CIOA 2- Carrot Improvement for Organic Agriculture With Added Grower and Consumer Value

CIOA 2- CARROT IMPROVEMENT FOR ORGANIC AGRICULTURE WITH ADDED GROWER AND CONSUMER VALUE

Sponsoring Institution

National Institute of Food and Agriculture

Project Status

TERMINATED

Funding Source

OTHER GRANTS

Reporting Frequency

Annual

Accession No.

1010332

Grant No.

2016-51300-25721

Project No.

ILLW-2016-04393

Proposal No.

2016-04393

Multistate No.

(N/A)

Program Code

113.A

Project Start Date

Sep 1, 2016

Project End Date

Aug 31, 2021

Grant Year

2016

Project Director
Simon, P.

Recipient Organization
AGRICULTURAL RESEARCH SERVICE
1815 N University
Peoria,IL 61604

Performing Department
(N/A)

Non Technical Summary
Organic growers need vegetable varieties that are adapted to organic growing conditions and have market qualities demanded by organic consumers. In carrots, weed competition, nutrient acquisition, nematodes, and disease pressure are particularly critical challenges to both fresh market carrots and carrot seed production, while flavor, appearance, and nutrition are key market qualities. This project will deliver improved carrot varieties for organic producers and consumers; improved understanding of cultivar performance in organic systems; improved understanding of how carrot genotypes interact with the root microbiome to access key nutrients under limiting environments and avoid heavy metal uptake; and a breeding model that may be adapted to other crops for organic cultivar development. Organic farmers, students, and industry stakeholders in six states will participate in the breeding, variety trials, and planning aspects of the project. Project results will be disseminated nationally. The project will train graduate and undergraduate students in plant breeding, soil microbial ecology, and vegetable trial development for organic systems through research and field assistant positions. New cultivars adapted to organic conditions will enhance organic vegetable production and organic farmer economic returns, thus facilitating expansion of organic agriculture in the USA. Publically available breeding lines, including germplasm with nematode resistance, will support organic seed industry development of additional new cultivars. The development of improved carrot varieties with greater tolerance to biotic and abiotic stress will bring broad environmental benefits by reducing the need for off-farm inputs. Organic seed companies, producers, and consumers will benefit from access to new cultivars.

Animal Health Component

Research Effort Categories

Basic

10%

Applied

80%

Developmental

10%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
201	1452	1081	60%
201	1452	1102	20%
201	1452	1100	20%

Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1452 - Carrot;

Field Of Science
1081 - Breeding; 1102 - Mycology; 1100 - Bacteriology;

Keywords

Goals / Objectives
1 - Conduct advanced on-farm crop research to advance organic production through a systems approach to breeding and on-farm assessment that includes: a) evaluating and breeding nutrient-rich, disease and nematode resistant carrots in infested fields; b) determining how carrot genotypes interact with their root microbiome to access key nutrients under limiting environments and avoid heavy metal uptake; c) trialing standard and organically available carrot cultivars and new breeding stocks on organic agricultural research stations and commercial organic growers' fields; and d) publishing results of agronomic, storage, and tasting analysis on the web and in print publications to inform growers and facilitate organic seed usage.2- Develop and demonstrate educational tools for Cooperative Extension personnel and other agricultural professionals, partnering with eOrganic to deliver online extension resources, including new educational publications, variety trial publications, and webinars related to organic carrot production and breeding topics. Additionally, the project will engage Cooperative Extension personnel through field days, agricultural conferences, and other outreach activities.3- Strengthen organic crop seed systems by breeding and releasing new publically available cultivars and breeding lines to the organic seed industry that address critical needs prioritized by organic stakeholders. Specific activities addressing this priority include: a) publically releasing new cultivars and inbred lines of nutrient-rich, disease and nematode resistant carrots with improved nutrient acquisition, weed tolerance, and long storage ability, with excellent flavor; b) developing new breeding populations that combine critical traits and advance future cultivar development; c) providing carrot breeding tools for seed companies, production information for growers, and flavor, nutritional quality, and environmental impact information for consumers about improved organic carrot germplasm; d) selecting for greater acquisition of key plant nutrients and reduced capacity to take up heavy metals; and e) evaluating diverse carrot germplasm for priority traits under organic management conditions in diverse environments and selecting and increasing promising populations to advance future breeding efforts.1 - Conduct advanced on-farm crop research to advance organic production through a systems approach to breeding and on-farm assessment that includes: a) evaluating and breeding nutrient-rich, disease and nematode resistant carrots in infested fields; b) determining how carrot genotypes interact with their root microbiome to access key nutrients under limiting environments and avoid heavy metal uptake; c) trialing standard and organically available carrot cultivars and new breeding stocks on organic agricultural research stations and commercial organic growers' fields; and d) publishing results of agronomic, storage, and tasting analysis on the web and in print publications to inform growers and facilitate organic seed usage.2- Develop and demonstrate educational tools for Cooperative Extension personnel and other agricultural professionals, partnering with eOrganic to deliver online extension resources, including new educational publications, variety trial publications, and webinars related to organic carrot production and breeding topics. Additionally, the project will engage Cooperative Extension personnel through field days, agricultural conferences, and other outreach activities.3- Strengthen organic crop seed systems by breeding and releasing new publically available cultivars and breeding lines to the organic seed industry that address critical needs prioritized by organic stakeholders. Specific activities addressing this priority include: a) publically releasing new cultivars and inbred lines of nutrient-rich, disease and nematode resistant carrots with improved nutrient acquisition, weed tolerance, and long storage ability, with excellent flavor; b) developing new breeding populations that combine critical traits and advance future cultivar development; c) providing carrot breeding tools for seed companies, production information for growers, and flavor, nutritional quality, and environmental impact information for consumers about improved organic carrot germplasm; d) selecting for greater acquisition of key plant nutrients and reduced capacity to take up heavy metals; and e) evaluating diverse carrot germplasm for priority traits under organic management conditions in diverse environments and selecting and increasing promising populations to advance future breeding efforts.

Project Methods
Focus Area1: Cultivar development and release - Sources of germplasm and breeding approaches - At least 200 carrot breeding stocks will be preliminarily evaluated for inclusion in the CIOA2 project from Simon's collection. Additional materials will be added to the research materials each year based on identification of promising lines from the extensive, annual USDA winter nursery evaluations.Preliminary breeding and selection: We anticipate at least 75 populations to be under development throughout CIOA2, dropping those performing poorly each cycle and adding an equivalent number of earlier generation segregating stocks based on their performance in the winter nursery at DREC. Seed production of earlier generation stocks will be done in small (1-2m) isolation cages in WI at the WMARS.Cultivar release: Mass selection of roots from more advanced breeding populations deemed suitable for release will be grown at DREC for summer seed increase at WA (OSARF) and WI (WMARS).Focus Area 2: Variety Trials - Participatory trials and breeding: The research team will meet each winter to prioritize advanced materials for testing in the national participatory network. Comparable commercial varieties in the same market classes as the CIOA2 materials in the trials will be identified by engaging organic seed companies and farmers participating in the trial network as well as the stakeholder advisory panel.A. Project managed trials: Research station locations represent major commercial carrot production areas for large- and small-scale growers in the respective regions: the San Joaquin Valley of California, the Columbia Basin of Washington, and maritime climate of Western Washington, the Central Sands of Wisconsin, and the Ohio Valley. Variety trials of 20-30 entries that showed promise in the winter nursery or received positive evaluations from stakeholders in previous project trials will be conducted each year on certified organic sites by project trial managers, Nunez (winter trial), Hoagland, Silva, and Waters (summer trials).B. National participatory trial network: Two regional participatory evaluation sites in each of the five regions (NE, SE, Midwest, PNW, and CA) comprised of organic seed companies and organic farms will evaluate elite materials with participatory stakeholder involvement. Selection protocols will be based on trial evaluation criteria and input from the stakeholder advisory panel and host farms to ensure a similar selection approach in each region.Focus Area 3: Understanding root microbiome interactions - Selection for nutrient management. Greenhouse trials will be conducted using 20 diverse carrot genotypes x 4 fertility rates (very low, low, medium and high) that vary in total and potentially mineralizable nutrients. Above and below ground biomass will also be analyzed with inductively coupled plasma-mass spectrometry (ICP-MS) (Perkins-Elmer, Waltham, MA) to quantify heavy metal uptake.Six genotypes with high NUE identified in the first trial will be included in a subsequent greenhouse trial to identify ideotypes that utilize enhanced root interactions with beneficial microbes to obtain nutrients using methods similar to those described in Zancarini et al., (2013b). Characterization of the active microbial community associated with carrot roots will be determined by subjecting RNA extracted from roots to RT-PCR. Plant macro- and micronutrients in above and below ground carrot tissue will be analyzed using ICP-MS.Cultivar association with arbuscular mycorrhizal fungi: To evaluate whether carrot cultivars differentially associated with varying species and strains of AMF and subsequently differ in their nutrient uptake and growth differs, trials investigating these relationships will be conducted at the Biotron Controlled Atmosphere Growth Facility (UW-Madison) as well as on the certified organic field plots at West Madison Agricultural Research Station (WMARS). Each cultivar will be inoculated with a single AMF species and strain. The species include Septoglomus deserticola, Rhizophagus intraradices, Rhizophagus clarus, and Funneliformis mosseae.Focus Area 4: Utilizing molecular markers to improve nematode resistance - Nematode resistance analyses: CIOA 2 entries will be screened for resistance to M. javanica and M. incognita each year. Entries scored as resistant or partially resistant in field screens will be re-screened in controlled inoculation tests in greenhouse pot screens with five-fold replication.Co-PD Roberts will assist the other investigators in assessing field test sites for root-knot nematode population levels and indices of root infection, using protocols described above.Development and application of gene markers: Total genomic DNA will be isolated from freeze-dried leaves, and SNP markers for six QTL developed by Parsons et al. (2015) will be mapped based on our knowledge of SNPs at the borders of QTL in the carrot genome sequence now available (Iorizzo et al., 2016).Focus Area 5: Evaluating and improving carrot flavor - Selection for carrot flavor: Initial organoleptic evaluation of the trial entries will employ slices taken at mid-root, and will be performed on all selected roots within two weeks of harvest as described by Simon (2000). Sweetness, harshness (primarily attributable to volatile terpenoids) (Senalik and Simon, 1987), and texture will be scored.A mixed model analysis of variance will be used to analyze data with taster and sample set considered random effects and variety considered fixed. Multiple Factor Analysis (MFA), an approach with a quantitative component based on distance between samples on the map and a qualitative, descriptive component, produces a consensus map interpreted using the comments and preference ratings given by the chefs.Field evaluation for foliar and seedborne diseases: Visual evaluations for foliar carrot diseases will be performed in all four organic trials in all four years of the project. Disease ratings will be taken at least three times each season at each location to monitor disease progress over time, and at an optimum time for specific soilborne diseases that might develop.Samples of seed harvested from some of the carrot entries and crosses will be tested for seedborne pathogens to screen the germplasm for entries that produce lower levels of seed infestation.Selection for carrot storage: Carrots will be placed in plastic bags with dry wood shavings, as is standard procedure to store breeding stocks (Peterson and Simon, 1986), and stored in refrigerated coolers (0.5 to 2o C) upon harvest. Postharvest storage quality will be evaluated (storage rot) on a monthly basis for 4 months postharvest.Evaluation and selection for root From each root, 2.5 g of tissue will be sampled mid-root and lyophilized.

