presented at agricultural economics and agribusiness meetings and in scientific publications. Cost and return results and consumer demand results is being presented to industry stakeholders in reports, websites and other media based tools. Issues briefs and short information bulletins are developed to inform carrot industry stakeholders on important opportunities about new varieties, and the general public is also expected to extensively use this information. Changes/Problems:Some data collection and outreach activities were delayed or omitted due to COVID restrictions. What opportunities for training and professional development has the project provided?Year 4 activities included grow-out of diverse carrot breeding stocks which are being distributed to stakeholders and general public contacts for project promotion and as educational materials. Forms to track the responses of recipients of materials were developed. Stakeholder training for database use was initiated through communication with stakeholders seeking information on project results and discussions at the Plant and Animal Genome meetings. As part of the education activities, undergraduate students, graduate students and post-doctorates are being trained in vegetable breeding, crop and seed production, disease protection and diagnosis, drought tolerance, stand establishment and bolting, genomic analysis and database development as they participate in research projects critical to the project achieving the research goals. Year 4 FARM SMART Carrot Activities continued those initiated in years 1-2 of the project including field production of colored carrots, field tours, and extensive exposure to elementary high school and college students, and members of the general public visiting and touring the Desert Research and Extension Center near El Centro, CA. In Davis, CA, the project allowed Student Farm undergraduate interns, volunteers and student employees to participate in carrot production in the UC Davis field teaching areas. As well as school children and chaperones. How have the results been disseminated to communities of interest?Educational events and conference presentations delivered in 2020 included: First PAG Workshop on Apiaceae: Simon, P.W. S.L. Ellison, D.Senalik. 2020. Trait Identification and Genomic Database Development for Carrot (Daucus carota) Improvement. XXVII Plant & Animal Genome, January 13, 2020, San Diego, California, USA. Iorizzo, M., H. Bostan, S.L. Ellison, D. Senalik, P.W. Simon. J.Curaba. 2020. Improved Hybrid de novo Genome Assembly, Gene Prediction and Annotation of Carrot (Daucus carota). XXVII Plant & Animal Genome, January 13, 2020, San Diego, California, USA. S.L. Ellison, Simon, P.W., D. Senalik. 2020. Genome-Wide Association Analysis of Carotenoids in Carrot. XXVII Plant & Animal Genome, January 13, 2020, San Diego, California, USA Van Deynze, A.. Hill, TA, Garcia-Llanos, A., Roberts, P.,Mathews, W. Ellison, S., Senalik, D., Loarca, J. and Simon, P. 2020. Characterization of the Tendency for Bolting among Carrot Germplasm Accessions. XXVII Plant & Animal Genome, January 13, 2020, San Diego, California, USA. Macko-Podgorni, A., K. Stelmach, K. Kwolek, D. Grzebelus. 2020. Abundance and Insertional Polymorphism of Carrot Mites and Demography of Daucus carota. XXVII Plant & Animal Genome, January 13, 2020, San Diego, California, USA. Van Deynze, A. 2020. Seed Biotechnology Center update. California Seed Association annual meeting. March 6, 2020, Carlsbad, CA. Nov. 20-21, 2019, oral presentation (L. du Toit). Carrot cavity spot. Pacific Northwest Vegetable Assoc. Annual Convention & Trade Show, Kennewick, WA. (200 people) February 24, 2020, oral presentation (H. Lee; R. Goldstein; D. A. Sumner), at UC Davis, CA; a seminar for undergraduates August 10, 2020, oral presentation (H. Lee; R. Goldstein; D. A. Sumner), 2020 Virtual Meeting, Agricultural & Applied Economics Association. Stakeholder events included: March 4 - 13, 2020, carrot harvest, PI collection evaluation and breeding pool development; and March 10 hybrid trials (P. Simon, M. Colley, J. Sidhu) at Desert Research and Extension Center, El Centro, CA Various dates, in vitro cavity spot inoculation protocol evaluation (L. du Toit) at Washington State University Mount Vernon, WA; carrot phenotyping for carotenoids, flavor, root shape and top size; breeding pool development (P. Simon, J. Dawson, S. Ellison) at the USDA, ARS Department of Horticulture, University of Wisconsin, Madison, WI January to March 2020, FARM SMART delivered carrot info/curriculum and harvested carrots (876 participants including kids, youth and adults). We also reached 15 teachers with carrot information and seed distribution. What do you plan to do during the next reporting period to accomplish the goals?Publish and release the carrot v3 assembly and release of the CarrotOmics database. A subset of field evaluations and research activities, and database development described for Year 4 will continue in Year 5 to re-test selected germplasm entries with more desirable performance to confirm previous results.. This will include evaluation of 300 PIs in DREC for sugar, flavor and pigment phenotyping, additional alternaria and nematode tolerance testing, and additional development of mapping populations for Mendelian genetic analysis. In addition, breeding pool seed will be produced and initial evaluations traits will be trialed and evaluated. GWAS analysis will be conducted and published on flavor, top size, alternaria and nematode resistance, stand establishment, bolting and water-stress (drought) tolerance. Addition of resequencing and GBS data and images to the CarrotOmics database will proceed. A stakeholder zoom meeting will be scheduled before February, 2021 to report project progress and to gather additional input from them on current and future project direction. Individual zoom or phone conference calls will be held in spring of 2021 with individual carrot production and processing industry companies and stakeholder groups, and with seed companies with carrot breeding programs to obtain more detailed input on traits of importance and types of publically available information this project can provide that is most useful for them. The CarrotOmics database will be discussed in detail. The surveys collected from U.S. carrot buyers will continue to be analyzed to measure how the organic trait and the baby-cut trait affect consumer decisions in carrot consumption. Preliminary results showed that U.S. carrot buyers are willing to pay for the organic trait (about $0.10 per pound) and the baby-cut trait (about $0.40 per pound), and the same survey exercise will be conducted again in October 2020 to confirm the previous results. Other nationwide surveys from U.S. carrot buyers will be conducted to analyze the relationship between carrot consumption and other carrot traits. Specifically, a set of surveys of U.S. carrot buyers will be conducted in 2021 to analyze how carrot consumers respond to different colors of carrots in shopping occasions. Another set of surveys will be collected from U.S. carrot buyers in 2021 to understand how carrot consumers respond to carrot products with leaves in shopping occasions. Survey responses will be summarized and preliminary analyzed. How much U.S. carrot buyers are willing to pay for those traits (different colors and carrot leaves) will be estimated. We will do addition consumer acceptance on-line surveys, assess shipment data during the pandemic relative to prior years and cost of production studies with current best practices. Outreach and educational events planned for Year 5 include- Presentations on the carrot SCRI project at: ASHS, August 5-9, 2021, Denver National Association of Plant Breeders, August 15-19, 2021 Cornell FARM SMART planned activities will include: distribute seed and curriculum to teachers, colored carrot curriculum kits for students, colored carrot virtual workshop with students, and agricultural careers program (explore carrots with middle school/high school students) ------- Websites, patents, inventions, or other community resources created: The carrot SCRI website includes a carrot database (phenotypic and genotypic data collected), project information, the project collaborators, breeding pool development, and relevant news. Carrot info was disseminated via FARM SMART social media including a carrot research blog https://ucanr.edu/blogs/blogcore/postdetail.cfm?postnum=43340.
Impacts
What was accomplished under these goals?
