Progress 09/01/23 to 08/31/24

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: Nothing Reported What opportunities for training and professional development has the project provided?The CIOA team advises carrot breeding and variety evaluation for small to medium scale seed companies and carrot farmers engaged in on-farm breeding. We also advise our colleagues at the Univ. of British Columbia enabling a growing network of CA on-farm carrot breeding activities. The project provides access to diverse genetics along with trainings to skill-up participants delivered through eOrganic and the Organic Seed Commons. These efforts are expanding the number of independent carrot breeders developing varieties for diverse climatic and market needs. As part of education activities, undergraduate students, graduate students, and post-doctorates are also 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, and present in professional conferences. Kayla Quintero (MS student at Purdue) investigating carrot genotype by microbiome by plant disease - received additional training, advanced experiments, and is continuing field trialing, data collection and analysis. Clare Talamy and Hannah Anderson (MS students at Univ. of Wisconsin-Madison) are investigating parallel field and greenhouse studies exploring whether the composition and functional potential of the carrot rhizosphere microbiome is governed by the chemical composition of root exudates. Avelina Gaston (MS student at UW-Madison) is receiving training for developing machine methodologies for testing carrot texture and for investigating the genetics of carrot root texture. Extension activities included creating new project promotion and educational materials for CIOA3, coordinating outreach and evaluation activities, presenting at multiple scientific and food industry conferences, and delivering trainings and educational events. Trials were conducted with organic seed company research farms. 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. Susana Cabrera-Mariz, Iowa State University, collaborated with CIOA to conduct research on carrot history, domestication, and cultural food pathways as a component of her MS thesis (2024 graduation). 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 to disseminate research updates, timely articles, and related project events (http://eorganic.info/carrotimprovement). 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. Project collaborators hosted public farmer field days in conjunction with trials at the project research sites. Field days coincided with timing of trial evaluations. How have the results been disseminated to communities of interest?Educational events and conference presentations delivered include: Webinars: 3/22/24. Unearthing the flavors of CANOVI-CIOA carrot trials and farm breeding club. https://seedalliance.org/2024/canovi-cioa-carrot-trials-webinar/ Field Days and Trainings: 3/5/24 field day for industry carrot breeders and production personnel to evaluate breeding materials from the project and from industry sources for agronomic performance and trialing of selected CIOA entries in comparison to available cultivars, El Centro, CA 5/14/24, Conventional carrot variety trial, Bakersfield, CA, University of California Cooperative Extension. 8/21/24 field day for industry carrot breeders and production personnel to evaluate breeding materials from the project and from industry sources for root-knot nematode resistance and agronomic performance, Coachella, CA 8/26/24 OSA Washington Researcher Field Day 9/13/24 West Madison Field Day, Madison, WI. Outreach activities presented on this project by the University of California, Desert Research and Extension Center, Holtville, CA: From 2023 to 2024 Farm Smart delivered carrot outreach programs in nutrition and production to over 2500 participants, which includes educators, K-12 students, and community members. Below is a summary of activities delivered: Farm to Summer - Carrots Led an interactive summer program where participants learned about the history of carrots, nutritional information, how they grow, and tasted a variety of carrot preparations, including the various colors. CARES Fall Festival- carrot planting Participants learned about carrots as they planted their own carrot seeds to take home Farm Tours- carrot presentation, research, harvesting While touring the facility, guests learned about colored carrot research taking place at the farm. Farm to Preschool Festival- carrot tasting and facts Participants tasted carrots and received recipes and information on nutritional value. Vegetable Adventures Field Trips- carrot harvesting and information Students who attended a Farm Smart program from March to April had the opportunity to learn what carrots need to grow, the history of colored carrots, their nutritional value, as well as an opportunity to harvest their own traditional and organic carrots. Teachers were also given resources to further enrich their lesson plans to include carrots. Community U-pick- carrot harvest and information Participants learned about colored carrots, the nutritional value of carrots, and were able to harvest carrots from the garden. Meetings: 3/23/24 Presentation to California Fresh Carrot Advisory Board Symposium on results of selection and breeding for combined nematode and cavity spot resistance and preferred agronomic performance. P Roberts, J. Sidhu, and P. Simon. Bakersfield CA (virtual meeting) 7/8/24 to 7/10/24 P. Roberts, P. Simon, B.-L. Huynh. Genetic mapping of resistance in carrot effective against multiple Meloidogyne hapla populations. 41st International Carrot Conference, Raleigh, NC. (oral presentation) 7/8/24 to 7/10/24 Colley MR, Dawson JC, Zystro J, Hoagland L, Liou M, Myers JR, Silva EM, and Simon PW. 2024. Multienvironment trials inform organic carrot testing and selection strategies. 