Progress 09/01/20 to 08/31/21

Outputs
Target Audience:Organic and conventional vegetable growers, marketers, and consumers; vegetable seed companies; plant science researchers in horticulture, plant breeding, plant pathology, nematology, soil science, and botany. 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 extension activities included creating new project promotion and educational materials for CIOA2, coordinating outreach and evaluation activities, presenting at multiple scientific and food industry conferences, and delivering trainings and educational events. The project communications team continued to support event outreach and track event participation and evaluation. We updated a promotional brochure that gives an overview of the project, and details about current research and research goals that was shared with growers, the carrot industry, researchers, and consumers at CIOA-related events. Each project collaborator received printed copies of the brochure to disseminate at outreach events. We also created a new scientific research poster about the project, presented at the IFOAM World Congress in September 2021 along with a proceedings paper. The IFOAM International Congress included a field tour on organic farms in France. We supplied carrot seed samples representing diverse carrot historical origins and types featured in the on-farm trial and provided an educational booklet on history and nutrition of carrot for participants. The trial entries also served as a taste testing participatory event. Trials were conducted with four organic seed company research farms - High Mowing Organic Seeds, Row 7 Seeds, Johnny's Selected Seeds, and Seed Peace/Wild Mountain Seeds. Each trial provided training on carrot trialing and seed production for employees and interns. These trials provided an opportunity for expansion of project impacts, testing materials in new regions, and soliciting input on evaluations from two organic seed companies. In late September, Colley and McKenzie delivered the OSA Annual Field Day field day highlighting the CIOA project and the breeding and trialing work at the OSA WA Research Farm. The OSA Annual Field day was hosted virtually in September attended by over 200 participants. OSA continues to advise on and support the carrot breeding and trialing work of our colleagues at the Univ. of British Columbia as well as sharing germplasm and mentoring farmers who have expressed interest in initiating on-farm breeding projects through their exposure to the CIOA project. As part of education activities, undergraduate students, graduate students and post-doctorates are being trained in vegetable breeding, crop and seed production, disease protection and diagnosis, and soil science with a focus on organic systems as they participate in research projects critical to the COIA Project achieving the research goals. In the past year 4 graduate students projects included CIOA research activities. To inform growers and consumers about the positive environmental impact of organic production systems, and about carrot nutritional quality and flavor we continued to update and use the web site developed through eOrganic in CIOA1-2 to disseminate research updates, timely articles, and related project events (http://eorganic.info/carrotimprovement). We created two new promotion brochures giving an overview of the project, and details about current research and research goals. One brochure was tailored for and shared with growers, the carrot industry, and researchers. A second version of the brochure was developed for and shared with a general audience at CIOA-related events. We created a new scientific research poster about the project and presented it at related scientific focused events/conferences. The project reached approximately 800 growers, carrot industry members, researchers, food industry representatives, and consumers in this period. A project field sign was also created and installed at each project location field site so field visitors could clearly identify the project plots, project goals, work, partners, and funder, and visit the website for additional information. Each of the four project collaborators hosted public farmer field days in conjunction with each trial at the project research sites. Field days coincided with timing of trial evaluations. In addition, this project is expanding graduate student and postdoc training, focused on research in organic systems and organic plant breeding. This includes one postdoc, Sahar Abdelrazek and graduate student Narda Silva at Purdue, and another postdoc, William Rolling, and two graduate students Kevser Ozel and Erin Lalor at UW. One visiting undergraduate scholars from Colombia (Leidy Meija, University of Caldes, Colombia) at Purdue and two graduate student scholars from Pakistan (Aneela Nijabat, University of Sargodha; Nadia Riaz, Lahore College for Women University) at UW received training by conducting research projects for their respective theses. Micaela Colley is publishing on CIOA 1 agronomic results results and CIOA 2 top growth trials as a component of her PhD thesis, data in process with plans to publish in 2021. The long-term impact of this important educational element is to establish the next generation of researchers, extension, and industry representatives with organic systems expertise. How have the results been disseminated to communities of interest?Educational events and conference presentations delivered include: Field Days and Trainings: 3/10/2021 CIOA/SCRI Carrot Harvest Public Field Day El Centro, CA45 2020 Organic Vegetable Field Day at University of Wisconsin-Madison, Purdue University, University of California - Riverside, and California Agriculture Extension were cancelled due to COVID Meetings: 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. Simon, P. et al. Carrot Improvement for Organic Agriculture and Consumer Value. International Federation of Organic Agriculture Movements World Congress. September 6-10, 2021. Blogposts OSA Blog, Farm to Flavor: Culinary Breeding in Carrots, 10/30/19,https://seedalliance.org/2019/farm-to-flavor-culinary-breeding-in-carrots/ OSA Blog, Breeding Carrots with Partners to Address Diverse Needs, 3/30/20,https://seedalliance.org/2020/cioa-ca-harvest2020/ Produce Grower, Soil microbiome can improve carrot resistance to deadly fungus, 7/22/20https://www.producegrower.com/article/carrots-greenhouse-study-purdue/ What do you plan to do during the next reporting period to accomplish the goals?This is the final reporting period for CIOA 2. All breeding and variety release efforts will continue to advance under CIOA 3. Selected field trialing and research activities described for Year 1-4 will continue in Year 5 - namely the winter 2020-21 winter root nursery is underway to produce stecklings to increase seed supplies of CIOA germplasm, especially breeding lines staged for release. In addition, seed increase of promising genetic stocks included in trials will be continued and resistance testing of ALB in WI and nematode resistance in CA will be continued in 2021. Marker work for nematode resistance will continue, and data will be summarized published.

Impacts
What was accomplished under these goals? This project addresses the critical needs of organic carrot producers by developing orange and novel colored carrots with improved disease and nematode resistance, improved weed competitiveness, and improved nutritional value and flavor. About 100,000 acres of carrots are grown annually in the U.S. The 2014 Census of Agriculture, estimated 14% of this carrot production is in organic systems, vs. 3% for vegetable crops overall. Organic production of carrots has significant pest and disease challenges. Over 80% of the U.S. carrot production land is infested with one or more species of root-knot nematodes. Alternaria leaf blight (ALB), other foliar diseases and cavity spot are major carrot diseases in virtually all production areas of the world. The needs for effective non-chemical methods of pest and disease control to the future of the US organic vegetable production are urgent. Carrots are among the slowest crops for growers to establish, often making weed control the most expensive cost of organic production. Flavor and nutritional value are the most important characteristics noted by consumers of organic foods and novel colors attract carrot consumers. This project is developing novel carrots improved for nutrition and flavor, integrated with critical pest and disease resistance and vigorous growth. This project also expands our understanding of root-microbiome interactions critical for growth and nutrient uptake of organically-grown carrots. Goals and annual progress: Long-term goals of this project are to: 1) deliver carrot cultivars with improved disease and nematode resistance, improved nutrient acquisition, seedling vigor and weed competitive traits, increased marketable yield, superior nutritional value, flavor and other culinary qualities, and storage quality for organic production; 2) determine how carrot genotypes interact with/influence, the root microbiome to access key nutrients under limiting environments and avoid heavy metal uptake; 3) inform growers about cultivar performance to maximize organic carrot production, markets, and organic seed usage; 4) inform consumers about the positive environmental impact of organic production systems and about carrot nutritional quality, flavor and culinary attributes; and 5) train undergraduate, graduate, and post-doctorate students in critical organic agriculture issues. Primary activities: Focus Area 1: Cultivar development and release New breeding populations (~50) were identified in the 2020-2021 winter root nursery. Continued advancement was done on nine orange breeding populations with improved flavor, carotene content, ALB and cavity spot resistance. Seven purple breeding populations with improved flavor, texture, and robust agronomic production qualities were also advanced. Four new breeding populations were started - three orange and one novel colored, from roots produced in the winter root nursery. Successful production of seed to increase stock for widespread and larger scale trials of novel colored populations slated for release was accomplished. True-breeding selections of P1129 were advanced. Advanced selections were trialed by five organic seed companies and formal release is underway for three populations from CIOA1 (R6636, R6220, Y1246). Commercial release plans are underway for release of the newly named 'Carnelian' red carrot variety (R6636) with High Mowing Organic Seeds. 'Carnelian' is slated for sale in the 2023 growing season. Focus Area 2: Variety trials on research stations and national participatory sites On-farm and on-station trials were radically impacted by covid-19, especially on-station trials at participating/collaborating Universities. Variety trials were held in WI, WA, and CA with participatory sites in OR, CO, VA, NY, ME, and VT. Included were 12 advanced breeding populations, check varieties, and selections from among 120 promising breeding populations. Flavor, marketability, productivity, pigment content and storage quality of selected CIOA entries was completed. Advanced lines were distributed to on-farm trials over two seasons as part of the Seed to Kitchen Collaborative trials in the upper midwest. Focus Area 3: Advancing research on root microbiome interactions Carrot taproots grown in a long-term field trial comparing organic and conventional management were colonized by an abundant and diverse assortment of bacteria and fungi, though endophytes were more diverse and had greater antagonistic activity against A. dauci in the organic system. Carrot genotype also affected endophyte abundance in taproots and potential for individual isolates to affect seed germination, seedling growth and ALB tolerance. Carrots do vertically transmit endophytic microbes within their seeds, and these microbes appear to play an important role in germination and early seedling performance. Many of these seedborne microbes appear to be part of a core microbiome in carrot. Carrot genotypes also vary in their potential to promote organic matter priming to scavenge nitrogen, tolerate cadmium (Cd) stress, and accumulate Cd in carrot taproots. The composition of AMF communities present in soil,also plays a significant role in mediating micronutrient and heavy metal uptake. Finally, carrot genotypes vary in their potential to alter soil microbial communities that influence susceptibility to pathogenic nematodes in subsequent generations, and N fertility management influences these relationships. Results of these studies demonstrate that carrot productivity is intimately connected to their root microbiomes. Soil management practices are critical in promoting beneficial carrot-soil-microbial relationships, though genotype also plays a role indicating that with further work it will be possible to select for these relationships. Focus Area 4: Utilizing molecular markers to improve nematode resistance CIOA2 advanced experimental selections and promising selections were included in field trialing at the UCR Coachella Valley Agricultural Research Station, Thermal, CA for resistance to the prevalent root-knot nematode M. incognita occurring in California. Additional carrot selections were advanced for seed production to be included in genetic analysis, molecular marker evaluation, and breeding line development. Molecular marker evaluation found a major M. hapla resistance gene on chromosome 9 which was fine-mapped to develop markers for breeders. Greenhouse tests were used to provide highly controlled screening conditions. Resistance traits for M. hapla, M. incognita, M. arenaria M. javanica were identified and confirmed in multiple greenhouse screenings Foliar diseases were diagnosed. Motley dwarf was identified for a third year in western WA trials, and also in central WA. ALB resistance was evaluated in central WI. Promising CIOA2 selections were identified where infection was very high and wide variation in resistance was observed. Cavity spot resistance was tested for advanced CIOA2 breeding selections in infested fields in CA and WA and selections advanced for breeding. Focus Area 5: Evaluating and improving carrot flavor, nutritional, and postharvest quality CIOA varieties varied in appearance, texture, flavor intensity, sweetness and harshness. Overall flavor was rated on all samples and was positively correlated with sweetness but negatively correlated with harshness. Flavor was rated on all samples by project staff each year of trials. CIOA varieties slated for release were evaluated for flavor by chefs in 2019, but not in 2020-2021 due to the COVID pandemic. Public educational events featured diverse advanced varieties at the second virtual OSA WA research farm field day (200+ attendees) in 2021. Mineral element profiles were assessed in diverse breeding materials since they are important for human nutrition, for plant health, and for microbiome interactions. Wide diversity was observed.

