Progress 09/15/23 to 09/14/24

Outputs
Target Audience:The audience 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 selected diverse carrots will be grown and managed annually by undergraduate students at land grant universities including this in California, North Carolina, Washington and Wisconsin. This diversity garden 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 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 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 provide critical feedback to project scientists about the performance of early-generation breeding stocks as perceived at the on-farm level. 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, 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. 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 2 outreach training activities included: Trained one post-doc (Iorizzo program) in genome sequencing and genomic analysis Trained 1 senior research associate and Trained one MSc student at UC Davis in carrot genetics and genomics for bolting Ongoing training in genetic mapping, diversity analysis, molecular marker development, gene expression analysis, and breeding methodology for two graduate students and one postdoc on carrot seed characteristics, early growth, stand establishment, carbohydrate composition analysis, and carotenoid accumulation (Simon and Dawson programs). Economist Dr. Lee continues on his postdoc completing research papers and initiating related work on carrot demand econometrics (Sumner program). Undergraduate assistants and junior researchers are gaining training in econometrics of carrot demand estimation of farm cost functions. Organic Seed Alliance hire Susana Cabrera-Mariz as a research and education associate. Cabera-Mariz published her MS thesis at Iowa State University including a chapter on carrot history, domestication and cultural food pathways. She will continue to develop and deliver outreach and education on this topic in the next year of the current project. (Colley program). How have the results been disseminated to communities of interest?Educational events and conference presentations delivered in 2022-23 included: At the 41st International Carrot Conference, July 8-10, 2024, Raleigh, NC. USDA-NIFA-SCRI Project Stakeholder and Advisory Panel meeting convened in person, presenting project results and soliciting feedback on project objectives all day July 8. Hosted Alternaria field trial demonstrating resistance of select SCRI lines to ALB in high pressure environment. Presentations on USDA-NIFA-SCRI Project research Julie Dawson, Tony Schuh, Keo Corak, and Phil Simon. Improving selection strategies for stand establishment Phil Roberts, Phil Simon, Bao-Lam Huynh. Genetic mapping of resistance in carrot effective against multiple Meloidogyne hapla populations. Douglas Senalik, William Rolling, Massimo Iorizzo, Shelby Ellison, Allen Van Deynze, Phil Simon. CarrotOmics - A community driven database supporting open science. Iorizzo M., R. Seth, M.A. Abid, P. Simon and P.F. Cavagnaro. Carrot anthocyanin genetics: recent advances and future prospectives. Abid M.A., J. Curaba, S. Esposito, P. Cavagnaro, V. D'Amelia and M. Iorizzo. Functional characterization of DcMYB11, an R2R3 MYB associated with the purple pigmentation of carrot petiole. At the Fourth Plant & Animal Genome Workshop on Apiaceae, January 13, 2024, San Diego, California, USA. Chaehee Lee, University of California - Davis, Crunching through Celery Genomic Resources for Breeding Resistance to Fusarium oxysporum Magdalena Klimek-Chodacka, University of Agriculture, Krakow, -, Poland, Early Attempts to Edit the Carrot Genome Using CRISPR Tools Rajesh Yarra, University of Wisconsin-Madison, CENH3-Based Haploid Induction in Carrot Alicja Macko-Podgorni, University of Agriculture in Krakow, Krakow, Poland, Genome-Wide Screening Reveals the Role of a Carrot Tourist Mite Family in Rewiring Lhy-Regulated Circadian Clock Network Massimo Iorizzo, North Carolina State University, Functional Characterization of DcMYB11, an R2R3 MYB Associated with the Purple Pigmentation of Carrot Petiole William Rolling, USDA, ARS and University of Wisconsin-Madison, Madison, Or, Y, and Y2 ... a Rec Encoding Gene Too? Genome-Wide Association Analyses in Carrot Diversity Panels Identify More Loci Involved in Carotenoid Accumulation At the California Seed Association Conference, September 25-26 2024, Monterey, CA. A. Van Deynze. Research progress at the Seed Biotechnology Center. Stakeholder events included: March 4-8, 2024, Carrot harvest trial, PI collection evaluation and breeding pool development; and March 7 hybrid trials and industry field day (P. Simon, M. Colley, J. Diaz, J. Sidhu) at Desert Research and Extension Center, El Centro, CA March 20, 2024, Presentation to California Fresh Carrot Advisory Board Symposium on results of selection and breeding for combined nematode resistance, cavity spot, and preferred agronomic performance (P Roberts, J. Sidhu, P. Simon) Bakersfield CA (virtual meeting) June 23, 2023, Conventional carrot variety trial, Bakersfield, CA, University of California Cooperative Extension. July 8, 2024, SCRI project meeting with Advisory Board. All co-PIs presented project progress and planned activities. July 8-10, 2024, PI Iorizzo hosted the 41st International Carrot Conference in Raleigh, NC. Conference