Carrots are a high-value crop worth $750M to US growers and the largest crop source of vitamin A in the US diet. Approx. 86% of the carrot production area and 94% of crop value is in fresh market carrots, with 85% of fresh market carrots grown in CA. WA and WI are the largest producers of carrots for processing. Nation-wide expansion of small-scale local vegetable markets has increased carrot production, and this trend contributes to the growing organic market share of the US production, estimated at 14%. Conventional and organic growers, processers, and seed industry breeders and their marker lab scientists were surveyed in 2014 and convened in 2015 to identify top traits deemed important for improving productivity, expanding product development, and strengthening economic viability. Based on this stakeholder input, this project addresses the critical needs of the carrot industry, to identify novel sources of genes for carrot improvement in future carrot breeding. We are identifying genes for improved resistance to diseases and pests, reliable crop production and tolerance to environmental stress, and enhanced consumer quality. To complement this gene discovery, we are developing a carrot database to provide breeders and other researchers with a platform to deliver information for carrot breeders to tap into the breadth of carrot genetic diversity; and establish a science-based foundation for long-term carrot improvement. Nutritional profiles and consumer attitudes toward carrots are being developed, the economic value of new breeding traits is being measured, and students are being educated. These new gene sources will be used in future breeding efforts to develop crop germplasm that requires less pesticide use and increased farm value; novel, high-value carrot products; and improved flavor and nutritional value for consumers. Longterm impacts are expected to increase crop consumption, benefit the environment and human health, and develop crop improvement strategies applicable to other crops. Project Objectives and Annual Progress: 1 Phenotype diverse carrot germplasm and breeding stocks to discover and describe previously uncharacterized variation for important traits. Variation in key traits identified by stakeholders are being phenotyped in a carrot germplasm collection that includes 694 diverse open-pollinated carrots from the USDA-NPGS and 70 public inbreds, referred to as the "PI collection". In year 4 screening of 21 M. incognita nematode resistant entries identified in previous years was conducted in field and greenhouse tests, and most resistant lines were also resistant to M. javanica while some entries were also resistant to M. hapla. Segregating progenies were produced, nematode-screened in the greenhouse and genotyped by GBS to map the new nematode resistance traits. At the cavity spot (Pythium violoae and P. sulcatum) field nursery site established at WSU in 2019, a subset of the PI collection has been evaluated and 5 PIs had less severe cavity spot symptoms than Purple Haze, the resistant check. Additional phenotyping is underway. In WI ~30 PIs were confirmed to have superior Alternaria resistance. Drought tolerance was evaluated in the UCR greenhouse with distinct genetic variation for tolerance in ~20 entries based on wilting indices and ability to recover upon re-watering following water-withholding. Bolting was evaluated in summer and winter crops where ~30% of PIs bolted at time of harvest, with high concordance between lines across locations and years. Inheritance is complex with epistasis and genotype x environment interaction. Three years of data have been taken on early establishment, height, and final stand establishment on the PI collection in WI. An association analysis has been conducted and will be submitted for publication in 2021. Mapping populations were created and F2 families were phenotyped for linkage mapping of stand establishment. Three years of data on the PI collection has been taken on harsh flavor and sweetness, carotenoids, anthocyanins, total dissolved solids, sugars, ionomic profile, and root shape. Data for all traits are being used for GWAS analysis. 2 - Develop an expanded carrot genomic database for breeders to catalogue genomic and phenotypic variation and track genes underlying important traits: DNA from single plants was extracted from the PI collection and resequenced at UC Davis and those same plants were phenotyped for several traits, Sequences were quality checked and mapped back to the v3 PacBio genome and SNPs and indels called to define the genetic diversity, population structure as well as initiate association analysis on traits measured on the plants phenotyped. In addition, to compare genotypes, DNA form a bulked sample of 25 seeds for each PI was extracted and sequenced using GBS. Initial analysis analyses indicate that at least two populations representing western and eastern carrots exist. Developed an improved genome assembly, gene prediction and annotation of carrot DH1. The new assembly v3, covers 440 Mb, all assembled into 9 chromosomes, with a contig N50 >6Mb. Compared with the previous assembly (v2), the v3 assembly include about 11% (54 Mb) new sequences, >21% (>100 Mb) extra sequence anchored to chromosome level, representing >189 fold increase in contig N50. In total, 36,216 genes were predicted, with >4,000 new gene models as compared to the previous gene prediction. The v3 genome has been successfully used to identify new candidate genes regulating the anthocyanin pathway in carrot root and petiole, and the acylation of the cyanidin derivatives. The sequence information will be used to detect SNPs and perform GWAS analysis. Also, integrated data from several QTL, transcriptome, gene annotation and functional analysis studies targeting anthocyanin genetics and genes in carrot, and anchored all these QTLs and genes to the v2 genome. These allowed identification of novel candidate genes controlling anthocyanin biosynthesis in carrot root and petiole. Initiate efforts to sequence the genome of a dark purple genotype using PacBio HiFi technology. The development of the carrot genome database was expanded to curate additional phenotypic and genotypic data. 3 - Initiate development and evaluation of breeding pools from diverse germplasm and breeding stocks, and detailed quality analysis: Roots with elite nematode and Alternaria resistance, low-bolting incidence, large tops, vigorous stand establishment, excellent flavor, and unique color are being intercrossed to develop breeding pools. To advance studies on bioefficacy evaluation of carrot nutritional quality, two gerbil and one chicken nutrition evaluation studies were completed. Carrot was found to be effective in improving animal nutrition in these studies. 4 - Evaluate the economic impacts of new carrot traits on grower practices and costs, and consumer decisions: Large U.S. surveys of self-reported carrot buyers were conducted to estimate expressed willingness to pay for carrot traits from 2019 to 2020. Specifically, we compared expressed willingness to pay for organic baby carrots, conventional baby carrots, organic full-sized carrots, and conventional full-sized carrots. We found evidence that consumers are willing to pay about $0.10 per pound for the organic trait, on average. The average willingness to pay is estimated to be about $0.40 per pound for the baby-cut trait, which is a trait for ease in consuming and cooking carrots. The results are robust across multiple surveys conducted from 2019 to 2020. The results indicate that consumers are willing to pay for trait differences when selecting carrot products.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Iorizzo M., Curaba J., Pottorff M., Ferruzzi G.M., Simon. P. and Cavagnaro P. 2020. Carrot anthocyanins genetics and genomics: status and perspectives to improve its application for the food colorant industry. Genes, 11: 906
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Curaba J., Bostan H., Cavagnaro P., Senalik D., Mengist M.F., Zhao Y., Simon P. and M. Iorizzo. 2020. Identification of an SCPL gene Controlling Anthocyanin Acylation in Carrot (Daucus carota L.) Root. Frontiers in Plant Science, 10:1770.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Iorizzo M., M. Pottorff, H. Bostan, S.L. Ellison, P.F. Cavagnaro, D. Senalik, D.M. Spooner and P.W. Simon. 2019. Recent advance in carrot genomics. ISHS Acta Horticulturae 1264: Proceedings of the II International Symposium on Carrot and Other Apiaceae. 10.17660/ActaHortic.2019.1264.9
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Cavagnaro P.F., F. Bannoud, M. Iorizzo, D. Senalik, S.L. Ellison and P.W. Simon. 2019. Carrot anthocyanins: nutrition, diversity and genetics. ISHS Acta Horticulturae 1264: International Symposium on Carrot and Other Apiaceae. 10.17660/ActaHortic.2019.1264.11
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Sowa, M., L. Mourao, J. Sheftel, M. Kaeppler, G. Simons, C. Davis, P.W. Simon, S. Tanumihardjo. Overlapping Vitamin A Interventions with Provitamin A Carotenoids and Preformed Vitamin A Fortificant Cause High Liver Retinol Stores in Male Mongolian Gerbils. Journal of Nutrition 150: 29122923. 2020. https://doi.org/10.1093/jn/nxaa142
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
du Toit, L., and Derie, M. 2020. Spot-on research. Establishing a carrot cavity spot nursery at Washington State University. Carrot Country, Spring 2020:4-9.