Publications

Type: Theses/Dissertations Status: Submitted Year Published: 2021 Citation: Kevser Ozel (MS) 2021 Thesis title: Identification and Genetic Mapping of New Sources of Nematode Resistance in Carrot (Daucus carota L.) M.S. Thesis, University of Wisconsin - Madison. 154p
Type: Theses/Dissertations Status: Published Year Published: 2021 Citation: Erin Lalor (MS) 2021 Thesis title: Variation of mineral element accumulation in a diverse carrot germplasm collection. M.S. Thesis, University of Wisconsin - Madison. 207p
Type: Theses/Dissertations Status: Submitted Year Published: 2020 Citation: Leidy Meija (Caldas University, Colombia) 2021 Project: Carrot genotype and nitrogen stress alter plant soil feedbacks and susceptibly to pathogenic nematodes
Type: Theses/Dissertations Status: Submitted Year Published: 2021 Citation: Hannah Komanapalli (Purdue University) 2021 Project: Carrot AMF elements
Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Simon, P. et al. 2021. Carrot Improvement for Organic Agriculture with Added Grower and Consumer Value. International Federation of Organic Agriculture Movements Organic World Congress, Rennes, France
Type: Journal Articles Status: Other Year Published: 2021 Citation: Carrot genotypes differ in their ability to stimulate soil microbial communities and scavenge nitrogen from organic materials in soil (in prep ⿿ target submission in November/December at the latest) Narda J. Triviñoa, Alejandro Rodriguez-Sancheza, Timothy Filleyb, James Camberatoc, Micaela Colleyd, Phill Simone, Lori Hoaglanda* - Will be submitted to Soil Biology and Biochemistry. Journal impact factor: 6.767 In preparation
Type: Journal Articles Status: Other Year Published: 2021 Citation: Keller-Pearson, M., L. Willems, B. Smith, A. Bortolazzo, A. Peterson, E.M. Silva, and Jean-Michel Ané. 202X. Arbuscular mycorrhizal fungi and carrot demonstrate contrasting responses to drought stress under organic agriculture management as revealed through a dual transcriptomic approach. In preparation

Progress 09/01/16 to 08/31/21

Outputs
Target Audience:Organic and conventional vegetable growers, marketers, and consumers; vegetable seed companies; plant science researchers in horticulture, plant breeding, plant pathology, nematology, soil science, and botany Changes/Problems:Some data collection and outreach activities were delayed or omitted due to COVD restrictions What opportunities for training and professional development has the project provided?Extension activities for all years included creating new project promotion and educational materials for CIOA2, coordinating outreach and evaluation activities, presenting at multiple scientific and food industry conferences, and delivering trainings and educational events. The project communications team continued to support event outreach and track event participation and evaluation. We updated a promotional brochure that gives an overview of the project, and details about current research and research goals that was shared with growers, the carrot industry, researchers, and consumers at CIOA-related events. Each project collaborator received printed copies of the brochure to disseminate at outreach events. We also created a new scientific research poster about the project, presented at the IFOAM World Congress in September 2021 along with a proceedings paper. The IFOAM International Congress included a field tour on organic farms in France. We supplied carrot seed samples representing diverse carrot historical origins and types featured in the on-farm trial and provided an educational booklet on history and nutrition of carrot for participants. The trial entries also served as a taste testing participatory event. Trials were conducted with four organic seed company research farms - High Mowing Organic Seeds, Row 7 Seeds, Johnny's Selected Seeds, and Seed Peace/Wild Mountain Seeds. Each trial provided training on carrot trialing and seed production for employees and interns. These trials provided an opportunity for expansion of project impacts, testing materials in new regions, and soliciting input on evaluations from two organic seed companies. In late September, Colley and McKenzie delivered the OSA Annual Field Day field day highlighting the CIOA project and the breeding and trialing work at the OSA WA Research Farm. The OSA Annual Field day was hosted virtually in September attended by over 200 participants. OSA continues to advise on and support the carrot breeding and trialing work of our colleagues at the Univ. of British Columbia as well as sharing germplasm and mentoring farmers who have expressed interest in initiating on-farm breeding projects through their exposure to the CIOA project. As part of education activities, undergraduate students, graduate students and post-doctorates are being trained in vegetable breeding, crop and seed production, disease protection and diagnosis, and soil science with a focus on organic systems as they participate in research projects critical to the COIA Project achieving the research goals. In the past year 4 graduate students projects included CIOA research activities. To inform growers and consumers about the positive environmental impact of organic production systems, and about carrot nutritional quality and flavor we continued to update and use the web site developed through eOrganic in CIOA1-2 to disseminate research updates, timely articles, and related project events (http://eorganic.info/carrotimprovement). We created two new promotion brochures giving an overview of the project, and details about current research and research goals. One brochure was tailored for and shared with growers, the carrot industry, and researchers. A second version of the brochure was developed for and shared with a general audience at CIOA-related events. We created a new scientific research poster about the project and presented it at related scientific focused events/conferences. The project reached approximately 800 growers, carrot industry members, researchers, food industry representatives, and consumers in this period. A project field sign was also created and installed at each project location field site so field visitors could clearly identify the project plots, project goals, work, partners, and funder, and visit the website for additional information. Each of the four project collaborators hosted public farmer field days in conjunction with each trial at the project research sites. Field days coincided with timing of trial evaluations. To demonstrate techniques and challenges associated with organic carrot seed production, seed increase plots were established for organic carrot seed production in two on-farm workshop. The seed increases at OSA research farm were also used in trainings on organic carrot breeding. Seed production for carrot germplasm to be released was initiated. In addition, this project is expanding graduate student and postdoc training, focused on research in organic systems and organic plant breeding. This includes one postdoc, Sahar Abdelrazek and graduate student Narda Silva at Purdue, and another postdoc, William Rolling, and graduate student Erin Lalor at UW. One visiting undergraduate scholars from Colombia (Leidy Meija, University of Caldes, Colombia) at Purdue and two graduate student scholars from Pakistan (Aneela Nijabat, University of Sargodha; Nadia Riaz, Lahore College for Women University) at UW received training by conducting research projects for their respective theses. Micaela Colley is publishing on CIOA 1 agronomic results results and CIOA 2 top growth trials as a component of her PhD thesis, data in process with plans to publish. The long-term impact of this important educational element is to establish the next generation of researchers, extension, and industry representatives with organic systems expertise. How have the results been disseminated to communities of interest?Educational events and conference presentations delivered include: Outreach: 9/17/16-9/18/16, Jefferson County Farm Tour, Chimacum, WA 9/26/2016, Organic Seed Alliance Research Farm Field Day, Chimacum, WA 11/4/16-11/6/16, CFSA Sustainable Agriculture Conference Preconference Research Intensive, Durham, NC 10/3/2016 Culinary Breeding Network Variety Showcase, Portland, OR 1/26/2017, Seed to Eaters Roundtable at EcoFarm, Pacific Grove, CA 2/2/17-2/4/17, Organicology Research Poster Session, Portland, OR 3/20/2017, CIOA2 poster and oral presentations, International Carrot Conference, Bakersfield, CA 6/29/2017, Southwest Purdue Agricultural Center Field Day, Vincennes, IN 8/7/17-8/9/17, National Association of Plant Breeders, Davis, CA 8/22/2017, Purdue Field Day at West Lafayette, West Lafayette, IN 8/24/2017, UW Madison hosted an Organic field Day at the West Madison Agricultural Research Station with good turn out from the organic seed sector. This was followed by a public Dinner and Outreach Event attended by over 200 people that evening, Madison, WI 9/7/17, Seed to Kitchen's Farm to Flavor Tasting, Madison, WI 3/13/18, Culinary Breeding Network's Variety Showcase, Oahu, HI 9/24/18, NYC Culinary Breeding Network's Variety Showcase, New York, NY 9/26/18, Seed to Kitchen's Farm to Flavor Tasting, Madison, WI 9/12/19 Seed to Kitchen's Farm to Flavor Tasting, Madison, WI Field Days and Trainings: 9/25/17 Research and Farmer Field Day, and Community Field Day and Tasting, Organic Seed Alliance Research Farm, Chimacum, WA 8/20/18 Organic Vegetable Field Day at University of Wisconsin-Madison's West Madison Agricultural Research Station, Madison, WI Participants were able to taste carrots developed through the CIOA1 project. 8/24/18 International Carrot Conference Field Tour of Carrot Research Projects, University of Wisconsin-Madison's Hancock Agricultural Research Station, Hancock, WI 8/22/19 Organic Vegetable Field Day at University of Wisconsin-Madison's West Madison Agricultural Research Station, Madison, WI Participants were able to taste carrots developed through the CIOA1 project. 9/30/19 Organic Seed Alliance Annual Field Day, OSA Research Farm, Chimacum, WA. Farmers and public were able to taste carrots and participate in making selections in breeding populations. 9/12/2019 Seed to Kitchen's Farm to Flavor Madison, WI 300 9/22/2019 Jefferson County Farm Tour Chimacum, WA 50 9/30/2019 5th Annual OSA Fall Field Day Chimacum, WA 120 2/12/20-2/15/20 Organic Seed Growers Conference Corvallis, OR 450 2/16/2020 CBN Variety Showcase Portland, OR 500 3/10/2021 CIOA/SCRI Carrot Harvest Public Field Day El Centro, CA45 Meetings: Simon, P. OREI PD Meeting, Washington, D.C.10/17-18/18 Colley, M, L. McKenzie, and P. Simon Organic Seed Growers Conference, Corvallis, OR 2/14-17/18 Silva, E. MOSES Organic Farming Conference, La Crosse, WI 2/22-24/18 Simon, P. ASHS, Washington, D.C.7/31 - 8/3/18 Simon, P. NAPB, Guelph, Ontario, Canada 8/7-10/18 Hoagland, L. Purdue Student Farm Field Day, West Lafayette, IN 8/20/18 All PIs, 39th Int'l. Carrot Conference, Madison, WI 8/22-24/18 Trivino, N. T. Combining pre-treatment of carrot roots (Daucus carota) with novel primer sets for better bacterial endophyte community characterization. HLA Research & Design Retreat, Layafette,IN May 8th-2019. Abdelrazek, S. and L.A Hoagland. Transmission and functional role of carrot endophyte communities. American Phytopathological Society (APS). Annual Meeting Cleveland, OH. Aug 3-8, 2019, (Oral) Abdelrazek, S and L.A Hoagland. Dynamics of endophyte communities associated with carrot. APS Annual Meeting , Cleveland, OH. Aug 3-8, 2019 (Poster). Hoagland, L. Characterizing carrot microbiomes and their potential role in plant and human health. North Central Region Plant Germplasm Repository Meeting, On-line, 2020. Dawson, J.C. Participatory Trialing for Direct-Market Vegetable Growers in the Upper Midwest. Washington State University Crop Science Seminar. Pullman, WA Jan 10, 2020. Dawson, J.C. Participatory Trialing for Direct-Market Vegetable Growers in the Upper Midwest. Michigan State University Horticulture and Plant, Soil and Microbial Sciences Seminar. East Lansing, MI, Jan 19, 2020. Simon, P. et al. Carrot Improvement for Organic Agriculture and Consumer Value. International Federation of Organic Agriculture Movements World Congress. September 6-10, 2021. Blogposts Seed Broadcast, "Getting Creative in the Kitchen with Chromatic Carrots", 10/13/16 Seed Broadcast, "Working Around the Calendar to Breed Organic Carrots", 3/10/17 Seed Broadcast, "This Weekend's Menu: Roasted Carrot Bolognese", 6/2/17 Seed Broadcast, "Join Us: Organic Seed Training in Indiana", 6/14/17 Seed Broadcast, "Evaluating the Fruits of Our Labor", 8/23/17 Seed Broadcast, "Join Us for Our Community Field Day and Tasting", 9/6/17 Seed Broadcast, "Business Member Spotlight: High Mowing Organic Seeds," https://seedalliance.org/2017/business-member-spotlight-high-mowing-organic-seeds/ Seed Broadcast, "Supporting Hawaii's Growing Seed Movement," https://seedalliance.org/2018/novic-team-brings-on-farm-training-to-hawaii/ Seed Broadcast, "Carrot Breeders Find Promising Results at Winter Nursery," https://seedalliance.org/2018/carrot-breeders-find-promising-results-at-the-winter-nursery-harvest/ Seed Broadcast, "Organic Carrot Breeding Intensive in Washington," https://seedalliance.org/2018/organic-carrot-breeding-intensive-washington-october/ Seed Broadcast, "'Glean & Clean' Proves to be a Bushel of Fun," https://seedalliance.org/2018/a-bushel-of-fun/ Seed Broadcast, "Organic Carrot Trials and Tastings in New York," https://seedalliance.org/2018/carrot-trials-and-tastings-in-new-york/ OSA Blog, Farm to Flavor: Culinary Breeding in Carrots, 10/30/19,https://seedalliance.org/2019/farm-to-flavor-culinary-breeding-in-carrots/ OSA Blog, Breeding Carrots with Partners to Address Diverse Needs, 3/30/20,https://seedalliance.org/2020/cioa-ca-harvest2020/ Produce Grower, Soil microbiome can improve carrot resistance to deadly fungus, 7/22/20https://www.producegrower.com/article/carrots-greenhouse-study-purdue/ What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? This project addresses the critical needs of organic carrot producers by developing orange and novel colored carrots with improved disease and nematode resistance, improved weed competitiveness, and improved nutritional value and flavor. About 100,000 acres of carrots are grown annually in the U.S. The 2014 Census of Agriculture, estimated 14% of this carrot production is in organic systems, vs. 3% for vegetable crops overall. Organic production of carrots has significant pest and disease challenges. Over 80% of the U.S. carrot production land is infested with one or more species of root-knot nematodes. Alternaria leaf blight (ALB), other foliar diseases and cavity spot are major carrot diseases in virtually all production areas of the world. The needs for effective non-chemical methods of pest and disease control to the future of the US organic vegetable production are urgent. Carrots are among the slowest crops for growers to establish, often making weed control the most expensive cost of organic production. Flavor and nutritional value are the most important characteristics noted by consumers of organic foods and novel colors attract carrot consumers. This project is developing novel carrots improved for nutrition and flavor, integrated with critical pest and disease resistance and vigorous growth. This project also expands our understanding of root-microbiome interactions critical for growth and nutrient uptake of organically-grown carrots. Goals and annual progress: Long-term goals of this project are to: 1) deliver carrot cultivars with improved disease and nematode resistance, improved nutrient acquisition, seedling vigor and weed competitive traits, increased marketable yield, superior nutritional value, flavor and other culinary qualities, and storage quality for organic production; 2) determine how carrot genotypes interact with/influence, the root microbiome to access key nutrients under limiting environments and avoid heavy metal uptake; 3) inform growers about cultivar performance to maximize organic carrot production, markets, and organic seed usage; 4) inform consumers about the positive environmental impact of organic production systems and about carrot nutritional quality, flavor and culinary attributes; and 5) train students in critical organic agriculture issues. Primary activities: Focus Area 1: Cultivar development and release New breeding populations (~250) were developed during this project. Continued advancement was done on nine orange breeding populations with improved flavor, carotene content, ALB and cavity spot resistance. Seven purple breeding populations with improved flavor, texture, and robust agronomic production qualities were also advanced. Four new breeding populations were started . Successful production of seed to increase stock of novel colored populations slated for release was accomplished. Advanced selections were trialed by five organic seed companies and formal release is underway for three populations from CIOA1 (R6636, R6220, Y1246). Commercial release plans are underway for release of the newly named 'Carnelian' red carrot variety (R6636) with High Mowing Organic Seeds. Focus Area 2: Variety trials on research stations and national participatory sites Variety trials were held in WI, WA, and CA with participatory sites in OR, CO, VA, NY, ME, and VT. Included were 12 advanced breeding populations, check varieties, and selections from among 127 promising breeding populations. Flavor, marketability, productivity, pigment content and storage quality of selected CIOA entries was completed. Advanced lines were distributed to on-farm trials over two seasons as part of the Seed to Kitchen Collaborative trials in the upper Midwest. Focus Area 3: Advancing research on root microbiome interactions A study to determine whether 4 carrot cultivars preferentially recruit AMF communities under organic management was carried out on five organic vegetable farms and the University of Wisconsin (UW) Research Station. Mean root colonization was significantly greater for one open pollinated variety which aligns with previous research where modern varieties of several crops demonstrate a loss of response to colonization by AMF to suggest that screening diverse genotypes may identify enhanced AMF colonization, to be used either directly be farmers or to be included in breeding programs. Interesting interactions in the role of AMF in increasing soil proteins in more highly disturbed environments were suggested. This can be characteristic of organic farms with their reliance on tillage and cultivation. Carrot taproots grown in a field trial comparing organic and conventional management were colonized by an abundant and diverse assortment of bacteria and fungi, though endophytes were more diverse and had greater antagonistic activity against A. dauci that causes ALB in the organic system. Carrot genotype also affected endophyte abundance in taproots and potential for individual isolates to affect seed germination, seedling growth and ALB tolerance. Carrots vertically transmit endophytic microbes within their seeds. These microbes play an important role in germination and early seedling performance and appear to be part of a core carrot microbiome. Carrot genotypes also vary in their potential to promote organic matter priming to scavenge nitrogen, tolerate cadmium (Cd) stress, and accumulate Cd in taproots. The composition of AMF communities present in soil also plays a major role in mediating micronutrient/heavy metal uptake. Carrot genotypes also vary in their potential to alter soil microbial communities that influence susceptibility to pathogenic nematodes in subsequent generations, and N fertility management influences these relationships. Results of these studies demonstrate that carrot productivity is intimately connected to root microbiomes. Soil management practices are critical in promoting beneficial carrot-soil-microbial relationships, though genotype also plays a role indicating that with further work it will be possible to select for these relationships. Focus Area 4: Utilizing molecular markers to improve nematode resistance CIOA2 advanced experimental selections and promising selections were included in field trialing for all 5 years at fields in CA with the prevalent root-knot nematode, M. incognita. Greenhouse tests were used to provide highly controlled screening conditions. Carrot selections were advanced for seed production to be included in genetic analysis, molecular marker evaluation, and breeding line development. Molecular marker evaluation found a major M. hapla resistance gene on chromosome 9 which was fine-mapped to develop markers for breeders. Resistance traits for M. hapla, M. incognita, M. arenaria and M. javanica were identified and confirmed in multiple greenhouse screenings Foliar diseases were diagnosed. Motley dwarf was identified for 3 years in western WA trials, and also in central WA. ALB resistance was evaluated in central WI where 34 promising CIOA2 selections were identified where infection was high and wide variation in resistance was observed. Cavity spot resistance was tested for advanced CIOA2 breeding selections in infested fields in CA and WA and 4 selections advanced for breeding. Focus Area 5: Evaluating and improving carrot flavor, nutritional, and postharvest quality CIOA varieties varied in appearance, texture, sweetness and harshness. Overall flavor was rated on all samples and was positively correlated with sweetness but negatively correlated with harshness. Flavor was rated on all samples each year of trials. Nutritional carotenoids and anthocyanins were evaluated for all advanced breeding lines. CIOA varieties slated for release were evaluated for flavor by chefs in 2019. Public educational events featured diverse advanced varieties at two virtual OSA WA research farm field day. and the Farm to Flavor event in Madison, WI (300+ attendees) in 2019.