41st International Carrot Conference, Raleigh, NC. (oral presentation) Blogposts Digging for carrots at the end of the rainbow. Organic Seed Alliance blogpost: https://eorganic.info/node/35347 OSA Blog, 2024 Unearthing the flavors of CANOVI-CIOA carrot trials and farm breeding club. https://seedalliance.org/2024/canovi-cioa-carrot-trials-webinar/ What do you plan to do during the next reporting period to accomplish the goals?Selected field trialing and research activities will continue in Year 4. The winter 2024-25 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 2024. Participatory trials with farmers and seed companies will continue to inform variety release and commercialization, including Ujamaa Seeds, High Mowing, and Johnny's in addition to other interested companies. We anticipate release of two orange, nantes populations with flavor and disease resistant backgrounds, as well as release of a purple-yellow-purple population with superior color and flavor in the next year or two based on ratings of uniformity and quality in trial evaluations. Genetic marker development for nematode resistance will continue, and data will be summarized and published. Continue investigations linking microbiomes, nutrient uptake, pathogen resistance, and root nutritional quality and storability among carrot genotypes Greenhouse trials investigating how different growth substrates influence carrot microbiomes and quality will be continued. Manuscripts covering research initiated in CIOA2 investigating relationships between carrot genotype, soil and root microbiomes, and physiological responses quantified using hyperspectral imaging and machine learning and the uptake of toxic heavy metals are in final preparation for publication. Future educational events planned for Year 4: -Hold an industry-stakeholder field day at the UC-DREC Research Station field trial for horticultural production trait and quality evaluation in March, 2025. (P. Simon, J. Sidhu). -Hold an industry-stakeholder field day at the UCR Coachella Research Station field trial for nematode resistance screening in summer 2025. (P. Roberts, P. Simon, T. Waters). -Present research results will be made to California Fresh Carrot Advisory Board Symposium, Spring 2025. (P. Roberts, P. Simon). Deliver an oral presentation to the Apiaceae Workshop at the 2025 Plant and Animal Genome Meetings (P. Simon, P. Roberts). Presentations on breeding for organic ag and the CIOA3 project may be delivered at selected regional vegetable growers meetings including the Great Lakes Fruit, Vegetable, and Farm Market Expo; Midwestern Organic and Sustainable Education Service (MOSES) Conference which are being held virtually. A poster of CIOA will be presented at the Organic Seed Growers' Conference. Corvallis, OR, February 27th -Mar 1st, 2025. Kayla Quintero (MS student at Purdue) will continue in her MS project, conducting studies investigating the role of carrot microbiomes in mediating resistance against Alternaria and other fungal pathogens. This will include both on-farm trials in Indiana, Vermont, North Carolina and Virginia, and greenhouse trials. At the University of Wisconsin a new MS student Clare Tallamy started at UW-Madison, she will continue microbiome and metabolomic analysis into year 3, whereby we will increase the number of carrot lines included in the analysis, increase the number of locations with field trials, as well as potentially utilizing a Liquid Chromatography-Mass Spectrometry approach to increase the resolution of metabolomic analysis. We anticipate a manuscript to be submitted for consideration at a peer-reviewed journal in late 2023/early 2024. . Also at UW-Madison, the Dawson lab will conduct storage and quality tests on harvested roots from field trials to evaluate the effects of links between microbiomes, nutrient uptake, pathogen resistance, and root nutritional quality and storability among carrot genotypes. The Simon and Dawson labs will conduct carrot texture analyses with a new graduate student Avelina Gaston. Field days with the University of California Cooperative Extension, Kern County, CA A participatory trial of CIOA germplasm will be organized using the Seedlinked platform with growers in the Upper Midwest.

Impacts
What was accomplished under these goals? Focus Area 1: Cultivar and breeding population development and release 1) Cultivar releases: Four breeding lines were submitted to the USDA for formal release including F7738 (superior flavor and cavity spot resistance), Nbh2306, Nb2159 and Nb3271 (root-knot nematode resistance to Meloidogyne incognita ). Farmers and seed companies trialed novel colored breeding lines "Sunset" and 'Fantasia' including trials by organic seed companies and by farmers of the BIPOC-led Ujamaa Seed Cooperative. Ujamaa introduced 'Fantasia' in commercial seed sales in spring 2024 and is collaborating with OSA on a seed increase for 2025 sales. On-farm and research station sites evaluated red colored breeding lines in WA, CA and Canada. 2) Advanced populations: More than 2043 entries were evaluated in the DREC winter nursery for qualities suitable for organic systems. From that evaluation 31 entries were selected for seed increase or crossing by OSA including orange, red, purple-red, mixed color, and purple selections. Thirty-six breeding populations produced at the OSA Research Farm were sent to the 2024 DREC winter nursery for evaluation and advanced selection with several grown as rootstock for seed company trials. 3) New breeding populations: Over 200 crosses or seed increases were made by the USDA and OSA to develop and advance new breeding populations combining priority agronomic and market qualities. These included new populations combining superior flavor and texture into lines with nematode and Alternaria leaf blight resistance, uniformity, and yield across multiple production areas. 4) Germplasm screening and regeneration: 19 entries of breeding populations were evaluated at OSA to assess readiness for release and suitability in organic systems and markets. New breeding populations of diverse red and yellow lines were advanced from root selections made at the DREC winter nursery. New seed sources of juicy texture were identified from the 2023-24 winter nursery field trials. Focus Area 2: Expand participatory variety trial and plant breeding network 1) Engagement with Ujamaa Seeds, High Mowing Organic Seeds, and Johnny's Selected Seeds in collaborative trials provided informative evaluation and expert feedback in advancing breeding lines for release. 2) In 2024, 3 farms and 3 research stations trialed breeding lines in WA, CA, IN, WI and BC. 3) To engage participants through online networking, OSA hosted a seed grower social and educational platform, the Organic Seed Commons. This space hosts a carrot breeding synergy group for coordinating trialing and education. In 2024 OSA outreach included a fall field day and a webinar presentation on CIOA participatory breeding and trials hosted with eOrganic and the Organic Seed Commons. 