- Type:
Theses/Dissertations
Status:
Submitted
Year Published:
2020
Citation:
Su Liu, 2020. Improved Hybrid de novo Genome Assembly, Resistance Gene Prediction and Annotation of Carrot (Daucus carota). MS thesis. North Carolina State University, Raleigh.
- Type:
Theses/Dissertations
Status:
Submitted
Year Published:
2020
Citation:
Coe. Kevin. 2020. Genetic analysis of domestication and carotenoid accumulation in carrot (Daucus carota L.) and the polyploidization of switchgrass (Panicum virgatum L.). Ph.D thesis. University of Wisconsin-Madison
- Type:
Theses/Dissertations
Status:
Submitted
Year Published:
2020
Citation:
Yildiz, Gunay. 2020. Genome Wide Association Analysis of Free Sugars in the Storage Roots of a Diverse Collection of Carrot (Daucus carota L.). MS thesis. University of Wisconsin-Madison.
|
Progress 09/01/18 to 08/31/19
Outputs
Target Audience:The audience for the web site being developed for this project includes all members of the scientific and breeding communities interested in phenotypic information important for crop production and improvement. Results are shared with stakeholders at international, national, regional and local grower and industry meetings and at field days. Carrot is a crop that the general public is familiar with, so approx. 40 selected diverse carrots are being grown and managed annually by undergraduate students at land grant universities including those in California, North Carolina, Washington and Wisconsin. This diversity garden approach is being the basis of interactive science outreach programs for K-12 students, undergraduate students, educational, and consumer groups in those states focusing on breeding, genetic diversity and nutrition. These diverse carrots are available to any field-based STEM and agricultural education institution. The FARM SMART program at the University of California Desert Research and Extension Center is developing an agricultural literacy component that incorporates agriculture (in particular an expanded awareness of carrots and other vegetables) in presentations to school (K-12) and community (adult) outreach programs in carrot nutrition and production. Markers and sequence information for traits phenotyped are available to stakeholders through conferences, web-accessible databases, and publications. Genomic tools are being demonstrated at workshops including hands-on training with presentations/webinars/videos developed to demonstrate approaches to marker discovery and marker assisted selection for breeders. The process of discovering plants with desirable carrot phenotypes are being described to the scientific and breeding communities in publications, webinars, and at meetings to instruct them on critical aspects of both the phenotype screening process as well as best procedures to utilize breeding pools developed by this project, and to initiate the development of breeding pools on their own. On-farm testing is being used to engage growers in participating in the evaluation of breeding pools, and for them to provide critical feedback to project scientists about the on-farm level performance of early-generation breeding stocks. Quality assessments of breeding pools by chefs and consumers also both inform those stakeholders about germplasm under development from this project, as well as provide feedback to project scientists about the progress achieved by this project in carrot improvement at the consumer level. Nutritional quality evaluations are being presented at horticulture, nutritional science, and grower meetings and in scientific and popular publications. Student and general public outreach staff and scientists involved in the project receive and dispense information from on-farm and consumer stakeholder testing. Information on economic impacts of carrot traits is being presented at agricultural economics and agribusiness meetings and in scientific publications. Cost and return results and consumer demand results is being presented to industry stakeholders in reports, websites and other media based tools. Issues briefs and short information bulletins are developed to inform carrot industry stakeholders on important opportunities about new varieties, and the general public is also expected to extensively use this information.The audience for the web site being developed for this project includes all members of the scientific and breeding communities interested in phenotypic information important for crop production and improvement. Results are shared with stakeholders at international, national, regional and local grower and industry meetings and at field days. Carrot is a crop that the general public is familiar with, so approx. 40 selected diverse carrots are being grown and managed annually by undergraduate students at land grant universities including those in California, North Carolina, Washington and Wisconsin. This diversity garden approach is being the basis of interactive science outreach programs for K-12 students, undergraduate students, educational, and consumer groups in those states focusing on breeding, genetic diversity and nutrition. These diverse carrots are available to any field-based STEM and agricultural education institution. The FARM SMART program at the University of California Desert Research and Extension Center is developing an agricultural literacy component that incorporates agriculture (in particular an expanded awareness of carrots and other vegetables) in presentations to school (K-12) and community (adult) outreach programs in carrot nutrition and production. Markers and sequence information for traits phenotyped are available to stakeholders through conferences, web-accessible databases, and publications. Genomic tools are being demonstrated at workshops including hands-on training with presentations/webinars/videos developed to demonstrate approaches to marker discovery and marker assisted selection for breeders. The process of discovering plants with desirable carrot phenotypes are being described to the scientific and breeding communities in publications, webinars, and at meetings to instruct them on critical aspects of both the phenotype screening process as well as best procedures to utilize breeding pools developed by this project, and to initiate the development of breeding pools on their own. On-farm testing is being used to engage growers in participating in the evaluation of breeding pools, and for them to provide critical feedback to project scientists about the on-farm level performance of early-generation breeding stocks. Quality assessments of breeding pools by chefs and consumers also both inform those stakeholders about germplasm under development from this project, as well as provide feedback to project scientists about the progress achieved by this project in carrot improvement at the consumer level. Nutritional quality evaluations are being presented at horticulture, nutritional science, and grower meetings and in scientific and popular publications. Student and general public outreach staff and scientists involved in the project receive and dispense information from on-farm and consumer stakeholder testing. Information on economic impacts of carrot traits is being presented at agricultural economics and agribusiness meetings and in scientific publications. Cost and return results and consumer demand results is being presented to industry stakeholders in reports, websites and other media based tools. Issues briefs and short information bulletins are developed to inform carrot industry stakeholders on important opportunities about new varieties, and the general public is also expected to extensively use this information. Changes/Problems:A no-cost project extension of one additional year will be requested What opportunities for training and professional development has the project provided?Year 3 activities included grow-out of diverse carrot breeding stocks which are being distributed to stakeholders and general public contacts for project promotion and as educational materials. Forms to track the responses of recipients of materials are being developed. Stakeholder training for database use was initiated through communication with stakeholders seeking information on project results. As part of the education activities, undergraduate students, graduate students and post-doctorates are being trained in vegetable breeding, crop and seed production, disease protection and diagnosis, drought tolerance, stand establishment and bolting, genomic analysis and database development as they participate in research projects critical to the project achieving the research goals. Year 3 FARM SMART Carrot Activities continued those initiated in years 1-2 of the project including field production of colored carrots, field tours, and extensive exposure to elementary high school and college students, and members of the general public visiting and touring the Desert Research and Extension Center near El Centro, CA. In Davis, CA, the project allowed Student Farm undergraduate interns, volunteers and student employees to participate in carrot production in the UC Davis field teaching areas. As well as school children and chaperones How have the results been disseminated to communities of interest?Educational events and conference presentations delivered in 2016-17 included: January 12-16, 2019, poster presentation (K. Coe) at Plant and Animal Genome Meeting February 18, 2019, Dept. Genetics Seminar series, (M. Iorizzo)NCSU Raleigh, NC March 12, 2019, oral presentations (P Roberts; P Simon; L. DuToit), California Carrot Symposium, Bakersfield, CA; hosted by California Fresh Carrot Advisory Board for carrot researchers, producers and processors. June 3-6, 2019, oral presentation (P. Simon) at CROPS, Huntsville, AL June 11, 2019, oral presentation (H. Bostan) at PHHI Seminar Series, RCCC-NCRC Kannapolis, NC July 22-25, 2019, oral presentation (P. Simon) at ASHS, Las Vegas, NV Stakeholder events included: Feb. 27- March 1, 2019, carrot harvest, PI collection demonstration and breeding pool development and March 5, hybrid trials (P. Simon, M. Colley, J. Sidhu, A. Van Deynze) at Desert Research and Extension Center, El Centro, CA October 8, 2019, carrot harvest and nematode evaluation (P. Roberts, P. Simon) at University of California Kearney Agricultural Center, Parlier, CA Various dates, in vitro cavity spot inoculation protocol evaluation (L. du Toit) at Washington State University Mount Vernon, WA; carrot phenotyping for carotenoids, flavor, root shape and top size; breeding pool development (P. Simon, S. Ellison) at the USDA, ARS Department of Horticulture, University of Wisconsin, Madison, WI What do you plan to do during the next reporting period to accomplish the goals?Field evaluations and research activities, and database development described for Year 3 will continue in Year 4. In addition, breeding pool seed will be produced and initial evaluations traits will be trialed and evaluated. The cavity spot nursery site in western WA will be planted again in 2020 with a diverse set of carrot germplasm from this SCRI project to help identify and select germplasm with greater resistance to cavity spot. Re-testing of germplasm entries with more desirable performance will be undertaken to confirm previous results. Data for publications on flavor, top size, alternaria and nematode resistance, bolting and water-stress (drought) tolerance will be summarized and preliminarily analyzed in preparation of GWAS analyses. Addition of resequencing and GBS data and images to the Carrotomics database will proceed. Nutritional bioefficacy and economic impact analyses will be advanced. Outreach and educational events planned for Year 4 include- Presentations on the carrot SCRI project will be delivered at: Plant and Animal Genome Meeting, Apiaceae Workshop, January National Association of Plant Breeders, Lincoln Nebraska, August 8-10, 2020 ASHS, August 15-19, 2020, Orlando, FL, 2020
Impacts
What was accomplished under these goals?