Publications

Type: Theses/Dissertations Status: Published Year Published: 2020 Citation: Narda Silva (MS) Characterizing carrot microbiomes and their potential role in soil organic matter decomposition. M.S. Thesis, Purdue University. 114p
Type: Theses/Dissertations Status: Submitted Year Published: 2021 Citation: Erin Lalor (MS) Variation of mineral element accumulation in a diverse carrot germplasm collection. M.S. Thesis, University of Wisconsin - Madison. 207p
Type: Theses/Dissertations Status: Submitted Year Published: 2021 Citation: Kevser Ozel (MS) Identification and Genetic Mapping of New Sources of Nematode Resistance in Carrot (Daucus carota L.) M.S. Thesis, University of Wisconsin - Madison. 154p
Type: Theses/Dissertations Status: Submitted Year Published: 2020 Citation: Leidy Meija (BS) Carrot genotype and nitrogen stress alter plant soil feedbacks and susceptibly to pathogenic nematodes BS Thesis, Purdue University
Type: Theses/Dissertations Status: Submitted Year Published: 2021 Citation: Hannah Komanapalli (BS) Carrot AMF elements. BS Thesis, Purdue University
Type: Journal Articles Status: Published Year Published: 2017 Citation: Simon, P.W., Zystro, J, Roberts, P.A., Waters, T., Colquhoun, J., Navazio, J., Colley, M., McCluskey, C., Hoagland, L., duToit, L., Silva, E., Nunez, J. The CIOA (Carrot Improvement for Organic Agriculture) Project: Location, cropping system, and genetic background influence carrot performance including top height and flavor. Acta Hort.1153: 1-8. 2017.
Type: Journal Articles Status: Published Year Published: 2017 Citation: Arbizu, C.I., P.Tas, P.W. Simon, D.M. Spooner Phylogenetic prediction of carrot leaf blight resistance in wild and cultivated species of carrots. Crop Sci. 57:2645-2653. 2017.
Type: Journal Articles Status: Published Year Published: 2018 Citation: Turner, S.D., P.L. Maurizio, W. Valdar, B.S. Yandell, and P.W. Simon. Dissecting the genetic architecture of shoot growth in carrot (Daucus carota L.) using a diallel mating design. G3 8:411-426. 2018.
Type: Journal Articles Status: Published Year Published: 2020 Citation: Keller-Pearson, M., Yang Liu, A. Peterson, K.Pederson, L. Willems, J.-M. An�, E.M. Silva. 2020. Inoculation with arbuscular mycorrhizal fungi has a more significant positive impact on the growth of open-pollinated heirloom varieties of carrots than on hybrid cultivars under organic management conditions. Agriculture, Ecosystems & Environment 289: 15.
Type: Journal Articles Status: Published Year Published: 2020 Citation: Abdelrazek, S., Simon, P., Colley, M., Mengiste, T., Sulba, Jyothi *Hoagland, L., 2020. Changes in the core endophytic mycobiome of carrot taproots in response to crop management and genotype Scientific Reports doi.org/10.1038/s41598-020-70683-x. Journal impact factor: 4.576
Type: Journal Articles Status: Published Year Published: 2020 Citation: Abdelrazek, S., Simon, P., Colley, M., Mengiste, T., *Hoagland, L., 2020. Crop management system and carrot genotype affect endophyte composition and Alternaria dauci suppression. PLOSOne doi.org/10.1371/journal.pone.0233783. Journal impact factor: 3.226

Progress 09/01/19 to 08/31/20

Outputs
Target Audience:Organic and conventional vegetable growers, marketers, and consumers; vegetable seed companies; plant science researchers in horticulture, plant breeding, plant pathology, nematology, soil science, and botany. Changes/Problems:Some data collection and outreach activities were delayed or omitted due to COVD restrictions What opportunities for training and professional development has the project provided?Year 4 extension activities included creating new project promotion and educational materials for CIOA2, coordinating outreach and evaluation activities, presenting at multiple scientific and food industry conferences, and delivering trainings and educational events. The project communications team continued to support event outreach and track event participation and evaluation. We updated a promotional brochure that gives an overview of the project, and details about current research and research goals that was shared with growers, the carrot industry, researchers, and consumers at CIOA-related events. Each project collaborator received printed copies of the brochure to disseminate at outreach events. We also created a new scientific research poster about the project and presented it at related scientific focused events/conferences. Trials were conducted with six organic seed company research farms - High Mowing Organic Seeds, Adaptive Seeds, Commonwealth Seeds, Row 7 Seeds, Johnny's Selected Seeds, and Seed rEvolution Now!. Each trial provided training on carrot trialing and seed production for employees and interns. These trials provided an opportunity for expansion of project impacts, testing materials in new regions, and soliciting input on evaluations from two organic seed companies. In late September, Colley and McKenzie delivered the OSA Annual Field Day field day highlighting the CIOA project and the breeding and trialing work at the OSA WA Research Farm. The OSA Annual Field day was attended by over approximately two dozen farmers, farmer-breeders and seed company representatives, and 100 members of the public. OSA continues to advise on and support the carrot breeding and trialing work of our colleagues at the Univ. of British Columbia as well as sharing germplasm and mentoring farmers who have expressed interest in initiating on-farm breeding projects through their exposure to the CIOA project. As part of education activities, undergraduate students, graduate students and post-doctorates are being trained in vegetable breeding, crop and seed production, disease protection and diagnosis, and soil science with a focus on organic systems as they participate in research projects critical to the COIA Project achieving the research goals. In the past year 4 graduate students projects included CIOA research activities. To inform growers and consumers about the positive environmental impact of organic production systems, and about carrot nutritional quality and flavor we continued to update and use the web site developed through eOrganic in CIOA1 to disseminate research updates, timely articles, and related project events (http://eorganic.info/carrotimprovement). We created two new promotion brochures giving an overview of the project, and details about current research and research goals. One brochure was tailored for and shared with growers, the carrot industry, and researchers. A second version of the brochure was developed for and shared with a general audience at CIOA-related events. We created a new scientific research poster about the project and presented it at related scientific focused events/conferences. The project reached approximately 800 growers, carrot industry members, researchers, food industry representatives, and consumers in this period. A project field sign was also created and installed at each project location field site so field visitors could clearly identify the project plots, project goals, work, partners, and funder, and visit the website for additional information. Each of the four project collaborators hosted public farmer field days in conjunction with each trial at the project research sites. Field days coincided with timing of trial evaluations. In addition, this project is expanding graduate student and postdoc training, focused on research in organic systems and organic plant breeding. This includes one postdoc, Sahar Abdelrazek and graduate student Narda Silva at Purdue, and another postdoc, William Rolling, and graduate student Erin Lalor at UW. One visiting undergraduate scholars from Colombia (Leidy Meija, University of Caldes, Colombia) at Purdue and two graduate student scholars from Pakistan (Aneela Nijabat, University of Sargodha; Nadia Riaz, Lahore College for Women University) at UW received training by conducting research projects for their respective theses. Micaela Colley is publishing on CIOA 1 agronomic results results and CIOA 2 top growth trials as a component of her PhD thesis, data in process with plans to publish in 2021. The long-term impact of this important educational element is to establish the next generation of researchers, extension, and industry representatives with organic systems expertise. How have the results been disseminated to communities of interest?Educational events and conference presentations delivered include: Outreach: September 12, 2019 Seed to Kitchen's Farm to Flavor Tasting, Madison, WI Field Days and Trainings: 9/30/19 Organic Seed Alliance Annual Field Day, OSA Research Farm, Chimacum, WA. Farmers and public were able to taste carrots and participate in making selections in breeding populations. 9/12/2019 Seed to Kitchen's Farm to Flavor Madison, WI 300 9/22/2019 Jefferson County Farm Tour Chimacum, WA 50 9/30/2019 5th Annual OSA Fall Field Day Chimacum, WA 120 2/12/20-2/15/20 Organic Seed Growers Conference Corvallis, OR 450 2/16/2020 CBN Variety Showcase Portland, OR 500 3/10/2020 CIOA/SCRI Carrot Harvest Public Field Day El Centro, CA 2020 Organic Vegetable Field Day at University of Wisconsin-Madison, Purdue University, University of California - Riverside, and California Agriculture Extension were cancelled due to COVID Meetings: Hoagland, L. Characterizing carrot microbiomes and their potential role in plant and human health. North Central Region Plant Germplasm Repository Meeting, On-line, 2020. Dawson, J.C. Participatory Trialing for Direct-Market Vegetable Growers in the Upper Midwest.Washington State University Crop Science Seminar. Pullman, WA Jan 10, 2020. Dawson, J.C. Participatory Trialing for Direct-Market Vegetable Growers in the Upper Midwest.Michigan State University Horticulture and Plant, Soil and Microbial Sciences Seminar. East Lansing, MI, Jan 19, 2020. Blogposts OSA Blog, Farm to Flavor: Culinary Breeding in Carrots, 10/30/19,https://seedalliance.org/2019/farm-to-flavor-culinary-breeding-in-carrots/ OSA Blog, Breeding Carrots with Partners to Address Diverse Needs, 3/30/20,https://seedalliance.org/2020/cioa-ca-harvest2020/ Produce Grower, Soil microbiome can improve carrot resistance to deadly fungus, 7/22/20https://www.producegrower.com/article/carrots-greenhouse-study-purdue/ What do you plan to do during the next reporting period to accomplish the goals?Selected field trialing and research activities described for Year 1-4 will continue in Year 5 - namely the winter 2020-21 winter root nursery is underway to produce stecklings to increase seed supplies of CIOA germplasm, especially breeding lines staged for release. In addition, seed increase of promising genetic stocks included in trials will be continued and resistance testing of ALB in WI and nematode resistance in CA will be continued in 2021. Marker work for nematode resistance will continue, and data will be summarized published. Future educational events planned for Year 5: Presentations on breeding for organic ag and the CIOA2 project may be delivered at selected regional vegetable growers meetings including the Pacific Northwest Vegetable Meeting; Seed Sovereignty Field Day/NOFA; Great Lakes Fruit, Vegetable, and Farm Market Expo; Midwestern Organic and Sustainable Education Service (MOSES) Conference which are being held virtually.