4) The Plant Prior Art Repository (PPAR) was envisioned as a tool for defensive publication for plant breeders and seed stewards to establish novel plant varieties and traits as prior art, and a PPAR toolkit on Intellectual Property was created for educational purposes. Informational materials are available to educate users how to protect released germplasm in the public domain. New CIOA germplasm releases are being registered in the public domain. They are being made publicly available and submitted to GRIN. Focus Area 3: Investigate links between microbiomes, nutrient uptake, pathogen resistance, and root nutritional quality and storability among carrot genotypes Two research projects focus on advancing our understanding of root-microbiome interactions. 1) The first, led by Hoagland and Colley and supported by graduate students K. Quintero and K. Zapf, aims to determine the extent to which genetic differences in elemental uptake and resistance to Alternaria are mediated by carrot microbiomes, and whether these beneficial relationships and outcomes can be enhanced through soil and crop management. During the summer of 2024, a set of carrot genotypes that vary in resistance to Alternaria were grown in on-farm field trials in 9 diverse locations across the country. Soil quality, Alternaria ratings, and yield were quantified at each site. Characterization of samples collected from these trials is underway. 2) A smaller on-farm participatory research trial was conducted in Indiana investigated whether a foliar amendment derived from organic substrates alters carrot leaf/root microbiomes, disease severity and quality of carrot taproots. 3) Carrot taproots from field trials in ME, VA, IL, NC, and WI were collected and stored for microbiome assessments associated with Alternaria resistance. 4) In the second study, building upon prior work showing that carrot cultivars exude chemically distinct root exudates that lead to the recruitment of compositionally distinct rhizosphere microbiomes, Freedman, Silva, and Dawson, and supported by grad student C. Tallamy, are evaluating the exudates of 6 carrot cultivars to determine if the chemically distinct root exudates that lead to the recruitment of compositionally distinct rhizosphere microbiomes are consistent across years and growing locations. They are also evaluating variation in root exudate-mediated recruitment of rhizosphere microbiomes across soil types to determine whether likely differences in rhizosphere microbiome composition are also associated with differences in within-root microbiome composition that may affect storability. Root exudates, roots, and soil have been sampled for evaluation of genetic variation and root exudate chemical composition. Focus Area 4: Utilize molecular markers to improve nematode resistance Research in this focus area utilizes molecular markers for nematode resistance to evaluate and select elite carrot populations. New and previously identified nematode resistance sources with M. incognita, M. javanica and M. hapla resistance were advanced in breeding selections and evaluated in two field trials in Coachella, CA and in greenhouse inoculation trials at UC Riverside with roots sent to WI for seed production. These entries were also evaluated in the DREC trial in 2024 to evaluate horticultural quality. Molecular markers are being developed for resistant alleles for all sources of resistance. Focus Area 5: Evaluate and improve carrot flavor, texture and color Assessment of carrot flavor was integrated into all germplasm evaluations and breeding activities since flavor is a priority trait necessary for the successful adoption of new cultivars with quality agronomic traits. Evaluations of texture were also initiated by a new graduate student, A. Gaston.

Publications

• Type: Peer Reviewed Journal Articles Status: Published Year Published: 2024 Citation: H M Anderson, GA Cagle, EL-W Majumder, E Silva, J Dawson, P Simon, ZB Freedman, Root exudation and rhizosphere microbial assembly are influenced by novel plant trait diversity in carrot genotypes, Soil Biology and Biochemistry, Volume 197, 2024
• Type: Websites Status: Published Year Published: 2024 Citation: CIOA web site - general project, carrot information, and gallery of carrots http://eorganic.info/carrotimprovement

Progress 09/01/22 to 08/31/23

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:none What opportunities for training and professional development has the project provided?CIOA team advises carrot breeding and variety evaluation for small to medium scale seed companies and carrot farmers engaged in on-farm breeding. We also advise our colleagues at the Univ. of British Columbia enabling a growing network of CA on-farm carrot breeding activities. The project provides access to diverse genetics along with trainings to skill-up participants delivered through eOrganic and the Organic Seed Commons. These efforts are expanding the number of independent carrot breeders developing varieties for diverse climatic and market needs. As part of education activities, undergraduate students, graduate students, and post-doctorates are also 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, and present in professional conferences. Kathleen Zapf (MS student at Purdue) investigating carrot genotype by microbiome by heavy metal/nutrient uptake - received additional training, completed experiments, presented data and is currently working on manuscripts. Hannah Anderson (MS student at Univ. of Wisconsin-Madison) investigated parallel field and greenhouse studies exploring whether the composition and functional potential of the carrot rhizosphere microbiome is governed by the chemical composition of root exudates. Avelina Gaston (MS student at UW-Madison) is receiving training for developing machine methodologies for testing carrot texture and for investigating the genetics of carrot root texture. Extension activities included creating new project promotion and educational materials for CIOA3, coordinating outreach and evaluation activities, presenting at multiple scientific and food industry conferences, and delivering trainings and educational events. Trials were conducted with organic seed company research farms. 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. Susana Cabrera-Mariz, Iowa State University, engaged in a 4 month research farm internship at Organic Seed Alliance, and is collaborating with CIOA to conduct research on carrot history, domestication, and cultural food pathways as her MS thesis (2024 graduation). 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 to disseminate research updates, timely articles, and related project events (http://eorganic.info/carrotimprovement). 