Carrots are a high-value crop worth $750M to US growers and the largest crop source of vitamin A in the US diet. Approx. 86% of the carrot production area and 94% of crop value is in fresh market carrots, with 85% of fresh market carrots grown in CA. WA and WI are the largest producers of carrots for processing. Nation-wide expansion of small-scale local vegetable markets has increased carrot production, and this trend contributes to the growing organic market share of the US production, estimated at 14%. Conventional and organic growers, processers, product developers, industry breeders, and genomic application labs were surveyed in 2014 and convened in 2015 to identify top traits deemed important for improving productivity, expanding product development, and strengthening economic viability. Based on this stakeholder input, this project addresses the critical needs of the carrot industry, to identify novel sources of genes for carrot improvement in future carrot breeding. We ware identifying genes for improved resistance to diseases and pests, reliable crop production and tolerance to environmental stress, and enhanced consumer quality. To complement this gene discovery, we are developing a carrot database to provide breeders and other researchers with a platform to deliver information for carrot breeders to tap into the breadth of carrot genetic diversity; and establish a science-based foundation for long-term carrot improvement. Nutritional profiles and consumer attitudes toward carrots are being developed, the economic value of new breeding traits is being measured, and students are being educated. These new gene sources will be used in future breeding efforts to develop crop germplasm that requires less pesticide use and increased farm value; novel, high-value carrot products; and improved flavor and nutritional value for consumers. Longterm impacts are expected to increase crop consumption, benefit the environment and human health, and develop crop improvement strategies applicable to other crops. Project Objectives and Annual Progress: 1 - Phenotype diverse carrot germplasm and breeding stocks to discover and describe previously uncharacterized variation for important traits. Variation in key traits identified by stakeholders are being phenotyped in a carrot germplasm collection that includes 694 diverse open-pollinated carrots from the USDA-NPGS and 70 public inbreds, referred to as the "PI collection". In year 3 approximately 100 carrot germplasm accessions with putative partial to high levels of nematode resistance to M. incognita in year 1 and 2 were screened in the greenhouse in year 2 where 21 entries had high levels of resistance. This set of 21 entries shown to have high levels of resistance in the greenhouse was confirmed to be resistant in the field at UC Kearney in year 3, and most resistant lines were also resistant to M. javanica. Some of the same lines were also found to carry resistance to M. hapla. Segregating progenies from some lines were produced, nematode-screened in the greenhouse, and leaf tissue sampled for DNA extraction and genotyping. Selected roots were sent to Wisconsin for breeding pool and mapping population development. A major field experiment is in progress at UC Riverside (UCR) to evaluate the drought tolerance in the PI collection building on a similar test started in Year 2 and completed in Year 3. Water was withheld from early-season onward and phenotypes for wilting and recovery after re-watering in late season were scored. The PI collection also evaluated in the greenhouse for drought tolerance. Preliminary analysis indicated distinct genetic variation for drought tolerance. Bolting was also evaluated in the UCR fields as well as in the Desert Research and Extension Center (DREC) where ~20-30% bolted. Phenotypic data was collected in the PI collection grown at DREC for carotenoids, pigmentation, plant height, total dissolved solids, flavor, sugars, ionomic profile, early flowering, and root shape. The PI collection was also tested in Hancock, WI where ~30% bolted at time of harvest, with high concordance between lines bolting in WI and CA. In WI ~30 PIs were confirmed to have superior Alternaria resistance and stand establishment, carotenoid content and flavor were also evaluated in WI. Imaged and phenotyped roots were genotyped, using GBS, and selfed for seed production. Breeding pool development is in progress. An in vitro lab trial was completed in year 3 at Washington State University Mount Vernon NWREC to screen germplasm for resistance to the two cavity spot pathogens, Pythium violae or P. sulcatum. The inoculation protocol successfully induced lesions for both species of Pythium that in preliminary results correlated well with field testing results .In addition, a cavity spot field nursery site was established at the NWREC for screening germplasm for resistance to both Pythium species. Plots were rated for cavity spot resistance as well as bolting, canopy height, and foliar color. Data from all phenotyping studies are being used for association studies and candidate gene analyses. 2 - Develop an expanded carrot genomic database for breeders to catalogue genomic and phenotypic variation and track genes underlying important traits: DNA was extracted from the PI collection and submitted for resequencing at UC Davis and the same plants that were sampled for resequencing were phenotyped. Development of an improved genome assembly, gene prediction and annotation of carrot DH1 was completed. The new assembly v3, cover 440 Mb, all assembled into 9 chromosomes, with a contig N50 >6Mb. Compared with the previous assembly (v2), the v3 assembly include about 11% (54 Mb) new sequences, >21% (>100 Mb) extra sequence anchored to chromosome level, and represent a >189 fold increase in contig N50. Using a combination of IsoSeq and Illumina transcriptome data, 36,216 genes were predicted, with >4,000 new gene models as compared to the previous gene prediction. The v3 genome has been successfully used to identify new candidate genes regulating the anthocyanin pathway in carrot root and petiole. The sequence information will be used to detect SNPs and perform GWAS analysis. The development of the carrot genome database was initiated to curate phenotypic and genotypic data. A single plant from each of the PI collection has been sequenced at 10 to 15X depth using Illumina Technology. These data are being mapped to the above genome to extract SNPs and indels to define the genetic diversity, population structure as well as initiate association analysis on traits measured on the same single plant phenotyped. 3 - Initiate development and evaluation of breeding pools from diverse germplasm and breeding stocks, and detailed quality analysis: Roots with elite nematode and Alternaria resistance, low-bolting incidence, large tops, vigorous stand establishment, excellent flavor, and unique color are being intercrossed to develop breeding pools. To advance studies on bioefficacy evaluation of carrot nutritional quality, two gerbil nutrition evaluation studies were completed, one with the carrot leaves and one with the high beta-carotene carrot roots. Also a chicken egg coloring study was completed. Carrot was found to be effective in improving animal nutrition in these studies. 4 - Evaluate the economic impacts of new carrot traits on grower practices and costs, and consumer decisions: Retail Scanner Data was analyzed for price differences across fresh carrot products sold in two metropolitan areas - Los Angeles (LA) and Atlanta (ATL). The largest selling form of carrots in each location was baby carrots. Despite price premiums over average carrot price of 20% in LA and 10% in ATL, baby carrots accounted for 40% and 49% of carrot sales, respectively. The results indicate that consumers are willing to pay trait differences when selecting carrot products.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Iorizzo M., Cavagnaro P.F., Bostan H., Zhao Y., Zhang J. and Simon PW. 2018. A cluster of MYB transcription factors regulates anthocyanin biosynthesis in carrot (Daucus carota L.) root and petiole. Frontier in Plant Science, 9:1927.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Titcomb, T., M. Kaeppler, J. Shannon, P.W. Simon, and S. Tanumihardjo. 2019. Carrot leaves maintain liver vitamin A concentrations in Mongolian gerbils regardless of the alpha- to beta-carotene ratio when beta-carotene equivalents are equalized. J. Nutrit. 149:951-958.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Titcomb T.J., M.S. Kaeppler, M.E. Cook, P.W. Simon, S.A. Tanumihardjo. 2019.Carrot leaves improve color and xanthophyll content of egg yolk in laying hens but are not as effective as commercially available marigold fortificant. Poult. Sci.; doi: 10.3382/ps/pez257.