was attended by 85 scientists and industry representatives, from 10 countries. August 20-22, 2024, Root-knot nematode (Meloidogyne incognita and M. javanica) trial and industry field day (P. Roberts, P. Simon) at UCR Coachella Valley Agricultural Research Station, Thermal, CA August 26, 2024, Organic Seed Alliance fall field day showcasing carrot trials and seed increases (~50 participants). September 17, 2024, Carrot hybrid trial (P. Simon) from Hancock, WI Miller Farm crop displayed on Univ. Wisconsin campus, Horticulture Annex, Madison, WI At UC Davis (A. Van Deynze) Hosted farm & garden field days at the Student Farm for nearly 1,900 elementary school students, Kindergarten to 6th grade (ages 5-12) Included 30+ schools from highly diverse Sacramento-area communities and over 100 teacher and parent chaperones. Activities were led by 35 UC Davis student educators from a variety of major. These undergraduate and graduate students train to become garden educators for a quarter and design new lessons, based on their interests and observations at the farm At UC-DREC (J. Diaz) Summary From July 1, 2023 to June 30, 2024 Farm Smart delivered carrot outreach programs in nutrition and production to 3,053 participants, which includes educators, K-12 students, and community members. Below is a summary of activities delivered. These programs were designed and delivered by Clarissa Abarca, Community Education Specialist and intern student, Fatima Gutierrez. 10/19/23 Julian Food Day - K-6th grade (186 participants) Provided an informational booth with the history of carrots, research done with colored carrots, other plants in the Umbelliferae family, and a colored carrot taste testing. 1/27/24 Farm to Preschool Festival - 0-5 year old and their families (1,446 participants) Colored carrot table highlighting the pigment power in each ofthe five carrot colors, and colored carrot taste testing. Presentations of "The Colorful World of Carrots", developed by our carrot intern, Fatima Guiterrez (148 participants) The presentation discussed the evolutionof the carrot, pigment power, nutritional value increased through research done by Dr. Phil Simon, observations of other plants in the Apiaceae family, and a colored carrot taste testing. 2/20/24 Southwest High School (90 participants) 2/27/24 ChLOE - Non-Formal STEM educators from across the U.S (17 participants) 3/7/24 Pheonix Rising High School (41 participants) Community Harvesting Events (255 participants) These events included carrot Harvesting, informational handouts with carrot nutritional benefits information, and summary of carrot research conducted at DREC. 2/21/24 Senior Citizen U-Pick (130 participants) 4/3/24 Public U-Pick for all ages (125 participants) Farm Tours (39 participants) Tours of the Desert Research and Extension Center. During each tour, we stopped at the fields where carrot research is being done. We provided information regarding the current project, improvements through previous carrot research such as the increase of nutritional benefits, what takes place during the field day with Dr. Simon, and the importance of continued research and outreach. 10/5/23 California Women of Agriculture (CWA) (6 participants) 2/7/24 Star Destinations - French Visitors (33 participants) Vegetable Adventures Field Trips - March through April (979 participants) Field trips for K-12th grade students across the Imperial County. This program is centered around teaching students everything plants need to grow. From topics such as soil types, the parts of the plant we eat, where seeds come from, to harvesting techniques that will be used during our time in the Farm Smart learning garden. Students observe carrot flowerheads that have gone to seed, the different colors of carrots, research done on carrots at our center, and get to harvest carrot themselves. What do you plan to do during the next reporting period to accomplish the goals? Meet with stakeholders at the 32nd Plant & Animal Genome Meeting, January, 2025 Initiate stakeholder meetings during the SCRI zoom meetings in the spring of 2025 to report project progress, invite feedback and gather additional input from them on current and future project direction. Continue field evaluations and research activities to advance studies for all project objectives. This will include: Complete sequencing and assembly the additional four samples and scaffolding of all the 36 samples. Complete sequencing RNA samples. Initiated genome annotation and comparative genome analysis. Initiate testing the genotyping platform. Genotype multi-parental and bi-parental mapping populations based on breeding pools developed in the first SCRI project and the genotyping platform currently being developed. Advance mapping of gene locations of economically important traits using multi-family linkage mapping and develop genomic prediction models for these traits based on cross-validation, to be further field-validated in years 3 and 4. Advancement of nematode resistant carrot materials will include combined phenotyping in infested field sites at Coachella, CA and in controlled inoculation greenhouse screenings at UC Riverside. Selected roots with nematode resistance and preferred agronomic qualities will be sent to WI for advancement and crossing in breeding pools. GBS-based marker development and RNAseq