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. Project collaborators hosted public farmer field days in conjunction with trials at the project research sites. Field days coincided with timing of trial evaluations. How have the results been disseminated to communities of interest?Educational events and conference presentations delivered include: Field Days and Trainings: OSA Washington Researcher Field Day, Sep 11, 2023 Webinar: McHenry County College, Carrot participatory plant breeding and on-farm trial evaluations, November 2nd, 2023. 8/17/22 West Madison Field Day, Madison, WI. 8/24/22 Collaborative Plant Breeding Field day at the West Madison Agricultural Research Station, Madison, WI 8/31/23 Field day for industry carrot breeder and production personnel to evaluate breeding materials from the project and from industry sources for root-knot nematode resistance and agronomic performance, Coachella, CA Outreach activities presented on this project by the University of California, Desert Research and Extension Center, Holtville, CA: From 2022 to 2023 Farm Smart delivered carrot outreach programs in nutrition and production to 2908 participants, which includes educators, K-12 students, and community members. Below is a summary of activities delivered: Farm to Summer - Carrots (45 participants) Led an interactive summer program where participants learned about the history of carrots, nutritional information, how they grow, and tasted a variety of carrot preparations, including the various colors. CARES Fall Festival- carrot planting (15 participants) Participants learned about carrots as they planted their own carrot seeds to take home Farm Tours- carrot presentation, research, harvesting (463) While touring the facility, guests learned about colored carrot research taking place at the farm. Farm to Preschool Festival- carrot tasting and facts (1116) Participants tasted carrots and received recipes and information on nutritional value. Vegetable Adventures Field Trips- carrot harvesting and information (992) Students who attended a Farm Smart program from March to April had the opportunity to learn what carrots need to grow, the history of colored carrots, their nutritional value, as well as an opportunity to harvest their own traditional and organic carrots. Teachers were also given resources to further enrich their lesson plans to include carrots. Community U-pick- carrot harvest and information (277) Participants learned about colored carrots, the nutritional value of carrots, and were able to harvest carrots from the garden. Meetings: Hoagland, L., 2023. Soil life and urban soil health assessments. Get the Dirt - Urban & Small Farm Soil Health Conference, Indianapolis, IN (oral presentation) Zapf., K., Simon, P., Lee, L., Hoagland, L., 2023. Carrot genotype and soil properties modulate heavy metal transfer factor on urban farms. Agronomy, Crop Science, Soil Science Societies International Meeting, St. Louis, MO. (poster presentation) Zapf, K. 2022. Interactions between carrot genotypes and soils on heavy metal uptake. Corteva Plant Science Symposium, West Lafayette, IN (poster presentation) Zapf, K., 2022. Are your carrots at risk for heavy metal uptake? Small Farm Conference, Danville IN (poster presentation) Zapf, K.. 2022/ Are your carrots at risk for heavy metal uptake? Indiana Horticulture Conference, West Lafayette, IN (poster presentation) 2/14/23 Presentation to California Fresh Carrot Advisory Board Symposium on results of selection and breeding for combined nematode and cavity spot resistance and preferred agronomic performance. P Roberts, J. Sidhu, and P. Simon. Bakersfield CA (virtual meeting) Anderson, H., E. Silva, J. Dawson, P. Simon, and Z.B. Freedman. Plant-Soil-Microbe Interactions in Organic Vegatable Cultivar Development. Marbleseed Organic Farming Conference, LaCrosse, WI. (2023). Anderson, H., E. Silva, J. Dawson, P. Simon, and Z.B. Freedman. Assessing the Influence of Root Exudation on Soil Microbial Recruitment across Cultivar Diversity in Organic Vegetable Production. Soil Science Society of America Annual Meeting. St. Louis, MO. (2023). Blogposts Digging for carrots at the end of the rainbow. Organic Seed Alliance blogpost: https://eorganic.info/node/35347 OSA Blog, Midwest Collaborative Plant Breeding Field Day https://seedalliance.org/2022/midwest-collaborative-plant-breeding-field-day-highlights/ 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 will continue in Year 3 - namely the winter 2023-24 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 2024. Marker work for nematode resistance will continue, and data will be summarized published. Future educational events planned for Year 2: Presentations on breeding for organic ag and the CIOA3 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. MS student Kathleen Zapf will finalize the results of her experiments investigating the role of carrot root microbiomes in mediating heavy metal uptake, submit publications and graduate in May 2024. Kayla Quintero (MS student at Purdue) will start in January 2024, and will conduct studies investigating the role of carrot microbiomes in mediating resistance against Alternaria and other fungal pathogens. This will include both on-farm trials in Indiana, Vermont and Virginia, and greenhouse trials. At the University of Wisconsin a new MS student Clare Tallamy started at UW-Madison, she will continue microbiome and metabolomic analysis into year 3, whereby we will increase the number of carrot lines included in the analysis, increase the number of locations with field trials, as well as potentially utilizing a Liquid Chromatography-Mass Spectrometry approach to increase the resolution of metabolomic analysis. We anticipate a manuscript to be submitted for consideration at a peer-reviewed journal in late 2023/early 2024. . Also at UW-Madison, the Dawson lab will conduct storage and quality tests on harvested roots from field trials to evaluate the effects of links between microbiomes, nutrient uptake, pathogen resistance, and root nutritional quality and storability among carrot genotypes. The Simon and Dawson labs will conduct carrot texture analyses with a new graduate student Avelina Gaston. At Organic Seed Alliance we will continue national de-centralized, participatory on-farm trials. We will also educate trial participants in opportunities for on-farm carrot breeding and provide access to CIOA breeding populations for their breeding activities. A participatory trial of CIOA germplasm will be organized using the Seedlinked platform with growers in the Upper Midwest.