- Type:
Book Chapters
Status:
Published
Year Published:
2019
Citation:
Simon P.W., Geoffriau E., Ellison S., Iorizzo M. 2019. Carrot Carotenoid Genetics and Genomics. In: Simon P., Iorizzo M., Grzebelus D., Baranski R. (eds) The Carrot Genome. Compendium of Plant Genomes. Springer International Publishing
- Type:
Book Chapters
Status:
Published
Year Published:
2019
Citation:
Ellison, S. 2019. Carrot Domestication. In: Simon P., Iorizzo M., Grzebelus D., Baranski R. (eds) The Carrot Genome. Compendium of Plant Genomes. Springer International Publishing.
- Type:
Book Chapters
Status:
Published
Year Published:
2019
Citation:
Iorizzo M., Ellison S., Pottorff M., Cavagnaro P.F. 2019. Carrot Molecular Genetics and Mapping. In: Simon P., Iorizzo M., Grzebelus D., Baranski R. (eds) The Carrot Genome. Compendium of Plant Genomes. Springer International Publishing.
- Type:
Book Chapters
Status:
Published
Year Published:
2019
Citation:
Cavagnaro P.F., and Iorizzo M. 2019. Carrot Anthocyanin Diversity, Genetics and Genomics. In: Simon P., Iorizzo M., Grzebelus D., Baranski R. (eds) The Carrot Genome. Compendium of Plant Genomes. Springer International Publishing.
- Type:
Book Chapters
Status:
Published
Year Published:
2019
Citation:
Iorizzo M., Macko-Podg�rni A., Senalik D., Van Deynze A., and Simon P.W. 2019. The Carrot Nuclear Genome and Comparative Analysis. In: Simon P., Iorizzo M., Grzebelus D., Baranski R. (eds) The Carrot Genome. Compendium of Plant Genomes. Springer International Publishing.
- Type:
Book Chapters
Status:
Published
Year Published:
2019
Citation:
Bostan H., Senalik D., Simon PW, and Iorizzo M. 2019. Carrot Genetics, Omics and Breeding Toolbox. In: Simon P., Iorizzo M., Grzebelus D., Baranski R. (eds) The Carrot Genome. Compendium of Plant Genomes. Springer International Publishing.
- Type:
Books
Status:
Published
Year Published:
2019
Citation:
Simon P., Iorizzo M., Grzebelus D., Baranski R. (eds) The Carrot Genome. Compendium of Plant Genomes. Springer International Publishing.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Sheftel , J., M. Sowa, L. Mourao, L.T. Zou�, C.R. Davis, P.W. Simon, and S.A. Tanumihardjo. 2019. Total adipose retinol concentrations are correlated with total liver retinol concentrations in male Mongolian gerbils, but only partially explained by chylomicron deposition assessed with total ?-retinol. Curr. Dev. Nutr. 3:nzy096.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Bannoud F., Ellison S., Paolinelli M., Horejsi T., Senalik D., Fanzone M., Iorizzo M., Simon P. (2019) Theor Appl Genet 132: 2485
|
Progress 09/01/17 to 08/31/18
Outputs
Target Audience:The audience for the web site to be developed for this project includes all members of the scientific and breeding communities interested in phenotypic information important for crop production and improvement. Results will be shared with stakeholders at international, national, regional and local grower and industry meetings and at field days. Carrot is a crop that the general public is familiar with, so approx. 40 selected diverse carrots will be grown and managed annually by undergraduate students at land grant universities including those in California, North Carolina, Washington and Wisconsin. This diversity garden approach will be the basis of interactive science outreach programs for K-12 students, undergraduate students, educational, and consumer groups in those states focusing on breeding, genetic diversity and nutrition. These diverse carrots will be available to any field-based STEM and agricultural education institution. The FARM SMART program at the University of California Desert Research and Extension Center will develop an agricultural literacy component that incorporates agriculture (in particular an expanded awareness of carrots and other vegetables) in presentations to school (K-12) and community (adult) outreach programs in carrot nutrition and production. Markers and sequence information for traits phenotyped will be available to stakeholders through conferences, web-accessible databases, and publications. Genomic tools will be demonstrated at workshops and will include hands-on training with presentations/webinars/videos developed to demonstrate approaches to marker discovery and marker assisted selection for breeders. The process of discovering plants with desirable carrot phenotypes will be described to the scientific and breeding communities in publications, webinars, and at meetings to instruct them on critical aspects of both the phenotype screening process as well as best procedures to utilize breeding pools developed by this project, and to initiate the development of breeding pools on their own. On-farm testing will be used to engage growers in participating in the evaluation of breeding pools, and for them to provide critical feedback to project scientists about the on-farm level performance of early-generation breeding stocks. Quality assessments of breeding pools by chefs and consumers also both inform those stakeholders about germplasm under development from this project, as well as provide feedback to project scientists about the progress achieved by this project in carrot improvement at the consumer level. Nutritional quality evaluations will be presented at horticulture, nutritional science, and grower meetings and in scientific and popular publications. Student and general public outreach staff and scientists involved in the project will receive and dispense information from on-farm and consumer stakeholder testing. Information on economic impacts of carrot traits will be presented at agricultural economics and agribusiness meetings and in scientific publications. Cost and return results and consumer demand results will be presented to industry stakeholders in reports, websites and other media based tools. Issues briefs and short information bulletins will be developed to inform carrot industry stakeholders on important opportunities about new varieties, and the general public is also expected to extensively use this information. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Year 2 activities included grow-out of diverse carrot breeding stocks which are being distributed to stakeholders and general public contacts for project promotion and as educational materials. Forms to track the responses of recipients of materials are being developed. Stakeholder training for database use was initiated through communication with stakeholders seeking information on project results. As part of the education activities, undergraduate students, graduate students and post-doctorates are being trained in vegetable breeding, crop and seed production, disease protection and diagnosis, and genomic analysis and database development as they participate in research projects critical to the project achieving the research goals. 2017/2018 FARM SMART Carrot Activities continued those initiated in year 1 of the project including field production of colored carrots, field tours, and extensive exposure to elementary high school and college students, and members of the general public visiting and touring the Desert Research and Extension Center near El Centro, CA. In Davis, CA, the project allowed Student Farm undergraduate interns, volunteers and student employees to participate in carrot production in the UC Davis field teaching areas. As well as school children and chaperones. How have the results been disseminated to communities of interest? January 13-17, 2018, poster presentation at Plant and Animal Genome Meeting June 11, 2018, oral presentation (S. Tanumihardjo),FASEB Retinoids Conference, Steamboat Springs, CO June 19, 2018, Gordon Research Conference on Carotenoids, Newry, ME July 31 - August 3, 2018, poster presentation (P. Simon) at ASHS, Washington, DC August 21-23 2018, poster and oral presentation (M. Iorizzo) oral presentation of population structure and potential core collection strategies (S. Ellison), poster (P. Simon) International Carrot Conference, Madison WI. September 20, 2018, oral presentations at International Apiaceae Meeting (P. Simon, M. Iorizzo, S. Ellison), September 19-22, 2018, Krakow, Poland. What do you plan to do during the next reporting period to accomplish the goals?All field evaluations and research activities, and database development described for Year 2 will continue in Year 3. In addition, third generation breeding pool seed will be produced for traits evaluated in Year 3. Cavity spot evaluation methodologies will be tested. Re-testing of germplasm entries with more desirable performance will be undertaken to confirm previous results. Data for publications on flavor, top size, alternaria and nematode resistance, and bolting will be summarized and preliminarily analyzed in preparation of GWAS analyses. Addition of resequencing and GBS data and images to the Carrotomics database will proceed. Nutritional bioefficacy and economic impact analyses will be advanced. Outreach and educational events planned for Year 2: Presentations on the carrot SCRI project will be delivered at: Plant and Animal Genome Meeting, January 1 ASHS, Las Vegas, NV, July 22-25, 2019
Impacts
What was accomplished under these goals?