based gene identification will be used to develop more accurate genome markers for marker-assisted selection. Advancement of cavity spot resistant carrot materials will include combined phenotyping in an inoculated field sites at Mount Vernon, WA and Shafter, CA. Selected roots with cavity spot resistance and preferred agronomic qualities will be sent to WI for advancement and crossing in breeding pools. GBS-based marker development will be initiated to develop more accurate genome markers for marker-assisted selection. OSA plans to continue selecting and increasing the nematode x flavor breeding pool and screening additional PI lines at the OSA research site in WA. Advance breeding pools grown on trial locations appropriate to include phenotyping Alternaria leaf blight, stand establishment, top size, and flavor. Alternaria breeding pools also to be evaluated selected under A. dauci pressure in on-farm trials in ME, NC, and VA. For bolting mapping populations, self/vernalize and harvest seed F2 plants, and plant additional 6-8 F2 populations over the winter at UC Davis to create F3 populations. Grow 1-3 F3 mapping populations in the field in spring and fall 2025, as well as genotype to study inheritance of bolting in specific backgrounds. Advance stand establishment plant growth phenotyping of ~200 carrot PIs and diallel populations Outreach and educational events planned for next year include- Presentations on the carrot SCRI project at meetings, outreach events, field days, etc. Presentations at the Plant and Animal Genome meetings (several co-PIs) Present data at the carrot SCRI project stakeholder meeting (all co-PIs) Continue outreach activities at the University of California, Desert Research and Extension Center (UC-DREC), Holtville, CA (P. Simon, M. Colley, J. Diaz, J. Sidhu) Present research results will be made to California Fresh Carrot Advisory Board Symposium, Spring 2025. (P. Roberts, P. Simon). Hold an industry-stakeholder field day at the UCR Coachella Research Station field trial for nematode resistance screening in summer 2025. (P. Roberts, P. Simon). Hold carrot stakeholder field days with the University of California Cooperative Extension, Kern County, CA (J. Sidhu) Cover carrot demand and the role of organic carrots in UC Davis MS course in Agricultural Economics and undergrad course in Economics of Agricultural Sustainability. Present new work on organic carrot demand at the Agricultural and Applied Economics meeting in August 2025 in Denver (D. Sumner, H Lee and O. Sambucci) At UC-DREC we are planning to conduct similar activities for the next reporting period. Deliver an educational webinar on the history and domestication of carrot (M. Colley and graduate student Cabrera-Mariz)

Impacts
What was accomplished under these goals? Carrots are a high-revenue crop with farm cash receipts of $1.82billion (2023) and are the largest crop source of vitamin A in the US diet. Approx 86% of the carrot acreage and 94% of crop value is sold in the fresh market, with 85% of fresh market carrots grown in CA. WA and WI are the other significant producers. Nationwide expansion of small-scale local vegetable markets has increased carrot production, and this trend contributes to the growing organic market share of US production, estimated at 19%. Conventional and organic carrot growers, processors, product developers, industry breeders, and genomic labs identified breeding priorities (listed below) and, based on follow-up stakeholder input in Jan 2021, those traits were confirmed as the top priorities for improving productivity, expanding product development, and strengthening economic viability. Improved cultivars with these characteristics will provide a cost-effective and environmentally responsible means to deliver an improved carrot crop to growers and consumers. However, carrot breeders will need new sources of favorable alleles, genomic resources to incorporate the alleles, and tested breeding stocks to develop superior cultivars efficiently. Based on stakeholder input, the Long-term Goals of this project are to: 1) release carrot germplasm with improved performance, from diverse carrot germplasm and breeding stocks, for traits important to growers and consumers; 2) generate genomics-based breeding tools to deliver phenotypic and genotypic information for carrot breeders to tap into the breadth of carrot genetic diversity; 3) establish a science-based research and outreach foundation for long-term carrot improvement that includes measures of economic value for producers and nutritional value for consumers; 4) train students and post-docs in carrot breeding and genetics, which was highlighted by industry stakeholders as an important goal to support longer-term carrot breeding; 5) engage stakeholders and the public to transfer project deliverables and educate them about importance of carrot research as well as carrot nutritional value. Based on this input, we have four research objectives for the current project. Project Objectives and Annual Progress: OBJECTIVE 1: Develop cost-effective genomic tools to advance breeding populations and integrate loci related to economically significant traits identified by stakeholders - Completed 32 haplotype-phased contig level genome assemblies. Chromosome level scaffolding and phasing using Hi-C data was completed for 6 