Impacts
What was accomplished under these goals? Focus Area 1: Cultivar and breeding population development and release 1) Cultivar releases:. R6636 is commercially available under the cultivar name 'Carnelian', and 2023 represented the second year of sales from High Mowing Organic Seeds. Farmers and seed companies trialed the diversity population named 'Fantasia' including a dozen farmers of the BIPOC-led Ujamaa Seed Cooperative. Ujamaa expressed interest in introducing 'Fantasia' in commercial seed sales in 2024. 2) Advanced populations: More than 1500 entries were evaluated in the DREC winter nursery for qualities suitable for organic systems. From that evaluation 212 entries were selected for seed increase by OSA including orange, red, purple-red, and purple selections. Thirty-six breeding populations produced at the OSA Research Farm were sent to the 2023 DREC winter nursery for evaluation and advanced selection with several grown as rootstock for seed company trials. 3) New breeding populations: Over 90 crosses were made to develop new breeding populations combining priority agronomic and market qualities New populations utilize marker assisted selection to be with the PPB network and breeding efforts of project partners. 4) Germplasm screening and regeneration: 121 entries of diverse carrot stocks were evaluated at OSA for suitability in organic systems and markets. Of these 121, 50 entries from the PI-breeding collection were grown as a representation of the history and diversity of history of carrot for educational purposes. Breeding populations were advanced of 17 populations at OSA including varied purple, yellow orange crosses, new strain crosses of red, advanced orange populations, rainbow mix ('Fantasia'). Cavity spot resistance screening identified CIOA entries F5367, U8284, and Nb8525 to present a fairly high level of resistance in field trials. Additional testing is needed to confirm these early observations. New seed sources of juicy texture were identified from the 2023-24 winter nursery field trials. Focus Area 2: Expand participatory variety trial and plant breeding network 1) Seed company engagement provided multiple project benefits to enhance participatory breeding in 2023 including evaluation and expert feedback to the breeding team on the qualities and commercial potential of CIOA populations and develops direct relationships for commercial availability and distribution of varieties once released. In 2023 High Mowing (Vermont), Peace Seeds (Colorado), Levine Seeds (Hawaii), and Ujamaa Seeds (National cooperative of BIPOC seed growers) all trialed advanced populations of CIOA lines to assess commercialization potential. Ujamaa has requested permission to sell 'Fantasia' in 2024 and other companies are providing feedback with intention of either commercializing CIOA lines or engaging in additional breeding efforts. 2) Fifty farmers across the US conducted on-farm trials of orange and novel color varieties and breeding populations coordinated through Seedlinked. To expand impacts trial coordinators collaboratd with the, CANOVI, the Canadian organic seed initiative who coordinated with 50 Canadian farmers in the same trial. Farmers reported on evalutions and engaged socially through Seedlinked (https://seedlinked.com/run-variety-trials-on-seedlinked/). January 2024 we will co-host a webinar on trial results through eOrganic and the Organic Seed Commons carrot breeding network (https://www.organicseedcommons.org/spaces/7291805/members/top ). 3) To engage participants through online networking, OSA hosts a new network through the Organic Seed Commons. The project created a carrot breeding synergy group within the OSC for coordinating trialing and education. In 2023 OSA's outreach included a fall field day and a webinar presentation on CIOA participatory breeding and trials for the McHenry County College in Illinois. 4) The Plant Prior Art Repository (PPAR) serves as the defensive publication for plant breeders and seed stewards to establish novel plant varieties and traits as prior art. Informational materials are being developed to educate users how to protect released germplasm in the public domain. New CIOA germplasm releases for PPB are being registered. Focus Area 3: Investigate links between microbiomes, nutrient uptake, pathogen resistance, and root nutritional quality and storability among carrot genotypes Two research projects focus on advancing our understanding of root-microbiome interactions. The first led by Hoagland and Colley verifies whether the composition and functional potential of microbiomes in carrot taproots are stable across a broad set of environments and determines if this influences crop field performance and quality. Greenhouse trials evaluate relationships between root microbiomes, disease resistance, and the quality and storability of carrot taproots. In that study: 1) Research investigating relationships between carrot genotype, feedback effects on soil microbial community structure, and resilience against parasitic nematodes has been completed. A manuscript covering this project is underway. 2) Research started in CIOA2 investigating relationships between carrot genotype, root microbiomes, and heavy metal uptake was continued with field and greenhouse trials. A manuscript covering the field trials is underway, and results of the greenhouse trials are being analyzed. 3) Trails were conducted in Purdue's automated controlled environment phenotyping facility (AAPF) to determine whether hyperspectral imaging could be used to quantify genetic differences in cadmium and uptake. A manuscript covering the results is underway. 4) Carrot taproots from field trials in Washington and Wisconsin were processed and stored for microbiome assessments associated with Alternaria resistance and genotypes were identified for a set of on-farm trials that will occur in 2024. The on-farm trials will be paired with greenhouse trials. 