Carrots are a high-value crop worth $750M to US growers and the largest crop source of vitamin A in the US diet. Approx. 86% of the carrot production area and 94% of crop value is in fresh market carrots, with 85% of fresh market carrots grown in CA. WA and WI are the largest producers of carrots for processing. Nation-wide expansion of small-scale local vegetable markets has increased carrot production, and this trend contributes to the growing organic market share of the US production, estimated at 14%. Conventional and organic growers, processers, product developers, industry breeders, and genomic application labs were surveyed in 2014 and convened in 2015 to identify top traits deemed important for improving productivity, expanding product development, and strengthening economic viability. Based on this stakeholder input, this project addresses the critical needs of the carrot industry, to identify novel sources of genes for carrot improvement in future carrot breeding. We will identify genes for improved resistance to diseases and pests, reliable crop production and tolerance to environmental stress, and enhanced consumer quality. To complement this gene discovery, we will develop a carrot database to provide breeders and other researchers with a platform to deliver information for carrot breeders to tap into the breadth of carrot genetic diversity; and establish a science-based foundation for long-term carrot improvement. Nutritional profiles and consumer attitudes toward carrots will be developed, the economic value of new breeding traits will be measured, and students will be educated. These new gene sources will be used in future breeding efforts to develop crop germplasm that requires less pesticide use and increased farm value; novel, high-value carrot products; and improved flavor and nutritional value for consumers. Longterm impacts are expected to increase crop consumption, benefit the environment and human health, and develop crop improvement strategies applicable to other crops. Project Objectives and Annual Progress: 1 - Phenotype diverse carrot germplasm and breeding stocks to discover and describe previously uncharacterized variation for important traits: Variation in root-knot nematode resistance and Alternaria leaf blight resistance, bolting incidence, and stand establishment was phenotyped in 694 diverse open-pollinated carrots from the USDA-NPGS carrot germplasm collection (PI collection) and 70 public inbreds; evaluation of consumer acceptance of color and flavor was initiated. In year 2 approximately 100 carrot germplasm accessions with putative partial to high levels of nematode resistance to M. incognita in year 1 were screened in the greenhouse in year 2 where 21 entries had high levels of resistance. This set of 21 entries shown to have high levels of resistance in the greenhouse was confirmed to be resistant in the field at UC Kearney, and most resistant lines were also resistant to M. javanica. Selected roots were sent to Wisconsin for breeding pool and mapping population development. A major field experiment is in progress at UC Riverside to evaluate the drought tolerance. Water was withheld from mid-season onward and phenotypes for wilting and recovery after re-watering in late season were scored. Bolting was also evaluated where about 20% bolted. These data will be used for association studies and candidate gene analyses. The 694 lines and 70 inbreds were also tested in Hancock, WI where approx 30% bolted at time of harvest, with high concordance between lines bolting in WI and CA. In WI approx. 30 PIs were confirmed to have superior Alternaria resistance. Stand establishment and flavor were also evaluated in WI and carotenoid content was quantified in 169 samples. Seed was produced on 41 selfed PIs. A field site was inoculated for the 2nd year with isolates of two primary cavity spot pathogens, Pythium violae and P. sulcatum, at WSU Othello, WA to establish a screening nursery but very limited cavity spot developed on carrots evaluated. Therefore, the site was abandoned and after consulting with the SCRI advisory team, a new field site was selected and inoculated at the WSU Mount Vernon, WA. In addition, a root inoculation protocol using colonized agar plugs is being evaluated to determine if root inoculation results correlate adequately with field screening results. Data was also collected on the PI and inbred collection grown in Hancock, WI for early germination, emergence and stand establishment. This data will be used for association analysis and the development of mapping populations to study this important phase of carrot development in more detail. 2 - Develop an expanded carrot genomic database for breeders to catalogue genomic and phenotypic variation and track genes underlying important traits: DNA was extracted from 792 PI and inbred plants and submitted for resequencing at UC Davis and the same plants that were sampled for resequencing were photographed at harvest, phenotyped for bolting, and sampled for flavor, sugar, and carotenoid analysis.. Over 500 PIs have been photographed and images will be uploaded to the carrot genome database. Population structure in the PI collection was analyzed and an association analysis for pigment color was conducted. We found that a genomic region containing the Or gene is important to carrot pigmentation and likely played a role in domestication. The Or gene has been described in other crop species but not in carrot. Our analysis used a large, diverse collection of germplasm to identify this region. This work was published in Genetics. The carrot genome assembly was assembled at chromosome level. In total, 415 Mb were anchored to pseudomolecules, which represents a 43 Mb increase over the previous assembly. Nanopore sequence and Hi-C data were generated and are currently used to verify the quality of the assembly and correct chimeric sequences. IsoSeq data from four libraries were obtained. Each library represented RNA from 4 tissues, including: 1) root phloem; 2) root xylem; 3) germinating seeds and; 4) upper part of the plant (pool RNA from petiole, leaves, and flower). The IsoSeq data is currently used to perform gene prediction and annotation and to identify tissue specific genes and isoforms. The development of the carrot genome database was initiated to curate phenotypic and genotypic data. This database is based on the mainlab Tripal modules provided by the Doreen Main group, and also used by CottonGen and other databases. 3 - Initiate development and evaluation of breeding pools from diverse germplasm and breeding stocks: Roots with elite nematode and Alternaria resistance, low-bolting incidence, large tops, vigorous stand establishment, excellent flavor, and unique color were intercrossed to develop F1 hybrids for the development of breeding pools. More than 300 PIs have been self-pollinated to begin creating breeding pools and establish segregating populations. To advance studies on bioefficacy evaluation of carrot nutritional quality, two gerbil nutrition evaluation studies were completed, one with the carrot leaves and one with the high beta-carotene carrot roots. Also a chicken egg coloring study was completed. Data are being analyzed. 4 - Evaluate the economic impacts of new carrot traits on grower practices and costs, and consumer decisions: Retail Scanner Data was analyzed for price differences across fresh carrot products sold in two metropolitan areas - Los Angeles (LA) and Atlanta (ATL). The largest selling form of carrots in each location was baby carrots. Despite price premiums over average carrot price of 20% in LA and 10% in ATL, baby carrots accounted for 40% and 49% of carrot sales, respectively. The results indicate that consumers are willing to pay trait differences when selecting carrot products.