genomes. DNA sequencing of 4 additional samples is ongoing. RNA extractions from roots, leaves, petioles, flowers, and germinating seeds completed for 29 samples. Preliminary analysis indicated that the genomes have very high contiguity and high collinearity with the DH1v3 genome assembly. Initiated development of the SNP catalog. Assessed genotyping platforms and selected DArT based on price and performance. DNA preparation for finalizing SNP catalog is ongoing. OBJECTIVE 2 Use multi-parental and biparental populations to map gene locations of economically important traits using optimized genomic-assisted strategies- Evaluated root-knot nematode (RKN) resistance in several bi- or tri-parental and single plant-derived populations segregating for resistance in three RKN-infested field sites for M. incognita (MI) and M. javanica (MJ) resistance response (Thermal, Coachella Valley, CA, 2024) and M. hapla resistance response (Othello, WA, successful in 2023; terminated by irrigation problem in 2024), and in inoculated greenhouse pot-screens at UCR to fine map resistance loci in the carrot genome. Plants were scored on a standard 0-8 scale for taproot and feeder root-galling symptoms. Selected roots were sent to WI for advancement and intercrossing. A primary focus is the strong resistance to MI found in Cape Market, which also exhibits resistance to other RKN species. Processed root samples for RNAseq analysis following inoculation with MJ using susceptible and resistant progeny from a population segregating for resistance locus Mj-1. F2 populations of RKN resistant by good flavor line crosses from the winter nursery were increased at the OSA research farm and sent to El Centro for the 2024 winter nursery harvest. Evaluated 55 diverse carrots in the WSU Carrot Cavity Spot (CS) Nursery in Mount Vernon, WA. Of these, 47 had reasonable plant stands to rate for incidence and severity of CS. Purple Haze was the only entry with no CS but 4 orange USDA breeding lines with F7737 or F7738 derivatives and 3 plant introductions (PIs) had <20% incidence and <10% severity of CS. Most resistant commercial cultivars had CS incidence of 22% or more. CS resistance of 56 diverse carrots was also evaluated in an inoculated field site in Shafter, CA for comparison to WSU results. Selected roots with the least CS were sent to WI to develop mapping populations. In Year 2 biparental F2 populations among 8 selected late and early bolting accessions as well as elite parents were grown in Davis, CA to evaluate bolting and selfed to develop F3 mapping populations to be genotyped in Years 3-4 for mapping and introgression of bolting loci. Established diversity pools for GWAS, biparental populations, and diallels and began evaluating stand establishment with digital phenotyping in the greenhouse. Evaluated ALB resistance and flavor in diversity pools for GWAS and in biparental populations. Evaluated and photo documented field trials of entries including breeding lines and PIs at the OSA research farm under organic conditions. Grew parental stocks and mapping populations in the El Centro, CA winter root nursery, and Hancock, WI summer root nursery for phenotyping flavor and pigment profiles. Drought tolerance of PIs and breeding stocks was evaluated in the greenhouse. Field trials conducted on-farm to evaluate resistance to ALB in Maine and Virginia. Resistant roots of ALB breeding pools were selected in ME under ALB pressure, to be regenerated in winter greenhouse Selected plants with superior performance for all traits phenotyped were intercrossed to develop new mapping populations and breeding pools. OBJECTIVE 3 Evaluate bioavailability of nutrients in selected breeding stocks with varying nutrient composition that may influence bioavailability- A comprehensive manuscript reporting pigment bioavailability results of the first acute feeding study in humans is being prepared for submission in early 2025. Carrot recipes for muffins made with the frozen purple carrots were acceptable for the chronic feeding study in humans with purple carrots based on consumer acceptance. The stability of anthocyanins in frozen purple carrots is being evaluated and a new LC/MS/MS system to quantify low levels of carrot anthocyanins is being developed. OBJECTIVE 4 Estimate economic costs and benefits value to buyers and the industry of improved traits and assess the broad societal value of these improvements- Completed econometric models of discrete choice econometric estimation of carrot demand response to price and alternative carrot product attributes that vary by demographic characteristics including age, gender, and region. Developed willingness-to-pay measures for organic, baby, and organic-baby attributes relative to each other and relative to conventional full-sized carrots. Used these models to develop estimates directly related to consumer-relevant traits developed in project breeding programs and other carrot product attributes that stakeholders have raised. Our use of CA county pesticide use data is well underway for assessing carrot improvements in pest and disease management and contributions of breeding program results that reduce costs. Trained several undergraduate research assistants and now employ junior research specialists who are learning new research skills related to carrot demand and cost estimation.