5) In the second study led by Freedman, Silva, and Dawson, a graduate student (Hannah Anderson; UW-Madison Soil Science MS program) analyzed the metabolome of rhizosphere and bulk soil from two time points across the growing season demonstrated that the four cultivars tested recruited distinct microbiomes to their rhizosphere, and this trend was not observed in the bulk soil where there was no cultivar effect. This suggests that the plant's governance of the soil microbiome does not extend very far from the root. The metabolomics analysis uncovered that the chemical signature of the plant root exudates was also distinct across cultivars and was most distinct for the heirloom variety and the nematode resistant variety. Interestingly, there were also detectable differences in the bulk soil metabolome across cultivars, suggesting that the plant chemical influence extends further into the soil than the plant's influence on the microbiome. . Focus Area 4: Utilize molecular markers to improve nematode resistance Research in this focus area utilizes molecular markers for nematode resistance to evaluate and select elite carrot populations. New and previously identified nematode resistance sources with M. incognita, M. javanica and(or) M. hapla resistance were advanced in breeding selections and evaluated in field trial in Coachella, CA (March-August 2023) and WSU Othello Station, WA (June-October 2023) and in greenhouse inoculation trials at UC Riverside and roots sent to WI. These entries were also evaluated in the DREC trial to evaluate horticultural quality. Molecular markers are being developed. Focus Area 5: Evaluate and improve carrot flavor, texture and color Assessment of carrot flavor was integrated into all germplasm evaluations and breeding activities since flavor is a priority trait necessary for the successful adoption of new cultivars with quality agronomic traits. Evaluations of texture were also initiated by a new UW-Madison MS student, Avelina Gaston.

Publications

• Type: Theses/Dissertations Status: Published Year Published: 2023 Citation: Anderson, H. (2023) Root exudation and rhizosphere microbial recruitment are influenced by novel cultivar development in organic carrot production. University of Wisconsin-Madison.
• Type: Journal Articles Status: Published Year Published: 2023 Citation: Trivi?o, N., Rodriguez-Sanchez, A., Filley, T., Camberato, J., Colley, M., Simon, P., Hoagland, L., 2023. Carrot genotypes differentially alter soil bacterial communities and decomposition of plant residue in soil. Plant and Soil doi.org/10.1007/s11104-023-05892-0.

Progress 09/01/21 to 08/31/22

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?CIOA team advises carrot breeding and variety evaluation for small to medium scale seed companies and carrot farmers engaged in on-farm breeding. We also advise our colleagues at the Univ. of British Columbia enabling a growing network of CA on-farm carrot breeding activities. The project provides access to diverse genetics along with trainings to skill-up participants delivered through eOrganic and the Organic Seed Commons. These efforts are expanding the number of independent carrot breeders developing varieties for diverse climatic and market needs. As part of education activities, undergraduate students, graduate students, and post-doctorates are also 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, and present in professional conferences. In year 1 co-PI Colley, completed her PhD including CIOA research on genotype by environment by management system interactions. Umut Bicim (BS student at Purdue University) received training and worked with post-doc Alejandro Rodriguez-Sanchez to quantify soil and root microbiomes in a carrot genotype X microbiome X pathogen resistance (nematode) experiment. Kathleen Zapf (MS student at Purdue) investigating carrot genotype X microbiome X heavy metal/nutrient uptake - received training and is conducting experiments. Hannah Anderson (MS student at Univ. of Wisconsin-Madison) investigating parallel field and greenhouse studies exploring whether the composition and functional potential of the carrot rhizosphere microbiome is governed by the chemical composition of root exudates. Extension activities included creating new project promotion and educational materials for CIOA3, coordinating outreach and evaluation activities, presenting at multiple scientific and food industry conferences, and delivering trainings and educational events. Trials were conducted with organic seed company research farms. 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. 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 to disseminate research updates, timely articles, and related project events (http://eorganic.info/carrotimprovement). 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. Project collaborators hosted public farmer field days in conjunction with trials at the project research sites. Field days coincided with timing of trial evaluations. How have the results been disseminated to communities of interest?Educational events and conference presentations delivered include: Outreach: August 21st 2022 Farm to Flavor Event, Madison Wisconsin Field Days and Trainings: OSA Washington Researcher Field Day, Sep 26, 2022 OSA Washington Community Field Day, Sep 26, 2022 Webinar: hosted on eOrganic and the Organic Seed Commons, Breeding carrots for production, resilience, flavor and fun in organic systems. https://eorganic.info/node/35336 Webinar: Breeding Carrots for Production, Resilience, Flavor and Fun in Organic Systems, March 31, 2022 -Viewed 1200 times since publishing / URL:https://www.youtube.com/watch?v=xdsg2NSPZ0w CIOA supported and presented at the International Carrot Conference, Aug 29-30, 2022 (~75 participants). Get the Dirt: Urban Agriculture Soil Health Conference (120 participants) West Lafayette, IN 2022. - Hoagland, L. - CIOA research investigating carrot genotype - heavy metal - microbiome research covered eOrganic webinar: Combining soil amendments