Publications
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2018
Citation:
Shelby L. Ellison, Claire H. Luby, Keo E. Corak, Kevin M. Coe, Douglas Senalik, Massimo Iorizzo, Irwin L. Goldman, Philipp W. Simon and Julie C. Dawson
GENETICS Early online October 23, 2018; https://doi.org/10.1534/genetics.118.301299
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Progress 09/01/16 to 08/31/17
Outputs
Target Audience:The audience for the web site to be developed for this project includes all members of the scientific and breeding communities interested in phenotypic information important for crop production and improvement. Results will be shared with stakeholders at international, national, regional and local grower and industry meetings and at field days. Carrot is a crop that the general public is familiar with, so approx. 40 selected diverse carrots will be grown and managed annually by undergraduate students at land grant universities including those in California, North Carolina, Washington and Wisconsin. This diversity garden approach will be the basis of interactive science outreach programs for K-12 students, undergraduate students, educational, and consumer groups in those states focusing on breeding, genetic diversity and nutrition. These diverse carrots will be available to any field-based STEM and agricultural education institution. The FARM SMART program at the University of California Desert Research and Extension Center will develop an agricultural literacy component that incorporates agriculture (in particular an expanded awareness of carrots and other vegetables) in presentations to school (K-12) and community (adult) outreach programs in carrot nutrition and production. Markers and sequence information for traits phenotyped will be available to stakeholders through conferences, web-accessible databases, and publications. Genomic tools will be demonstrated at workshops and will include hands-on training with presentations/webinars/videos developed to demonstrate approaches to marker discovery and marker assisted selection for breeders. The process of discovering plants with desirable carrot phenotypes will be described to the scientific and breeding communities in publications, webinars, and at meetings to instruct them on critical aspects of both the phenotype screening process as well as best procedures to utilize breeding pools developed by this project, and to initiate the development of breeding pools on their own. On-farm testing will be used to engage growers in participating in the evaluation of breeding pools, and for them to provide critical feedback to project scientists about the on-farm level performance of early-generation breeding stocks. Quality assessments of breeding pools by chefs and consumers also both inform those stakeholders about germplasm under development from this project, as well as provide feedback to project scientists about the progress achieved by this project in carrot improvement at the consumer level. Nutritional quality evaluations will be presented at horticulture, nutritional science, and grower meetings and in scientific and popular publications. Student and general public outreach staff and scientists involved in the project will receive and dispense information from on-farm and consumer stakeholder testing. Information on economic impacts of carrot traits will be presented at agricultural economics and agribusiness meetings and in scientific publications. Cost and return results and consumer demand results will be presented to industry stakeholders in reports, websites and other media based tools. Issues briefs and short information bulletins will be developed to inform carrot industry stakeholders on important opportunities about new varieties, and the general public is also expected to extensively use this information.The audience for the web site to be developed for this project includes all members of the scientific and breeding communities interested in phenotypic information important for crop production and improvement. Results will be shared with stakeholders at international, national, regional and local grower and industry meetings and at field days. Carrot is a crop that the general public is familiar with, so approx. 40 selected diverse carrots will be grown and managed annually by undergraduate students at land grant universities including those in California, North Carolina, Washington and Wisconsin. This diversity garden approach will be the basis of interactive science outreach programs for K-12 students, undergraduate students, educational, and consumer groups in those states focusing on breeding, genetic diversity and nutrition. These diverse carrots will be available to any field-based STEM and agricultural education institution. The FARM SMART program at the University of California Desert Research and Extension Center will develop an agricultural literacy component that incorporates agriculture (in particular an expanded awareness of carrots and other vegetables) in presentations to school (K-12) and community (adult) outreach programs in carrot nutrition and production. Markers and sequence information for traits phenotyped will be available to stakeholders through conferences, web-accessible databases, and publications. Genomic tools will be demonstrated at workshops and will include hands-on training with presentations/webinars/videos developed to demonstrate approaches to marker discovery and marker assisted selection for breeders. The process of discovering plants with desirable carrot phenotypes will be described to the scientific and breeding communities in publications, webinars, and at meetings to instruct them on critical aspects of both the phenotype screening process as well as best procedures to utilize breeding pools developed by this project, and to initiate the development of breeding pools on their own. On-farm testing will be used to engage growers in participating in the evaluation of breeding pools, and for them to provide critical feedback to project scientists about the on-farm level performance of early-generation breeding stocks. Quality assessments of breeding pools by chefs and consumers also both inform those stakeholders about germplasm under development from this project, as well as provide feedback to project scientists about the progress achieved by this project in carrot improvement at the consumer level. Nutritional quality evaluations will be presented at horticulture, nutritional science, and grower meetings and in scientific and popular publications. Student and general public outreach staff and scientists involved in the project will receive and dispense information from on-farm and consumer stakeholder testing. Information on economic impacts of carrot traits will be presented at agricultural economics and agribusiness meetings and in scientific publications. Cost and return results and consumer demand results will be presented to industry stakeholders in reports, websites and other media based tools. Issues briefs and short information bulletins will be developed to inform carrot industry stakeholders on important opportunities about new varieties, and the general public is also expected to extensively use this information. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Year 1 activities included grow-out of diverse carrot breeding stocks which are being distributed to stakeholders and general public contacts for project promotion and as educational materials. Forms to track the responses of recipients of materials are being developed. Stakeholder training for database use was initiated through communication with stakeholders seeking information on project results. As part of the education activities, undergraduate students, graduate students and post-doctorates are being trained in vegetable breeding, crop and seed production, disease protection and diagnosis, and genomic analysis and database development as they participate in research projects critical to the project achieving the research goals. 2016/2017 FARM SMART Carrot Activities included: in September 2016: California Ag in the Classroom Conference, Sacramento, CA, where we led a carrot themed "Taste of California" table at the annual Ag in the Classroom conference dinner; and introduced California educators from across the state to the colored carrot research taking place at the University of California, Desert Research and Extension Center. The dinner included a display on colored carrots, information on current research from Dr. Simon, information on the history of carrots, packets of carrot seeds to take back to their classrooms, colored carrot tastings, and lesson plan development specifically related to the research. Lesson plans included an emphasis on carrots and carrot diversity, and health benefits of disease-preventive pigments that give plants their distinctive colors. Participants left with a better understanding of the history of carrots and methods to incorporate carrots into their varying grade levels and educational institutions. Conference attendance was over 300 educators. In January-February, 2017: The FARM SMART Winter Visitor Program provided field tours to close to 1000 participants from across the United States and Canada with hands-on activities including carrot harvesting, carrot recipe demonstrations, and carrot sampling. FARM SMART was able to introduce the research and history of the colored carrots, offer harvesting of colored and traditional carrots, and provided nutritional values of the different colored carrots. Participants were also introduced to carrot harvesting methods and carrot production facts for Imperial County and California. In March-April, 2017: The FARM SMART K-12 Field Trips provided carrot education through outreach to over 7500 participants in our K-12 field trip program. Students who attended a FARM SMART program from March to April had the opportunity to learn what carrots need to grow, the history of colored carrots, their nutritional value, as well as an opportunity to harvest their own traditional and organic carrots. Teachers were also given resources to further enrich their lesson plans to include carrots. In April-May, 2017: Imperial Valley College Ag Students were provided carrot research information and introduced to colored carrots, with over 30 visiting community college agriculture students in attendance. Students had the opportunity to harvest traditional and colored carrots from the FARM SMART garden and experiment with colored carrot recipes. In Davis, CA, the project allowed Student Farm undergraduate interns, volunteers and student employees to participate in carrot production in the UC Davis Student Farm Market Garden and Ecological Garden teaching areas. This numbered 50-60 students each academic quarter. Students involved in our undergraduate courses PLS 193 and PLS 49 also learned about how carrots are grown and had the opportunity to harvest and consume fresh product. This numbered roughly 80 students over 3 quarters. In addition during spring quarter we hosted 2000 school children and about 200 chaperones on this site. About half of those students and their chaperones learned about and/or harvested and ate carrots during these educational activities. How have the results been disseminated to communities of interest?Educational events and conference presentations delivered in 2016-17 included: March 19, 2017, SCRI Advisory Panel meeting, Bakersfield, CA March 20, 2017, SCRI poster and oral presentations, International Carrot Conference, Bakersfield, CA August 30, 2017, SCRI PD meeting, Traverse City, MI What do you plan to do during the next reporting period to accomplish the goals?All field evaluations and research activities, and database development described for Year 1 will continue in Year 2. In addition, first generation breeding pool seed will be produced for traits evaluated in Year 1. Educational events planned for Year 2: Presentations on the carrot SCRI project will be delivered at the Plant and Animal Genome Meeting, January 13-18, 2018, San Diego, CA; ASHS Meeting, July 31-August 3, 2018, Washington,DC, International Carrot Conference, August 21-23, Madison, WI, and International Apiaceae Meeting, September 19-22, 2018, Krakow, Poland. -------
Impacts
What was accomplished under these goals?