Publications

• Type: Peer Reviewed Journal Articles Status: Published Year Published: 2024 Citation: Simon, P.W., Rolling, W., Senalik, D., Dawson, J., Tanumihardjo, S., Spalding, E., Iorizzo, M., Van Deynze, A., Hill, T., Sumner, D., Goodrich, B., Ullman, K., Roberts, P., du Toit, L., Waters, T., Colley, M., McKenzie, L., Sidhu, J., Diaz, J. and Meng, Y. (2024). The carrot SCRI project taps into carrot diversity to develop genetic and genomic resources, evaluate nutrient bioavailability, and assess factors influencing grower and consumer decisions. Acta Hortic. 1393, 277-286
• Type: Peer Reviewed Journal Articles Status: Published Year Published: 2024 Citation: Loarca, J., Liou, M., Dawson, J.C. and Simon, P.W. (2024) Evaluation of shoot-growth variation in diverse carrot (Daucus carota L.) germplasm for genetic improvement of stand establishment. Front. Plant Sci. 15:1342512.
• Type: Peer Reviewed Journal Articles Status: Published Year Published: 2024 Citation: Loarca, J., Liou, M., Dawson, J.C. and Simon, P.W. (2024) Advancing utilization of diverse global carrot (Daucus carota L.) germplasm with flowering habit trait ontology. Front. Plant Sci. 15:1342513.

Progress 09/15/22 to 09/14/23

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: 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. 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 1 outreach training activities include One student (Lee; Sumner program) completed PhD on carrot demand and is now completing papers during post-doc training. Trained 1 post-doc (Iorizzo program) in genome sequencing and genomic analysis. Ongoing training in genetic mapping, diversity analysis, molecular marker development, gene expression analysis, and breeding methodology for two graduate students and one postdoc on carrot seed characteristics, early growth, stand establishment, carbohydrate composition analysis, and carotenoid accumulation (Simon and Dawson). Organic Seed Alliance hosted a paid 4 month internship for Susana Cabrera-Mariz. Susana gained hands-on experience in carrot seed production and variety evaluation and went on to undertake a research project on carrot history, domestication and cultural food pathways as a component of her Masters thesis at Iowa State University (Colley). How have the results been disseminated to communities of interest?Educational events and conference presentations delivered in 2022-23 included: M. Iorizzo. Recent advances in characterizing the carrot genome. International Carrot and Other Apiaceae Symposium, October 2-5, 2023, York, UK. P. Simon et al. The carrot SCRI project taps into carrot diversity to develop genetic and genomic resources, evaluate nutrient bioavailability, and assess factors influencing grower and consumer decisions. International Carrot and Other Apiaceae Symposium, October 2-5, 2023, York, UK. M. Iorizzo. Omics approach to uncover the origin of high carotenoid orange carrots. 66th Annual Congress Italian Society of Italian Genetics, September 5-8, 2023, Bari, Italy. Third Plant & Animal Genome Workshop on Apiaceae, January 14, 2023, San Diego, California, USA. W. Rolling - Introducing the tools and data available at the CarrotOmics database D. Grzebelus - The impact of transposable elements on the carrot genome - the past, the present and the future M. Iorizzo - Analysis of global carrot germplasm identifies genomic signatures of domestication and improvement and uncovers the origin of high carotenoid orange carrots K. Corak - Genetic mapping of QTL associated with canopy height in connected carrot populations A. Macko-Podgorni - Carrot MITEs provide binding sites for Myb-like TFs regulating the circadian clock P.W. Simon - Sources of abiotic stress tolerance in diverse carrot germplasm Stakeholder events included: February 14, 2023 Presentation to California Fresh Carrot Advisory Board Symposium on results of selection and breeding for combined nematode resistance, cavity spot, and preferred agronomic performance (P Roberts, J. Sidhu, P. Simon) Bakersfield CA (virtual meeting) March 6-10, 2023, Carrot harvest trial, PI collection evaluation and breeding pool development; and March 7 hybrid trials (P. Simon, M. Colley, J. Diaz, J. Sidhu) at Desert Research and Extension Center, El Centro, CA In vitro cavity spot inoculation protocol evaluation (L. du Toit) at Washington State University Mount Vernon, WA August 30-31, 2023, Root-knot nematode (Meloidogyne incognita) trial (P. Roberts, P. Simon) at UCR Coachella Valley Agricultural Research Station, Thermal, CA September 11th, 2023, Organic Seed Alliance fall field day. September 19, 2023 Carrot hybrid trial (P. Simon) from Hancock, WI Miller Farm crop displayed on Univ. Wisconsin campus, Horticulture Annex, Madison, WI Outreach activities presented on this project by