Impacts
What was accomplished under these goals? This project addresses the critical needs of organic carrot producers by developing orange and novel colored carrots with improved disease and nematode resistance, improved weed competitiveness, and improved nutritional value and flavor. About 100,000 acres of carrots are grown annually in the U.S. The 2014 Census of Agriculture, estimated 14% of this carrot production is in organic systems, vs. 3% for vegetable crops overall. Organic production of carrots has significant pest and disease challenges. Over 80% of the U.S. carrot production land is infested with one or more species of root-knot nematodes. Alternaria leaf blight (ALB), other foliar diseases and cavity spot are major carrot diseases in virtually all production areas of the world. The needs for effective non-chemical methods of pest and disease control to the future of the US organic vegetable production are urgent. Carrots are among the slowest crops for growers to establish, often making weed control the most expensive cost of organic production. Flavor and nutritional value are the most important characteristics noted by consumers of organic foods and novel colors attract carrot consumers. This project is developing novel carrots improved for nutrition and flavor, integrated with critical pest and disease resistance and vigorous growth. This project also expands our understanding of root-microbiome interactions critical for growth and nutrient uptake of organically-grown carrots. Goals and annual progress: Long-term goals of this project are to: 1) deliver carrot cultivars with improved disease and nematode resistance, improved nutrient acquisition, seedling vigor and weed competitive traits, increased marketable yield, superior nutritional value, flavor and other culinary qualities, and storage quality for organic production; 2) determine how carrot genotypes interact with/influence, the root microbiome to access key nutrients under limiting environments and avoid heavy metal uptake; 3) inform growers about cultivar performance to maximize organic carrot production, markets, and organic seed usage; 4) inform consumers about the positive environmental impact of organic production systems and about carrot nutritional quality, flavor and culinary attributes; and 5) train undergraduate, graduate, and post-doctorate students in critical organic agriculture issues. Primary activities: Focus Area 1: Cultivar development and release New breeding populations (~45) were identified in the 2019-2020 winter root nursery. Three new orange breeding populations with improved flavor, carotene content, ALB and cavity spot resistance were advanced. The two purple breeding populations with improved flavor, texture, and robust agronomic production qualities were also advanced. Seven new breeding populations were started - one orange and six of novel colors, from roots produced in the winter root nursery. Successful production of seed to increase stock for widespread and larger scale trials of novel colored populations slated for release was accomplished. True-breeding selections of P1129 were advanced. Advanced selections were trialed by five organic seed companies and formal release is underway for three populations from CIOA1 (R6636, R6220, Y1246). Project partners are currently discussing release of the red carrot R6636 with one seed company. Focus Area 2: Variety trials on research stations and national participatory sites On-farm and on-station trials were radically impacted by covid-19, especially on-station trials at participating/collaborating Universities. Variety trials were held in WI, WA, and CA with participatory sites in OR, CO, VA, NY, ME, and VT. Included were 12 advanced breeding populations, check varieties, and selections from among 120 promising breeding populations. Flavor, marketability, productivity, pigment content and storage quality of selected CIOA entries was completed. Focus Area 3: Advancing research on root microbiome interactions A study to determine whether 4 carrot cultivars preferentially recruit AMF communities under organic management was carried out on five organic vegetable farms and the University of Wisconsin (UW) Research Station. Mean root colonization was significantly greater for one open pollinated variety which aligns with previous research where modern varieties of several crops demonstrate a loss of response to colonization by AMF to suggest that screening diverse genotypes may identify enhanced AMF colonization, to be used either directly be farmers or to be included in breeding programs. AMF-associated soil proteins were not correlated to carrot cultivar at different farm sites but interesting interactions in the role of AMF in increasing soil proteins in more highly disturbed environments were suggested. This can be characteristic of organic farms with their reliance on tillage and cultivation indicating that it would be valuable to further investigate the role of cultivar selection and AMF inoculation on soil aggregation in heavily tilled/cultivated phases of the organic crop rotation, and in intensive vegetable production. Carrot taproots were found to be colonized by an abundant and diverse assortment of bacteria and fungi with greater diversity in organic management than conventional soils. Carrot genotype affected endophyte abundance in taproots and potential for individual isolates to affect seed germination, seedling growth and ALB tolerance was evaluated. Benefits of endophytes on carrot growth were greatest when plants were subjected to ALB stress, highlighting the importance of environmental conditions and the potential functional role of endophytes. This study demonstrates that endophytes can play an important role in improving carrot performance and mediating stress caused by ALB. Studies evaluating carrot root microbiome effects on nitrogen scavenging and heavy metal uptake are underway. Focus Area 4: Utilizing molecular markers to improve nematode resistance CIOA2 advanced experimental selections and promising selections were included in field trialing for resistance to prevalent root-knot nematodes occurring in California. Selected carrots were advanced for seed production to be included in genetic analysis, molecular marker evaluation, and breeding line development. Molecular marker evaluation this year found a major M. hapla resistance gene which is being fine-mapped to develop markers for breeders. Greenhouse tests were used to provide highly controlled screening conditions. Resistance traits for M. hapla, M. incognita and M. javanica were identified. Foliar diseases were diagnosed. Motley dwarf was identified for a third year in western WA trials, and also in central WA. ALB resistance was evaluated in central WI. Promising CIOA2 selections were identified where infection was high and wide variation in resistance was observed. Cavity spot resistance was tested for advanced CIOA2 breeding selections in infested fields in CA and WA and selections advanced for breeding. Focus Area 5: Evaluating and improving carrot flavor, nutritional, and postharvest quality CIOA varieties varied in appearance, texture, flavor intensity, acidity, sweetness and harshness. Overall flavor was rated on all samples and was positively correlated with sweetness but negatively correlated with harshness. Carrot flavor evaluation from the 2020 growing season is in progress. CIOA varieties slated for release were evaluated for flavor by chefs in 2019, but not in 2020 due to the COVID pandemic. Public educational events featured diverse advanced varieties at the first virtual OSA WA research farm field day and the Farm to Flavor event in Madison, WI (300+ attendees) in 2019.

Publications

Type: Journal Articles Status: Published Year Published: 2020 Citation: Abdelrazek, S., Simon, P., Colley, M., Mengiste, T., Sulba, Jyothi *Hoagland, L., 2020. Changes in the core endophytic mycobiome of carrot taproots in response to crop management and genotype Scientific Reports doi.org/10.1038/s41598-020-70683-x
Type: Journal Articles Status: Published Year Published: 2020 Citation: Abdelrazek, S., Simon, P., Colley, M., Mengiste, T., *Hoagland, L., 2020. Crop management system and carrot genotype affect endophyte composition and Alternaria dauci suppression. PLOSOne doi.org/10.1371/journal.pone.0233783
Type: Theses/Dissertations Status: Submitted Year Published: 2020 Citation: Narda Silva.Characterizing carrot microbiomes and their potential role in soil organic matter decomposition. M.S. Thesis, Purdue University.
Type: Theses/Dissertations Status: Submitted Year Published: 2020 Citation: Leidy Meija. Carrot genotype and nitrogen stress alter plant soil feedbacks and susceptibly to pathogenic nematodes. B.S. thesis , Purdue University