Carrots are a high-value crop worth $750M to US growers and the largest crop source of vitamin A in the US diet. Approx. 86% of the carrot production area and 94% of crop value is in fresh market carrots, with 85% of fresh market carrots grown in CA. WA and WI are the largest producers of carrots for processing. Nation-wide expansion of small-scale local vegetable markets has increased carrot production, and this trend contributes to the growing organic market share of the US production, estimated at 14%. Conventional and organic growers, processers, product developers, industry breeders, and genomic application labs were surveyed in 2014 and convened in 2015 to identify top traits deemed important for improving productivity, expanding product development, and strengthening economic viability. Based on this stakeholder input, this project addresses the critical needs of the carrot industry, to identify novel sources of genes for carrot improvement in future carrot breeding. We will identify genes for improved resistance to diseases and pests, reliable crop production and tolerance to environmental stress, and enhanced consumer quality. To complement this gene discovery, we will develop a carrot database to provide breeders and other researchers with a platform to deliver information for carrot breeders to tap into the breadth of carrot genetic diversity; and establish a science-based foundation for long-term carrot improvement. Nutritional profiles and consumer attitudes toward carrots will be developed, the economic value of new breeding traits will be measured, and students will be educated. These new gene sources will be used in future breeding efforts to develop crop germplasm that requires less pesticide use and increased farm value; novel, high-value carrot products; and improved flavor and nutritional value for consumers. Longterm impacts are expected to increase crop consumption, benefit the environment and human health, and develop crop improvement strategies applicable to other crops. Project Objectives and Annual Progress: 1 - Phenotype diverse carrot germplasm and breeding stocks to discover and describe previously uncharacterized variation for important traits: Variation in root-knot nematode resistance and Alternaria leaf blight resistance, bolting incidence, and stand establishment was phenotyped in 694 diverse open-pollinated carrots from the USDA-NPGS carrot germplasm collection (PI collection) and breeding stocks; evaluation of consumer acceptance of color and flavor was initiated. A major field experiment was conducted at the University of California Riverside's Coachella Valley Agricultural Research Station, Thermal, CA to determine the resistance/susceptibility of the carrot germplasm collection to the root-knot nematode Meloidogyne incognita. The trial included 694 carrot Plant Introductions (PIs) obtained from USDA, grown on 1-m length two-row plots, replicated twice. Susceptible control line Imperator 58 was grown in every fifth plot. The field was heavily infested with the nematode, with high pre-plant densities uniformly distributed across the field. The trial was planted in late March, 2017 and the roots assayed for nematode infection on roots (root-galling index, 0-9 scale) in mid-August, 2017. Stand-counts as a measure of stand establishment were taken after 6 weeks. The trial was also used to score the bolting phenotype of each entry, scored in May and June. Results of the nematode response assays revealed 73 of the 694 entries (10.5%) with putative partial to high levels of resistance, of which 13 (1.9%) entries had very high resistance responses. Taproots of all putative resistant entries were collected and shipped to Wisconsin for crossing and seed production. About 80 entries of these putative resistance sources were grown in greenhouse pots at UC Riverside, inoculated with M. incognita 3-weeks after emergence, and are currently awaiting assessment for root-galling and egg production scores to confirm the levels of resistance. We measured bolting in the trials carried out in Coachella Valley, CA (a desert location with high heat (120°F) that promotes bolting) by counting plants and bolted plants to calculate percent bolting. Of the 694 lines tested 47% bolted. Similarly, of the 694 lines tested in Hancock, WI, 31% bolted at time of harvest. There was high concordance between lines bolting in Hancock and those bolting in Coachella Valley. Trials will be repeated in 2018. These data will be used for association studies and candidate gene analyses. We identified 32 PIs with superior Alternaria resistance. Stand establishment was evaluated in WI. Flavor evaluation is underway. Cavity spot evaluation field preparation was initiated by establishing a nursery at the WSU Othello REU in central Washington. The 0.3-acre site was fumigated with Vapam HL in March 2017, inoculated by spreading ~400 liters of a sand-cornmeal inoculum (mix of ~200 liters of inoculum of each of Pythium sulcatum and P. ultimum), and then planted with a blend of non-treated seed of six carrot cultivars that are highly susceptible to cavity spot (provided by seed companies). In late summer, the carrot roots were disked into the nursery site to promote establishment of cavity spot inoculum. 2 - Develop an expanded carrot genomic database for breeders to catalogue genomic and phenotypic variation and track genes underlying important traits: PI and breeding stock samples were collected and DNA was extracted for GBS and/or resequencing. We are currently analyzing population structure in the collection and preparing phenotypic data for association analyses. Over 500 PIs have been photographed and images will be uploaded to the carrot genome database currently under development. A new carrot genome assembly using Pacific Bioscience long read sequencing technology has been developed. The carrot assembly V3.0 covers 436Mb with a contig N50 of 3.3 Mb. Compared with the carrot genome assembly V2.0 this new assembly captured about 15Mb of new sequence, and represents a 172-fold improvement in terms of sequence contiguity. Assembly validation and chromosome anchoring is currently ongoing. RNA from six different tissues including germinating seeds, leaf, flower, petiole, phloem and xylem has been extracted and is ready to use for sequencing with Pacific Bioscience long read technology. These sequences will be used to perform gene prediction and annotation. Phylogenetic prediction of Alternaria resistance was analyzed using part of the carrot germplasm base. The development of the carrot genome database was initiated to curate phenotypic and genotypic data. This database is based on the mainlab Tripal modules provided by the Doreen Main group, which are used by CottonGen and other databases. 3 - Initiate development and evaluation of breeding pools from diverse germplasm and breeding stocks: Roots with elite nematode and Alternaria resistance, low-bolting incidence, vigorous stand establishment, excellent flavor, and unique color were stored and are being vernalized for upcoming use in seed production in the development of breeding pools. More than 300 PIs have been self-pollinated to begin creating breeding pools and establish segregating populations. Two gerbil nutrition evaluation studies were completed, one with the carrot leaves and one with the high beta-carotene carrot roots. Also a chicken egg coloring study was completed. Data are being analyzed. 4 - Evaluate the economic impacts of new carrot traits on grower practices and costs, and consumer decisions: Activities will be initiated later in the project.
Publications
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