the University of California, Desert Research and Extension Center (UC-DREC), Holtville, CA (J. Diaz, S. Amparano, Y. Meng): From 2022 to 2023 Farm Smart delivered carrot outreach programs in nutrition and production to 2908 participants, which includes educators, K-12 students, and community members. Below is a summary of activities delivered: o Farm to Summer - Carrots (45 participants) o Led an interactive summer program where participants learned about the history of carrots, nutritional information, how they grow, and tasted a variety of carrot preparations, including the various colors. o CARES Fall Festival- carrot planting (15 participants) o Participants learned about carrots as they planted their own carrot seeds to take home o Farm Tours- carrot presentation, research, harvesting (463) - While touring the UC-DREC facility, guests learned about colored carrot research taking place at the farm. o Native Sons of the Golden West (20) o BUHSD- AP Environment (5) o Master gardener Tour (35) o SHS CTE- health Sciences (25) o Brawley CTE health Sciences (40) o SHS CTE health Sciences (23) o SHS_CTE health Sciences (21) o Calexico FFA Field Day (31) o Senior U-Pick (258) o IVROP Ready for Life (5) o Farm to Preschool Festival- carrot tasting and facts (1116) ? Participants tasted carrots and received recipes and information on nutritional value. - Vegetable Adventures Field Trips at UC-DREC - carrot harvesting and information (992) o 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. - Community U-pick at UC-DREC - carrot harvest and information (277) o Participants learned about colored carrots, the nutritional value of carrots, and were able to harvest carrots from the garden. What do you plan to do during the next reporting period to accomplish the goals? Initiate stakeholder meetings during the SCRI zoom meetings in the winter of 2023-24 to report project progress, invite feedback and gather additional input from them on current and future project direction. Meet with stakeholders preceding the International Carrot Conference in Raleigh, NC, July, 2024 Continue field evaluations and research activities to advance studies for all project objectives. This will include: Complete sequencing all samples for the pan genome and initiated sequencing RNA samples. Continue assembling genomes. Initiate efforts to develop the genotyping platform. Genotype multi-parental and bi-parental mapping populations based on breeding pools developed in the first SCRI project and the genotyping platform currently being developed. Advance mapping of gene locations of economically important traits using multi-family linkage mapping and develop genomic prediction models for these traits based on cross-validation, to be further field-validated in years 3 and 4. Advancement of nematode resistant carrot materials will include combined phenotyping in infested field sites at Coachella, CA and in controlled inoculation greenhouse screenings at UC Riverside. Selected roots with nematode resistance and preferred agronomic qualities will be sent to WI for advancement and crossing in breeding pools. GBS-based marker development and RNAseq based gene identification will be used to develop more accurate genome markers for marker-assisted selection. Advancement of cavity spot resistant carrot materials will include combined phenotyping in infested field sites at Mt. Vernon, WA. Selected roots with cavity spot resistance and preferred agronomic qualities will be sent to WI for advancement and crossing in breeding pools. GBS-based marker development will be initiated to develop more accurate genome markers for marker-assisted selection. OSA plans to continue selecting and increasing the nematode x flavor breeding pool and screening additional PI lines at the OSA research site in WA. Advance breeding pools grown on trial locations appropriate to include phenotyping Alternaria leaf blight, stand establishment, top size, and flavor. Outreach and educational events planned for next year include- Presentations on the carrot SCRI project at meetings, outreach events, field days, etc. Presentations at the Plant and Animal Genome meetings (several PIs) Organize the international carrot conference in Raleigh NC, July 9-10 (M. Iorizzo) Present data at the carrot SCRI project stakeholder meetings (all) Hold an industry-stakeholder field day at the UCR Coachella Research Station field trial for nematode resistance screening in summer 2024. (P. Roberts, P. Simon). Present research results will be made to California Fresh Carrot Advisory Board Symposium, Spring 2024. (P. Roberts, P. Simon). Continue outreach activities at the University of California, Desert Research and Extension Center (UC-DREC), Holtville, CA (P. Simon, M. Colley, J. Diaz, J. Sidhu) Cover carrot demand and the role of organic carrots in UC Davis MS course in Agricultural Economics and undergrad course in Economics of Agricultural Sustainability. Present new work on organic carrot demand at the Agricultural and Applied Economics meeting in July 2024 (D. Sumner) Present on carrot participatory plant breeding at the Eco-breeds conference in Slovenia, January 2024. (M. Colley) Deliver an educational webinar on the history and domestication of carrot (M. Colley and graduate student Cabrera-Mariz)