Progress 09/01/18 to 08/31/19

Outputs
Target Audience:Organic and conventional vegetable growers, marketers, and consumers; vegetable seed companies; plant science researchers in horticulture, plant breeding, plant pathology, nematology, soil science, and botany 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 extension activities included creating new project promotion and educational materials for CIOA2, coordinating outreach and evaluation activities, presenting at multiple scientific and food industry conferences, and delivering trainings and educational events. The project communications team continued to support event outreach and track event participation and evaluation. We created a new promotional brochure giving an overview of the project, and details about current research and research goals that was shared with growers, the carrot industry, researchers, and consumers at CIOA-related events. Each project collaborator received printed copies of the brochure to disseminate at outreach events. We also created a new scientific research poster about the project and presented it at related scientific focused events/conferences. Replicated trials were conducted on two organic seed company research farms in the NE and SE (High Mowing Organic Seed and Southern Exposure Seed Exchange) and they provided training on carrot trialing and seed production. These two trials provided an opportunity for expansion of project impacts, testing materials in new regions, and soliciting input on evaluations from two organic seed companies. Fall, 2019, Colley and McKenzie delivered a field day and workshop on organic carrot plant breeding at the OSA research farm in WA with over two dozen farmer-breeders and seed company representatives present. Several participants expressed interest in initiating on-farm breeding projects and the CIOA team plans to support these efforts by advising and sharing of germplasm. As part of education activities, undergraduate students, graduate students and post-doctorates are being trained in vegetable breeding, crop and seed production, disease protection and diagnosis, and soil science with a focus on organic systems as they participate in research projects critical to the COIA Project achieving the research goals. In the past year 4 graduate students projects included CIOA research activities. To inform growers and consumers about the positive environmental impact of organic production systems, and about carrot nutritional quality and flavor we continued to update and use the web site developed through eOrganic in CIOA I to disseminate research updates, timely articles, and related project events (http://eorganic.info/carrotimprovement). We created two new promotion brochures giving an overview of the project, and details about current research and research goals. One brochure was tailored for and shared with growers, the carrot industry, and researchers. A second version of the brochure was developed for and shared with a general audience at CIOA-related events. We created a new scientific research poster about the project and presented it at related scientific focused events/conferences. The project reached approximately 800 growers, carrot industry members, researchers, food industry representatives, and consumers in this period. A project field sign was also created and installed at each project location field site so field visitors could clearly identify the project plots, project goals, work, partners, and funder, and visit the website for additional information. Each of the four project collaborators hosted public farmer field days in conjunction with each trial at the project research sites. Field days coincided with timing of trial evaluations. To demonstrate techniques and challenges associated with organic carrot seed production, seed increase plots were established for organic carrot seed production in two on-farm workshop. The seed increases at OSA research farm were also used in trainings on organic carrot breeding. Seed production for carrot germplasm to be released was initiated. In addition, this project is expanding graduate student training, focused on research in organic systems and organic plant breeding. One student, Sahar Abdelrazk, completed her PhD in December 2018, and another graduate student, Narda Silva, is preparing to graduate with her MS in May 2019. Two visiting undergraduate scholars from Latin America received training by conducting research projects for their senior theses. One, Gabriella Santos (Zamorano University, Honduras) completed a project in spring 2018, and another, Leidy Mejas (University of Caldes, Colombia) is currently conducting an experiment. Finally, an undergraduate student at Purdue, Hannah Komanapelli, is currently conducted a project as part of her honors thesis. The long-term impact of this important educational element is to establish the next generation of researchers, extension, and industry representatives with organic systems expertise. How have the results been disseminated to communities of interest?Educational events and conference presentations delivered include: Outreach: September 12, 2019 Seed to Kitchen's Farm to Flavor Tasting, Madison, WI Field Days and Trainings: August 22, 2019 Organic Vegetable Field Day at University of Wisconsin-Madison's West Madison Agricultural Research Station, Madison, WI Participants were able to taste carrots developed through the CIOA1 project. Meetings: Trivino, N. T. Combining pre-treatment of carrot roots (Daucus carota) with novel primer sets for better bacterial endophyte community characterization. HLA Research & Design Retreat, May 8th-2019. Layafette,IN Abdelrazek, S. and L.A Hoagland. Transmission and functional role of carrot endophyte communities. American Phytopathological Society (APS). Annual Meeting Aug 3-8, 2019, Cleveland, OH. (Oral) Abdelrazek, S and L.A Hoagland. Dynamics of endophyte communities associated with carrot. APS Annual Meeting Aug 3-8, 2019, Cleveland, OH. (Poster). Blogposts Seed Broadcast, "Business Member Spotlight: High Mowing Organic Seeds," https://seedalliance.org/2017/business-member-spotlight-high-mowing-organic-seeds/ Seed Broadcast, "Supporting Hawaii's Growing Seed Movement," https://seedalliance.org/2018/novic-team-brings-on-farm-training-to-hawaii/ Seed Broadcast, "Carrot Breeders Find Promising Results at Winter Nursery," https://seedalliance.org/2018/carrot-breeders-find-promising-results-at-the-winter-nursery-harvest/ Seed Broadcast, "Organic Carrot Breeding Intensive in Washington," https://seedalliance.org/2018/organic-carrot-breeding-intensive-washington-october/ Seed Broadcast, "'Glean & Clean' Proves to be a Bushel of Fun," https://seedalliance.org/2018/a-bushel-of-fun/ Seed Broadcast, "Organic Carrot Trials and Tastings in New York," https://seedalliance.org/2018/carrot-trials-and-tastings-in-new-york/ What do you plan to do during the next reporting period to accomplish the goals?All field trialing and research activities described for Year 1-3 will continue in Year 4. In addition, seed increase of promising genetic stocks included in trials will be continued and expanded. Future educational events planned for Year 4: Presentations on breeding for organic and the CIOA2 project will be delivered at selected regional vegetable growers meetings including the Pacific Northwest Vegetable Meeting, Kennewick, WA; Seed Sovereignty Field Day/NOFA, Dartmouth, MA; Great Lakes Fruit, Vegetable, and Farm Market Expo, Grand Rapids, MI; Organic Seed Growers Conference, Corvallis, OR; Organicology Conference, Portland, OR; Organic Agriculture Research Symposium; Midwestern Organic and Sustainable Education Service (MOSES) Conference, LaCrosse, WI; ASHS, Orlando. The project team holds an annual planning meeting in conjunction with the Organic Agriculture Research Symposium.

Impacts
What was accomplished under these goals? This project addresses the critical needs of organic carrot producers by developing orange and novel colored carrots with improved disease and nematode resistance, improved weed competitiveness, and improved nutritional value and flavor. About 100,000 acres of carrots are grown annually in the U.S. The 2014 Census of Agriculture, estimated 14% of this carrot production is in organic systems, vs. 3% for vegetable crops overall. Organic production of carrots has significant pest and disease challenges. Over 80% of the U.S. carrot production land is infested with one or more species of root-knot nematodes. Alternaria leaf blight (ALB), other foliar diseases and cavity spot are major carrot diseases in virtually all production areas of the world. The needs for effective non-chemical methods of pest and disease control to the future of the US organic vegetable production are urgent. Carrots are among the slowest crops for growers to establish, often making weed control the most expensive cost of organic production. Flavor and nutritional value are the most important characteristics noted by consumers of organic foods and novel colors attract carrot consumers. This project is developing novel carrots improved for nutrition and flavor, integrated with critical pest and disease resistance and vigorous growth. This project also expands our understanding of root-microbiome interactions critical for growth and nutrient uptake of organically-grown carrots. Goals and annual progress: Long-term goals of this project are to: 1) deliver carrot cultivars with improved disease and nematode resistance, improved nutrient acquisition, seedling vigor and weed competitive traits, increased marketable yield, superior nutritional value, flavor and other culinary qualities, and storage quality for organic production; 2) determine how carrot genotypes interact with/influence, the root microbiome to access key nutrients under limiting environments and avoid heavy metal uptake; 3) inform growers about cultivar performance to maximize organic carrot production, markets, and organic seed usage; 4) inform consumers about the positive environmental impact of organic production systems and about carrot nutritional quality, flavor and culinary attributes; and 5) train undergraduate, graduate, and post-doctorate students in critical organic agriculture issues. Primary activities: Focus Area 1: Cultivar development and release Detailed crop improvement plans for diverse breeding materials were developed and seed increases of promising selections were initiated for national trial evaluation. Approx. 85 new breeding populations were identified in our winter root nursery. Three new orange breeding populations with improved flavor, carotene content, ALB and cavity spot resistance were advanced. Two purple breeding populations with improved flavor, texture and color were also developed. A final round of selection and seed increase of three novel colored populations slated for release from CIOA1 (R6636, R6220 and Y1246) were selected in the 2019 winter nursery and grown to seed. Half-sib family selection to removed recessive orange roots from the purple P1129 population was exercised. Advanced selections were trialed by four organic seed companies and formal release is underway. Focus Area 2: Variety trials on research stations and national participatory sites Variety trials were held in IN, WI, WA, and CA with participatory sites in WA, VA, and VT. Included were 12 advanced breeding populations, check varieties, and selections from among 34 promising breeding populations. Flavor, carotenoid and anthocyanin content and storage quality of all CIOA entries was completed. Focus Area 3: Advancing research on root microbiome interactions In year 3, the relationship between carrot genotype and arbuscular mycorrhizal fungi associations under organic production conditions was evaluated, including four carrot cultivars (two heirlooms and two hybrids) of carrots and their propensities to benefit from inoculation with isolates of arbuscular mycorrhizal fungi in organic field conditions with and without late-season water restriction. Inoculants included geographically-distinct isolates from four species (Funneliformis mosseae, Rhizophagus clarus, R. intraradices, and Septoglomus deserticola). Carrot cultivars differed significantly in their response to inoculation, with heirloom cultivars demonstrating a higher propensity to benefit compared to hybrid cultivars. However, there was no consistent benefit or cost associated with inoculation, regardless of water conditions. Results were published and research expanded in 2019 to investigate interactions between carrot cultivar and the native soil microbiome on working organic farms, to determine if different carrot genetics respond differently to variation in soil biology. Data is being analyzed with evaluations continuing. Carrot taproots were found to be colonized by an abundant and diverse assortment of bacteria and fungi with greater diversity in organic management than conventional soils. Carrot genotype affected endophyte abundance in taproots and potential for individual isolates to affect seed germination, seedling growth and ALB tolerance was evaluated. Benefits of endophytes on carrot growth were greatest when plants were subjected to ALB stress, highlighting the importance of environmental conditions and the potential functional role of endophytes. This study demonstrates that endophytes can play an important role in improving carrot performance and mediating stress caused by ALB. Studies evaluating carrot root microbiome effects on nitrogen scavenging and heavy metal uptake are underway. Focus Area 4: Utilizing molecular markers to improve nematode resistance CIOA2 advanced experimental selections and promising selections were included in field trialing for resistance to prevalent root-knot nematodes occurring in California. Selected carrots were advanced for seed production to be included in genetic analysis, molecular marker evaluation, and breeding line development. Molecular marker evaluation this year narrowed genomic regions flanking the six major nematode resistance genes identified to date. Three new genomic regions contributing to resistance were discovered in 2018, and are being fine-mapped to develop markers for breeders. Continuation of greenhouse and field-screening for nematode resistance were carried out using sites in Parlier, CA. Greenhouse tests were used to provide highly controlled screening conditions. Resistance traits for M. hapla, M. incognita and M. javanica were identified. Foliar diseases were diagnosed when identity was uncertain. Motley dwarf was identified for a second year in Chimicum, WA trials. ALB resistance was evaluated in central Wisconsin. Promising CIOA2 selections were identified where infection was high and wide variation in resistance was observed. Cavity spot resistance was tested for advanced CIOA2 breeding selections in infested fields in CA and WA and selections advanced for breeding. Focus Area 5: Evaluating and improving carrot flavor, nutritional, and postharvest quality CIOA varieties were evaluated in November 2018, in separate groupings for different colors. Evaluation included appearance and texture, as well as flavor intensity, acidity, sweetness and harshness. Overall flavor was rated on all samples and was positively correlated with sweetness but negatively correlated with harshness. Carrot flavor evaluation from the 2019 growing season is in progress. CIOA varieties slated for release were evaluated for flavor by chefs evaluated for flavor. Public educational events also featured diverse advanced varieties, at the OSA WA research farm field day and the Farm to Flavor event in Madison, WI (300+ attendees) in 2019. Breeding lines from CIOA2 were shared with attendees at the and public taste test data was collected.