and varietal development to prevent pathogens and heavy metal uptake (2022). Hoagland, L. - CIOA research investigating carrot genotype - heavy metal - microbiome research covered Improving nutrient use efficiency and crop productivity with soil health. Bi County Soils Workshop. Delphi, IN (2022) - Hoagland, L. - CIOA research investigating carrot genotype X microbiome X NUE research covered 8/17/22 West Madison Field Day, Madison, WI. 8/24/22 Collaborative Plant Breeding Field day at the West Madison Agricultural Research Station, Madison, WI Meetings: International Carrot Conference: Colley and McKenzie, "Creating connections, igniting inspiration and imagination, and having fun through Participatory Plan Breeding". http://www.internationalcarrots.org/uploads/1/2/7/7/127726097/2022_icc_conference_-_program_book_final.pdf Hoagland, L. How are Purdue researchers using the plant using the national plant germplasm collections? North Central Regional Plant Germplasm Repository Meeting, On-line (2022). Hoagland, L. Organic vs. conventional cropping systems: impacts on root microbiomes and their functions. III International Organic Fruit Symposium and I International Organic Vegetable Symposium. On-line (2021) Blogposts Digging for carrots at the end of the rainbow. Organic Seed Alliance blogpost: https://eorganic.info/node/35347 and https://seedalliance.org/2022/digging-for-carrots-at-the-end-of-the-rainbow/ OSA Blog, Midwest Collaborative Plant Breeding Field Day https://seedalliance.org/2022/midwest-collaborative-plant-breeding-field-day-highlights/ 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 will continue in Year 2 - namely the winter 2022-23 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 2023. Marker work for nematode resistance will continue, and data will be summarized published. Future educational events planned for Year 2: Presentations on breeding for organic ag and the CIOA3 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. New post-doc Dr. Marian Luis will start at Purdue University and conduct research investigating carrot genotype X microbiome X pathogen resistance/taproot quality experiments. MS student Kathleen Zapf will continue her studies investigating carrot genotype X microbiome X heavy metal/nutrient uptake experiments. Publications submitted. Microbiome and metabolomic analysis will continue into year 2, whereby we will increase the number of carrot lines included in the analysis as well as potentially utilizing a Liquid Chromatography-Mass Spectrometry approach to increase the resolution of analysis. We will also enhance the portion of the analysis dedicated to better understanding how each carrot line will impact important microbial functions. The MS student on the project will defend her MS thesis in Winter, 2023 and possibly stay to complete her PhD on this project. We anticipate a manuscript to be submitted for consideration at a peer-reviewed journal in late 2023/early 2024 as well as data to be disseminated as presentations at the West Madison Field Day and a meeting of international scope like the Soil Science Society of America Annual Meeting. At the University of Wisconsin the Dawson lab will conduct storage and quality tests on harvested roots from field trials to evaluate the effects of links between microbiomes, nutrient uptake, pathogen resistance, and root nutritional quality and storability among carrot genotypes. The Simon lab will conduct carrot texture analyses with a new graduate student.

Impacts
What was accomplished under these goals? Focus Area 1: Cultivar and breeding population development and release 1) Cultivar releases: Three new varieties bred during CIOA 1-2 are now ready for commercial release with formal releases from the USDA and Organic Seed Alliance (R6220, Y1246, and R6636). In 2022, 5 organic seed companies evaluated the 3 varieties to determine interest in commercialization. R6636 was produced on 2 participatory organic farms and is now available commercially from High Mowing Organic Seeds under the name Carnelian. Other releases are advancing to commercialization. 2) Advanced populations: More than 1500 entries were evaluated in the DREC winter nursery for qualities suitable for organic systems. From that evaluation 95 entries were selected for seed increase by OSA including orange, red, purple-red, and purple selections. 70 breeding populations produced at the OSA Research Farm were sent to the 2023 DREC winter nursery for evaluation and advanced selection with several grown as rootstock for seed company trials. 3) New breeding populations: Over 75 crosses were made to develop new breeding populations combining priority agronomic and market qualities - flavor, novel visual appearance, and agronomic traits including Alternaria leaf blight resistance, root-knot nematode resistance, cavity spot resistance, early stand establishment and seedling vigor, and high nutritional value. New populations utilize marker assisted selection to be with the PPB network and breeding efforts of project partners. 4) Germplasm screening and regeneration: 72 entries of diverse carrot stocks were evaluated at OSA for suitability in organic systems and markets and 18 advanced populations were increased at OSA. Focus Area 2: Expand participatory variety trial and plant breeding network 1) To expand the number of farms and seed companies participating in the project through participatory on-farm trials and on-farm plant breeding (PPB), on-farm trials included small seed companies in VT, CO, and ME with plans to expand in 2023. 2) Using the online platform SeedLinked to collect and share trial evaluations participant evaluations informed release decisions of new varieties. Trial coordination will be implemented in 2023 to evaluate advanced populations. 