Impacts
What was accomplished under these goals? Carrots are a high-revenue farm crop with farm cash receipts of $1.171 billion in 2022 and carrots are the largest crop source of vitamin A in the US diet. Approx. 86% of the carrot acreage and 94% of crop value is sold in the fresh market, with 85% of fresh market carrots grown in CA. Washington and Wisconsin are the other significant producers. Nationwide expansion of small-scale local vegetable markets has increased carrot production, and this trend contributes to the growing organic market share of US production, estimated at 14%. Conventional and organic carrot growers, processors, product developers, industry breeders, and genomic labs identified breeding priorities (listed below) and, based on follow-up stakeholder input in Jan 2021, those traits were confirmed as the top priorities for improving productivity, expanding product development, and strengthening economic viability. Improved cultivars with these characteristics will provide a cost-effective and environmentally responsible means to deliver an improved carrot crop to growers and consumers. However, carrot breeders will need new sources of favorable alleles, genomic resources to incorporate the alleles, and tested breeding stocks to develop superior cultivars efficiently. Based on stakeholder input, the Long-term Goals of this project are to: (1) release carrot germplasm with improved performance, from diverse carrot germplasm and breeding stocks, for traits important to growers and consumers; (2) generate genomics-based breeding tools to deliver phenotypic and genotypic information for carrot breeders to tap into the breadth of carrot genetic diversity; (3) establish a science-based research and outreach foundation for long-term carrot improvement that includes measures of economic value for producers and nutritional value for consumers; and (4) train students and post-docs in carrot breeding and genetics, which was highlighted by industry stakeholders as an important goal to support longer-term carrot breeding; 5) engage stakeholders and the public to transfer project deliverables and educate them about importance of carrot research as well as carrot nutritional value. Based on this input, we have four research objectives for the current project. Project Objectives and Annual Progress: Objective 1: Develop cost-effective genomic tools to advance breeding populations and integrate loci related to economically significant traits identified by stakeholders - Released the DH1v3 genome assembly and annotation. Completed mining SNPs data from diversity panel and identified SNPs associated with alpha and beta-carotene content. SNPs data will be used to develop the SNPs catalog to design the genotyping platform. Initiated efforts to sequence the genomes for the pangenome. Completed DNA extractions from 32 samples. Initiated sequencing and testing genome assembly pipeline. Four haplotype level genome assemblies were developed. Preliminary quality assessment indicated that the genomes have very high contiguity and are highly collinear with the DH1v3 genome assembly. Objective 2: Use multi-parental and biparental populations to map gene locations of economically important traits using optimized genomic-assisted strategies - Evaluated root-knot nematode resistance in several bi- or tri-parental and single plant-derived breeding populations segregating for resistance in two nematode-infested field sites for M. incognita resistance response (Thermal, Coachella Valley, CA) and M. hapla resistance response (Othello, WA), and in inoculated greenhouse pot-screens at UCR. Plants were scored on a standard 0-8 scale for taproot and feeder root-galling symptoms on an individual plant basis. Selected roots were sent to WI for advancement and crossing in breeding pools. These phenotypic data sets are being used for fine mapping of resistance loci in the carrot genome. A primary focus is the very strong resistance to M. incognita found in single plant selections from the variety Cape Market, which also exhibits resistance to other Meloidogyne species. Collected root materials following inoculation with M. javanica using susceptible and resistant progeny from a population segregating for resistance locus Mj-1. Root tissues were frozen at -80C and will be used