Publications

Type: Journal Articles Status: Awaiting Publication Year Published: 2020 Citation: Keller-Pearson, M., Yang Liu, A. Peterson, K.Pederson, L. Willems, J.-M. An�, E.M. Silva. 2020. Inoculation with arbuscular mycorrhizal fungi has a more significant positive impact on the growth of open-pollinated heirloom varieties of carrots than on hybrid cultivars under organic management conditions. Agriculture, Ecosystems & Environment 289: 15.
Type: Journal Articles Status: Submitted Year Published: 2020 Citation: Abdelrazek, S., Simon, P., Colley, M., Mengiste, T., Hoagland, L., (submitted). Crop management system and carrot genotype affect endophyte composition and Alternaria dauci suppression. PLOSOne

Progress 09/01/17 to 08/31/18

Outputs
Target Audience: Organic and conventional vegetable growers, marketers, and consumers; vegetable seed companies; plant science researchers in horticulture, plant breeding, plant pathology, nematology, soil science, botany Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Year 2 extension activities included creating new project promotion and educational materials for CIOA2, coordinating outreach and evaluation activities, presenting at multiple scientific and food industry conferences, and delivering trainings and educational events. The project communications team continued to support event outreach and track event participation and evaluation. We created a new promotional brochure giving an overview of the project, and details about current research and research goals that was shared with growers, the carrot industry, researchers, and consumers at CIOA-related events. Each project collaborator received printed copies of the brochure to disseminate at outreach events. We also created a new scientific research poster about the project and presented it at related scientific focused events/conferences. Replicated trials were conducted on two organic seed company research farms in the NE and SE (High Mowing Organic Seed and Southern Exposure Seed Exchange) and they provided training on carrot trailing and seed production. These two trials provided an opportunity for expansion of project impacts, testing materials in new regions, and soliciting input on evaluations from two organic seed companies. An on-farm trial was also conducted in Hawaii at Counter Culture Farm on Oahu. This trial added a tropical environment for testing material and one of the CIOA entries (Brasilia) performed well. Fall, 2018, Simon, Colley and McKenzie delivered a workshop on organic carrot plant breeding at the OSA research farm in WA with over a dozen farmer-breeders and seed company representatives present. Several participants expressed interest in initiating on-farm breeding projects in 2019 and the CIOA team plans to support these efforts by advising and sharing of germplasm. As part of education activities, undergraduate students, graduate students and post-doctorates are being trained in vegetable breeding, crop and seed production, disease protection and diagnosis, and soil science with a focus on organic systems as they participate in research projects critical to the COIA Project achieving the research goals. In the past year 4 graduate students projects included CIOA research activities. To inform growers and consumers about the positive environmental impact of organic production systems, and about carrot nutritional quality and flavor we continued to update and use the web site developed through eOrganic in CIOA I to disseminate research updates, timely articles, and related project events (http://eorganic.info/carrotimprovement). We created two new promotion brochures giving an overview of the project, and details about current research and research goals. One brochure was tailored for and shared with growers, the carrot industry, and researchers. A second version of the brochure was developed for and shared with a general audience at CIOA-related events. We created a new scientific research poster about the project and presented it at related scientific focused events/conferences. The project reached approximately 800 growers, carrot industry members, researchers, food industry representatives, and consumers in this period. A project field sign was also created and installed at each project location field site so field visitors could clearly identify the project plots, project goals, work, partners, and funder, and visit the website for additional information. Each of the four project collaborators hosted public farmer field days in conjunction with each trial at the project research sites. Field days coincided with timing of trial evaluations. To demonstrate techniques and challenges associated with organic carrot seed production, seed increase plots were established for organic carrot seed production in two on-farm workshop. The seed increases at OSA research farm were also used in trainings on organic carrot breeding. . Seed production for carrot germplasm to be released was initiated. In addition, this project is expanding graduate student training, focused on research in organic systems and organic plant breeding. The long-term impact of this important educational element is to establish the next generation of researchers, extension, and industry representatives with organic systems expertise. How have the results been disseminated to communities of interest?Educational events and conference presentations delivered in 2017-2018 include: Outreach: September 7, 2017, Seed to Kitchen's Farm to Flavor Tasting, Madison, WI March 13, 2018, Culinary Breeding Network's Variety Showcase, Oahu, HI September 24, 2018, NYC Culinary Breeding Network's Variety Showcase, New York, NY September 26, 2018, Seed to Kitchen's Farm to Flavor Tasting, Madison, WI Field Days and Trainings: September 25, 2017, Research and Farmer Field Day, and Community Field Day and Tasting, Organic Seed Alliance Research Farm, Chimacum, WA August 20, 2018, Organic Vegetable Field Day at University of Wisconsin-Madison's West Madison Agricultural Research Station, Madison, WI Participants were able to taste carrots developed through the CIOA1 project. August 24, 2018, International Carrot Conference Field Tour of Carrot Research Projects, University of Wisconsin-Madison's Hancock Agricultural Research Station, Hancock, WI Meetings: October 17-18, 2018, OREI PD Meeting, Washington, D.C. February 14-17, 2018, Organic Seed Growers Conference, Corvallis, OR February 22-24, 2018, MOSES Organic Farming Conference, La Crosse, WI July 31-August 3, 2018, ASHS, Washington, D.C. August 7-10, 2018, NAPB, Guelph, Ontario, Canada August 20, 2018, Purdue Student Farm Field Day, West Lafayette, IN August 22-24, 2018 39th Int'l. Carrot Conference, Madison, WI Upcoming: September 11, 2018, Fundamentals of Organic Plant Breeding Intensive and Field Day, Mineral, VA September 19-22, 2018, Apiaceae Meeting, Krakow, Poland September 22, 2018, Seed Saving and Variety Improvement Workshop, Shelter Island, NY September 26, 2018, Farm to Flavor, a public dinner and outreach event attended by about 330 people in, Madison, WI featuring dishes by participating chefs. Carrots from the CIOA project were one of the featured varieties and attendees received information about the project October 1, 2018, Research and Farmer Field Day, and Community Field Day and Tasting, Organic Seed Alliance Research Farm, Chimacum, WA October 9, 2018, Organic Carrot Breeding Workshop, Organic Seed Alliance Research Farm, Chimacum, WA November 15-16, 2018, Pacific Northwest Vegetable Association Meeting, Washington February 14-16, 2019, Organicology, Portland, OR Blogposts Seed Broadcast, "Business Member Spotlight: High Mowing Organic Seeds," 9/28/17, https://seedalliance.org/2017/business-member-spotlight-high-mowing-organic-seeds/ Seed Broadcast, "Supporting Hawaii's Growing Seed Movement," 3/22/18, Seed Broadcast, "Carrot Breeders Find Promising Results at Winter Nursery," 3/22/18, Seed Broadcast, "Organic Carrot Breeding Intensive in Washington," 9/14/18, Seed Broadcast, "'Glean & Clean' Proves to be a Bushel of Fun," 10/17/18, Seed Broadcast, "Organic Carrot Trials and Tastings in New York," 10/26/18, https://seedalliance.org/2018/carrot-trials-and-tastings-in-new-york/ What do you plan to do during the next reporting period to accomplish the goals?All field trialing and research activities described for Year 1-2 will continue in Year 3. In addition, seed increase of promising genetic stocks included in trials will be continued and expanded. Future educational events planned for Year 3: Presentations on breeding for organic and the CIOA2 project will be delivered at selected regional vegetable growers meetings including the Pacific Northwest Vegetable Meeting, Kennewick, WA (Q4, 2018); Seed Sovereignty Field Day/NOFA, Dartmouth, MA; Great Lakes Fruit, Vegetable, and Farm Market Expo, Grand Rapids, MI; Organic Seed Growers Conference, Corvallis, OR; Organicology Conference, Portland, OR; Organic Agriculture Research Symposium; Midwestern Organic and Sustainable Education Service (MOSES) Conference, LaCrosse, WI; ASHS, Las Vegas. The project team holds an annual planning meeting in conjunction with the Organic Agriculture Research Symposium.

Impacts
What was accomplished under these goals? This project addresses the critical needs of organic carrot producers by developing orange and novel colored carrots with improved disease and nematode resistance, improved weed competitiveness, and improved nutritional value and flavor. About 100,000 acres of carrots are grown annually in the U.S. The 2014 Census of Agriculture, estimated 14% of this carrot production is in organic systems, vs. 3% for vegetable crops overall. Organic production of carrots presents several significant challenges from pests and diseases. Over 80% of the U.S. carrot production land is infested with one or more of the common species of root-knot nematodes. Alternaria leaf blight, other foliar diseases and cavity spot are major carrot diseases in virtually all production areas of the world. It is urgent and vital to the future of the US organic vegetable industry that effective non-chemical methods of nematode and leaf blight control be developed. Carrots are one of the slowest crops for growers to establish and grow. This often makes weed control the most expensive cost of organic carrot production. Flavor and nutritional value are the most important characteristics noted by consumers of organic foods. Among novel colored carrots are breeding stocks with some of the most vigorous growing seedlings and large tops. This project is developing novel carrots improved for nutrition and flavor, integrated with critical pest and disease resistance and vigorous growth. This project also expands our understanding of root-microbiome interactions critical for growth and nutrient uptake of organically-grown carrots. Goals and annual progress: The long-term goals of this project are to: 1) deliver carrot cultivars with improved disease and nematode resistance, improved nutrient acquisition, seedling vigor and weed competitive traits, increased marketable yield, superior nutritional value, flavor and other culinary qualities, and storage quality for organic production; 2) determine how carrot genotypes interact with, or influence, the root microbiome to access key nutrients under limiting environments and avoid heavy metal uptake; 3) inform growers about cultivar performance to maximize organic carrot production, markets, and organic seed usage; 4) inform consumers about the positive environmental impact of organic production systems and about carrot nutritional quality, flavor and culinary attributes; and 5) train undergraduate, graduate, and post-doctorate students in critical organic agriculture issues. Primary activities: Focus Area 1: Cultivar development and release We have developed detailed breeding plans for diverse breeding materials and have initiated seed increases of promising selections to be grown at all national trial sites. Selection of new breeding populations for CIOA2 in our winter root nursery identified ~85 new germplasm sources for evaluations. Seed was produced and included in the winter root nursery. Three new orange breeding populations have been created with a combination of flavor, enhanced carotene content, Alternaria and cavity spot resistance. Two purple breeding populations have also been created with a focus on excellent flavor,texture and color. A final round of selection and seed increase of two populations slated for release from CIOA1 (Purple-Orange 1129 and Red 6636) will be initiated this winter. Focus Area 2: Variety trials on research stations and national participatory sites Variety trials were held in Indiana, Wisconsin, Washington, and California and participatory sites in Washington, Hawaii, Maine, Virginia and Vermont. Included were 12 advanced breeding populations check varieties, plus selections from among an additional 34 potentially promising breeding populations that varied among trial sites. Roots from trial locations were sampled for nutritional pigment and flavor analysis. Focus Area 3: Advancing research on root microbiome interactions Arbuscular mycorrhizal fungi (AMF) beneficially interact with host plants by colonizing host roots, forming structures called arbuscules that facilitate the movement of water and nutrients, most notably phosphorus, in exchange for plant sugars. AMF can boost host performance during drought and other stresses. We evaluated organically grown carrot cultivars to compare the influence of different AMF species on carrot growth during varying water-limiting soil conditions. Carrot cultivars differed in their response to water limitation. Benefits to carrot growth differed according to cultivar-mycorrhizal species pairing. In addition to AMF, an abundant and diverse assortment of other microbial taxa that can help carrots acquire nitrogen and withstand biotic and abiotic stress also colonizes carrots. We identified these microbes within the seeds and taproots of a diverse set of carrot genotypes and demonstrated that they have potential to improve seedling establishment, help carrots acquire nitrogen and phosphorous, and withstand assault by Alternaria dauci, a key carrot pest. Microbial populations in carrot roots that are antagonistic to A. dauci, were greater in organic than conventional farming systems, demonstrating the value of greater soil health in organic systems. Carrot genotype also affected the composition of these microbes indicating that it may be possible to select for these beneficial plant-microbial relationships in breeding programs. Additional studies to determine whether carrot root microbiomes can enhance nitrogen scavenging and exclude heavy metal uptake are underway, along with evaluation of new processing and imaging tools to enhance recovery of carrot endophytes and improve phenotypic evaluation of carrot characteristics. Focus Area 4: Utilizing molecular markers to improve nematode resistance CIOA2 advanced experimental selections and additional potentially promising selections were included in field trialing for resistance to the most prevalent root-knot nematodes occurring in California. Selected carrots were advanced for seed production to be included in the genetic analysis, molecular marker evaluation, and breeding line development. Molecular marker evaluation underway has developed molecular markers for narrower genomic regions flanking the six major nematode resistance genes identified to date. Three new genomic regions contributing to resistance were discovered in 2018, and are being fine-mapped to develop markers for breeders. Foliar diseases were diagnosed when identity was uncertain. Motley dwarf was identified for a second year in Chimicum, WA trials. Alternaria leaf blight resistance was evaluated and promising selections identified in CIOA2 selections in central Wisconsin, Infection was high and wide variation in resistance was observed. Cavity spot resistance was tested for advanced CIOA2 breeding selections in infested fields in California and selections advanced for breeding. Focus Area 5: Evaluating and improving carrot flavor, nutritional, and postharvest quality CIOA varieties were evaluated by chefs participating in vegetable flavor evaluations including two varieties slated for release. These varieties were also tasted by attendees at the international carrot conference in Madison, WI in August 2018. The attendees included representatives from most of the major carrot breeding, seed and production companies globally. Public educational events also featured these two varieties, at the Variety Showcase in NYC September 24th and the Farm to Flavor event in Madison, WI on September 26th. Taste evaluations by project personnel and participating chefs on orange, red and purple breeding lines as well as check varieties are anticipated in November, to provide quantitative and qualitative feedback on their culinary qualities. Evaluation of flavor, carotenoids and anthocyanins of all CIOA carrots is ongoing. Postharvest storage quality (rots, sprouting) is being noted.