3) To engage participants through online networking, OSA hosts a new network through the Organic Seed Commons. The project created a carrot breeding synergy group within the OSC for coordinating trialing and education, currently for 16 members. A carrot breeding webinar co-hosted with eOrganic trained participants in fundamentals of carrot genetics and selection. The research team submitted 7 CIOA varieties in conference field trials, presented a CIOA poster, and delivered an oral presentation. Yr 1 outreach featured the CIOA trials in the annual OSA activities reported in the Field Day list. Storage and quality tests on harvested roots from field trials are evaluated in Focus Area 3. 4) The Plant Prior Art Repository (PPAR) serves as the defensive publication for plant breeders and seed stewards to establish novel plant varieties and traits as prior art. Publishing plant varieties and traits in the repository puts these inventions into the public domain and protects them from patenting. CIOA partners are working with the US Patent Office to promote its use to ensure varieties and traits published as prior art are not awarded patents to other individuals or companies. Informational materials are being developed to educate users how to protect released germplasm in the public domain. New CIOA germplasm releases for PPB will be registered. Focus Area 3: Investigate links between microbiomes, nutrient uptake, pathogen resistance, and root nutritional quality and storability among carrot genotypes Two research projects focus on advancing our understanding of root-microbiome interactions. The first led by Hoagland and Colley verifies whether the composition and functional potential of microbiomes in carrot taproots are stable across a broad set of environments (CA, WI, IN, VT, VI), and determines if this influences crop field performance and quality. Corresponding greenhouse trials evaluate relationships between root microbiomes, disease resistance, and the quality and storability of carrot taproots. In that study: 1) Research started in CIOA2 investigating relationships between carrot genotype, feedback effects on soil microbial community structure, and resilience against parasitic nematodes was continued. Root endophyte and soil microbiome analyses from greenhouse studies were sequenced and bioinformatic analyses are underway. 2) Research started in CIOA2 investigating relationships between carrot genotype, root microbiomes, and heavy metal uptake was continued with a second round of field trials on 10 urban farms across Indiana. 3) A preliminary trial was conducted in Purdue's automated controlled environment phenotyping facility (AAPF) to assess carrot growth and timing for quantifying plant performance using hyperspectral imaging and CT root scanning. A follow-up experiment to identify the best wavelengths and algorithms for quantifying differences in carrot genotype responses to heavy metals and estimate uptake is underway. A further experiment integrating microbiome dynamics is expected in the spring. 4) Carrot taproots from field trials in Washington and Wisconsin were processed and stored for microbiome and other assays that will begin, and publications covering results are expected in the next year. In the second study led by Freedman, Silva, and Dawson, a graduate student (Hannah Anderson; UW-Madison Soil Science MS program) started January 2022. Parallel field and greenhouse studies explored the relationship between composition, functional potential of the carrot rhizosphere microbiome, and chemical composition of root exudates. The first-year effort included a field trial and a greenhouse trial with four carrot cultivars. The field experiment was a success, and the greenhouse experiment was not, due to relatively weak carrot growth. From the field experiment, samples were taken for microbiome analysis from two soil compartments, including the rhizosphere (i.e. soil directly in contact with the carrot taproot) as well as bulk soil (that is, soil in the plot, but not in contact with the taproot) at three time points across the growing season. DNA has been extracted from all samples and is being sequenced for microbial community analysis in the coming months. For metabolomics, a protocol was developed and used to extract root exudates from carrot roots. Samples were sent for metabolomic analysis of rhizosphere and bulk soil from two time points across the growing season. Relationships between carrot root exudate chemistry, soil microbiome characteristics, and carrot quality are being evaluated. Focus Area 4: Utilize molecular markers to improve nematode resistance Research in this focus area utilizes molecular markers for nematode resistance to evaluate and select elite carrot populations. Molecular markers are being developed to confirm the identity of resistance genes segregating in breeding stocks derived from these sources and utilize those markers to select parental roots with resistance alleles from multiple genes to assure strong resistance during the breeding process. One new nematode resistance source was identified with M. incognita resistance was advanced and evaluated in trials in Coachella, CA, and roots sent to WI. These entries were also evaluated in the DREC trial to evaluate horticultural quality. Focus Area 5: Evaluate and improve carrot flavor, texture and color Assessment of carrot flavor was integrated into all germplasm evaluations and breeding activities since flavor is a priority trait necessary for the successful adoption of new cultivars with quality agronomic traits. Organoleptic and machine evaluations of texture were also initiated.

Publications

• Type: Theses/Dissertations Status: Published Year Published: 2022 Citation: Colley, M. (2022) Critical Experiences in Participatory Approaches to build up Organic Plant Breeding and Organic Seed Systems. Wageningen University and Research. https://edepot.wur.nl/578477
• Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Colley, M and McKenzie, L. (2022) Creating connections, igniting inspiration and imagination, and having fun through participatory plant breeding with carrots. 40th International Carrot Conference.