for RNAseq analysis, to identify the Mj-1 gene sequence. Selected F2 cross-populations of nematode resistant and flavor breeding lines in the winter nursery and increased at the OSA research farm. Seed from this population was harvested and sent to El Centro for the 2024 winter nursery harvest. Evaluated 78 Plant Introductions and check cultivars in a cavity-spot inoculated field site in Mt. Vernon, WA and storage roots were scored on a 0-5 scale for symptoms. Among PIs evaluated, 9 new sources of resistance were identified. Selected roots were sent to WI for advancement and crossing to develop mapping populations. Selected 20 consistently early bolting and 20 consistently late bolting genotypes focusing on cultivated (like) types based on results from previous SCRI tested in 5 environments in spring and summer planted carrots in WI and CA. These are being crossed systematically to create multiple-parent and F2 populations among themselves and with elite germplasm. They will be genotyped tested in Year 2-4 for mapping and introgression of bolting loci. Evaluated and photo documented field trials of 121 entries including breeding lines and PI lines at the OSA research farm under organic conditions. Also grew parental stocks and mapping populations in the El Centro, CA, winter root nursery, and Hancock, WI, summer root nursery for phenotyping flavor, carotenoid and anthocyanin profiles, Alternaria leaf blight resistance (WI only), and stand establishment. Drought tolerance of PI and breeding stocks was evaluated in the greenhouse, and selected plants from this phenotyping effort, as well as selected plants from the UCR nematode resistance screening were intercrossed or self-pollinated to develop new mapping populations and breeding pools. Objective 3: Evaluate bioavailability of nutrients in selected breeding stocks with varying nutrient composition that may influence bioavailability - Work in the animal model has been completed and was recently published. The first acute feeding study in humans was completed and the PhD Student finished her degree in June 2023. We are currently merging two of her dissertation chapters into one comprehensive manuscript to be submitted in early 2024. Started reviewing carrot recipes from former human studies to adapt for the chronic feeding study in humans with the purple carrot. We have hired a graduate student and are hiring a postdoc for upcoming studies. OBJECTIVE 4: Estimate economic costs and benefits value to buyers and the industry of improved traits and assess broad societal value of these Improvements - Finalized paper on projected demand for organic carrots, (Lee, Sumner, Goldstein) that is to be submitted at the end of 2023. Initiated use of California public data by county of pesticide use to account for carrot pest and disease management and contribution of breeding to reduce costs.

Publications

• Type: Journal Articles Status: Published Year Published: 2023 Citation: Coe K, H. Bostan, W. Rolling, S. Turner-Hissong, A. Macko-Podg�rni, D. Senalik, S.Liu, J. Curaba, M.F. Mengist, D. Grzebelus, A. Van Deynze, J. Dawson, S. Ellison, P. Simon and M. Iorizzo. 2023. Analysis of global carrot germplasm identifies genomic signatures of domestication and improvement and uncovers the origin of high carotenoid orange carrots. Nature Plants, 9, 16431658 (2023).
• Type: Conference Papers and Presentations Status: Awaiting Publication Year Published: 2023 Citation: Iorizzo M., K. Coe, H. Bostan, W. Rolling, S. Turner-Hissong, A. Macko-Podg�rni, D. Senalik, R. Seth, S.Liu, J. Curaba, M.F. Mengist, D. Grzebelus, A. Van Deynze, J. Dawson, S. Ellison and P. Simon. Recent advances in characterizing the carrot genome. Proceedings of the III International Symposium on Carrot and Other Apiaceae. (In press).
• Type: Journal Articles Status: Published Year Published: 2023 Citation: Corak, K.E., Genger, R.K.,Simon, P.W. and Dawson, J.C. 2023. Comparison of genotypic and phenotypic selection of breeding parents in a carrot (Daucus carota) germplasm collection. Crop Science 63:4. 1998-2011.
• Type: Journal Articles Status: Published Year Published: 2023 Citation: Kaeppler MS, Smith JB, Davis CR, Simon PW, Tanumihardjo SA. Anthocyanin and lycopene contents do not affect ?-carotene bioefficacy from multicolored carrots (Daucus carota L.) in male Mongolian gerbils. J Nutr. 2023;153(1):76-87.
• Type: Theses/Dissertations Status: Published Year Published: 2023 Citation: Lee, Hanbin. 2023. Economics of Food Attributes Linked to Farm Practices. PhD UC Davis, Agricultural and Resource Economics.
• Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: M. Iorizzo. Omics approach to uncover the origin of high carotenoid orange carrots. 66th Annual Congress Italian Society of Italian Genetics, September 5-8, 2023, Bari, Italy