Publications

Type: Journal Articles Status: Published Year Published: 2018 Citation: Turner, S.D., P.L. Maurizio, W. Valdar, B.S. Yandell, and P.W. Simon. Dissecting the genetic architecture of shoot growth in carrot (Daucus carota L.) using a diallel mating design. G3 8:411-426. 2018.

Progress 09/01/16 to 08/31/17

Outputs
Target Audience: Organic and conventional vegetable growers, marketers, and consumers; vegetable seed companies; plant science researchers in horticulture, plant breeding, plant pathology, nematology, soil science, botany Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Year 1 extension activities included creating new project promotion and educational materials for CIOA2, coordinating outreach and evaluation activities, presenting at multiple scientific and food industry conferences, and delivering trainings and educational events. The project communications team continued to support event outreach and track event participation and evaluation. We created a new promotional brochure giving an overview of the project, and details about current research and research goals that was shared with growers, the carrot industry, researchers, and consumers at CIOA-related events. Each project collaborator received printed copies of the brochure to disseminate at outreach events. We also created a new scientific research poster about the project and presented it at related scientific focused events/conferences. Replicated trials were conducted on two organic seed company research farms in the NE and SE (High Mowing Organic Seed and Southern Exposure Seed Exchange) and they provided training on carrot trailing and seed production. These two trials provided an opportunity for expansion of project impacts, testing materials in new regions, and soliciting input on evaluations from two organic seed companies. As part of education activities, undergraduate students, graduate students and post-doctorates are being trained in vegetable breeding, crop and seed production, disease protection and diagnosis, and soil science with a focus on organic systems as they participate in research projects critical to the COIA Project achieving the research goals. Collaborators hosted public farmer field days in conjunction with each trial. Field days coincided with timing of trial evaluations. To inform growers and consumers about the positive environmental impact of organic production systems, and about carrot nutritional quality and flavor we continued to update and use the web site developed through eOrganic in CIOA I to disseminate research updates, timely articles, and related project events (http://eorganic.info/carrotimprovement). We created a new promotion brochure giving an overview of the project, and details about current research and research goals that was shared with growers, the carrot industry, researchers, and consumers at CIOA-related events. Additionally, we created a new scientific research poster about the project and presented it at related scientific focused events/conferences. The project reached approximately 800 growers, carrot industry members, researchers, food industry representatives, and consumers in this period. A project field sign was also created and installed at each project location field site so field visitors could clearly identify the project plots and visit the website for additional information. To demonstrate techniques and challenges associated with organic carrot seed production, seed increase plots were established for organic carrot seed production in two on-farm workshops. Seed production for carrot germplasm to be released was initiated. In addition, this project is expanding graduate student training, focused on research in organic systems and organic plant breeding. The long-term impact of this important educational element is to establish the next generation of researchers, extension, and industry representatives with organic systems expertise. How have the results been disseminated to communities of interest?Educational events and conference presentations delivered in 2016-2017 include: 9/17/16-9/18/16, Jefferson County Farm Tour, Chimacum, WA 9/26/2016, Organic Seed Alliance Research Farm Field Day, Chimacum, WA 11/4/16-11/6/16, CFSA Sustainable Agriculture Conference Preconference ResearchIntensive, Durham, NC 10/3/2016 Culinary Breeding Network Variety Showcase, Portland, OR 1/26/2017, Seed to Eaters Roundtable at EcoFarm, Pacific Grove, CA 2/2/17-2/4/17, Organicology Research Poster Session, Portland, OR 3/20/2017, CIOA2 poster and oral presentations, International Carrot Conference, Bakersfield, CA 6/29/2017, Southwest Purdue Agricultural Center Field Day, Vincennes, IN 8/7/17-8/9/17, National Association of Plant Breeders, Davis, CA 8/22/2017, Purdue Field Day at West Lafayette, West Lafayette, IN 8/24/2017, UW Madison hosted an Organic field Day at the West Madison Agricultural Research Station with good turn out from the organic seed sector. This was followed by a public Dinner and Outreach Event attended by over 200 people that evening, Madison, WI Blogposts Seed Broadcast, "Getting Creative in the Kitchen with Chromatic Carrots", 10/13/16 Seed Broadcast, "Working Around the Calendar to Breed Organic Carrots", 3/10/17 Seed Broadcast, "This Weekend's Menu: Roasted Carrot Bolognese", 6/2/17 Seed Broadcast, "Join Us: Organic Seed Training in Indiana", 6/14/17 Seed Broadcast, "Evaluating the Fruits of Our Labor", 8/23/17 What do you plan to do during the next reporting period to accomplish the goals?All field trialing and research activities described for Year 1 will continue in Year 2. In addition, seed increase of promising genetic stocks included in trials will be expanded. Future educational events planned for Year 2: Presentations on breeding for organic and the CIOA2 project will be delivered at selected regional vegetable growers meetings including the Pacific Northwest Vegetable Meeting, Kennewick, WA; Carolina Farm Stewards Association Conference; Seed Sovereignty Field Day/NOFA, Dartmouth, MA; Great Lakes Fruit, Vegetable, and Farm Market Expo, Grand Rapids, MI; Organic Seed Growers Conference, Corvallis, OR; Organicology Conference, Portland, OR; Organic Agriculture Research Symposium; Midwestern Organic and Sustainable Education Service (MOSES) Conference, LaCrosse, WI; ASHS, Washington DC; International Carrot Conference, Madison, WI; and International Apiaceae Meeting, Krakow, Poland. The project team holds an annual planning meetings in conjunction with the Organic Agriculture Research Symposium.

Impacts
What was accomplished under these goals? This project addresses the critical needs of organic carrot producers by developing orange and novel colored carrots with improved disease and nematode resistance, improved weed competitiveness, and improved nutritional value and flavor. About 100,000 acres of carrots are grown annually in the U.S. The 2014 Census of Agriculture, estimated 14% of this carrot production is in organic systems, vs. 3% for vegetable crops overall. Organic production of carrots presents several significant challenges from pests and diseases. Over 80% of the U.S. carrot production land is infested with one or more of the common species of root-knot nematodes. Alternaria leaf blight, other foliar diseases and cavity spot are major carrot diseases in virtually all production areas of the world. It is urgent and vital to the future of the US organic vegetable industry that effective non-chemical methods of nematode and leaf blight control be developed. Carrots are one of the slowest crops for growers to establish and grow. This often makes weed control the most expensive cost of organic carrot production. Flavor and nutritional value are the most important characteristics noted by consumers of organic foods. Among novel colored carrots are breeding stocks with some of the most vigorous growing seedlings and large tops. This project is developing novel carrots improved for nutrition and flavor characteristics, integrated with critical pest and disease resistance traits, and vigorous growth. This project also expands our understanding of root-microbiome interactions critical for growth and nutrient uptake of organically-grown carrots. Goals and annual progress: The long-term goals of this project are to: 1) deliver carrot cultivars with improved disease and nematode resistance, improved nutrient acquisition, seedling vigor and weed competitive traits, increased marketable yield, superior nutritional value, flavor and other culinary qualities, and storage quality for organic production; 2) determine how carrot genotypes interact with, or influence, the root microbiome to access key nutrients under limiting environments and avoid heavy metal uptake; 3) inform growers about cultivar performance to maximize organic carrot production, markets, and organic seed usage; 4) inform consumers about the positive environmental impact of organic production systems and about carrot nutritional quality, flavor and culinary attributes; and 5) train undergraduate, graduate, and post-doctorate students in critical organic agriculture issues. Primary activities: Focus Area 1: Cultivar development and release We have developed detailed breeding plans for diverse breeding materials and have initiated seed increases of promising selections to be grown at all national trial sites. Preliminary selection of potential new breeding populations for CIOA2 in our winter root nursery identified ~85 new germplasm sources for inclusion in future evaluations. Seed was produced in our summer seed nursery and included in the 2017-18 winter root nursery. Three new orange breeding populations have been created - one with a focus on superior flavor, a second with a combination of flavor, enhanced carotene content, with Alternaria and cavity spot resistance, and a third with enhanced carotene content and flavor. A final round of selection and seed increase of two populations slated for release from CIOA1 (Purple-Orange 1129 and Red 6636) will be initiated this winter. Focus Area 2: Variety trials on research stations and national participatory sites Variety trials where held on four research stations across the nation by co-PIs in Indiana, Wisconsin, Washington, and California and 2 participatory sites in Virginia and Vermont. These trials included 12 advanced breeding populations and commercially available check varieties common to all sites plus selections from among an additional 34 potentially promising breeding populations that varied among trial sites. Roots of all breeding populations and checks from trial locations were sampled for nutritional pigment and flavor analysis. Trial results are being summarized and analyzed. Focus Area 3: Advancing research on root microbiome interactions Arbuscular mycorrhizal fungi (AMF) beneficially interact with host plants by colonizing host roots, forming structures called arbuscules that facilitate the movement of water and nutrients, most notably phosphorus, in exchange for plant sugars. AMF can boost host performance during drought and other stresses. We evaluated organically grown carrot cultivars to compare the influence of different AMF species on carrot growth during varying water-limiting soil conditions. Carrot cultivars differed in their response to water limitation. Benefits to carrot growth differed according to cultivar-mycorrhizal species pairing. Uptake of sufficient nitrogen (N) during critical periods of plant growth is challenging in organic farming systems. At the same time, as production in urban and marginal areas increases worldwide, heavy metal uptake from contaminated soil has become an important food safety consideration. We observed differences in root architecture and microbial community structure among carrot genotypes. Genotypic differences in N and heavy metal uptake were also observed in carrot, but their relationship with various root characteristics has not yet been determined. Among a wide range of carrot germplasm evaluated, N and carbon partitioning among soil and root components was tracked using stable isotopes. Functional root characteristics are being identified using root imaging, analytical chemistry and microbial community profiling. Focus Area 4: Utilizing molecular markers to improve nematode resistance CIOA2 advanced experimental selections and additional potentially promising selections were included in field trialing in Irvine, California for resistance to the most prevalent root-knot nematodes occurring in California and other warm-season carrot production areas (Meloidogyne javanica and M. incognita). Selected carrots from these populations were advanced for seed production to be included in the genetic analysis, molecular marker evaluation, and breeding line development. Molecular marker evaluation underway has progressed to develop molecular markers for narrower genomic regions flanking the six major M. incognita resistance genes identified to date. GBS mapping has been completed and fine-mapping is underway. Foliar diseases were diagnosed when identity was uncertain. Alternaria leaf blight resistance (ALBR) was evaluated in CIOA2 advanced experimental selections and additional potentially promising selections in central Wisconsin, Infection was high and wide variation in resistance was observed. An investigation of the association between ALBR and phylogenetic relationships in diverse carrots revealed top height to be associated with resistance. Cavity spot (caused by Pythium sp.) resistance was tested for advanced CIOA2 breeding selections in infested fields in California and selections advanced for breeding. Focus Area 5: Evaluating and improving carrot flavor, nutritional, and postharvest quality Flavor evaluation of fresh carrot is underway and will be completed for carrots from all trials. Chefs who have been participating in vegetable flavor evaluations featuring different varieties that are showing promise for organic agriculture are expected to provide a more detailed flavor test of two varieties carrots developed through the CIOA1 project that are being trialed and released during CIOA2. Taste evaluations by seven chefs on orange, red and purple breeding lines as well as check varieties are anticipated to provide quantitative and qualitative feedback on their culinary qualities later this year. Samples were collected to evaluate carrot nutritional carotenoids and anthocyanins with HPLC for all entries of all field trials. Postharvest storage quality (rots, sprouting) is being noted for all of these samples.

Publications

Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Simon, P.W., Zystro, J, Roberts, P.A., Waters, T., Colquhoun, J., Navazio, J., Colley, M., McCluskey, C., Hoagland, L., duToit, L., Silva, E., Nunez, J. The CIOA (Carrot Improvement for Organic Agriculture) Project: Location, cropping system, and genetic background influence carrot performance including top height and flavor. Acta Hort.1153: 1-8. 2017.
Type: Journal Articles Status: Published Year Published: 2017 Citation: Arbizu, C.I., P.Tas, P.W. Simon, D.M. Spooner Phylogenetic prediction of carrot leaf blight resistance in wild and cultivated species of carrots. Crop Sci. 57:2645-2653. 2017.