Progress 09/15/23 to 09/14/24
Outputs
Target Audience:Our target audience in this second year has encompassed several segments of society, from gene bank customers to farmers to scientists to consumers: a) Outside Advisory Committee, with a broad composition b) Gene bank customers: plant breeders in the public and private sectors (demonstration field trial of seed increase) Farmers: field days in California, Delaware, and South Carolina c) Farmers: field days in California, Delaware, and South Carolina d) Scientists: field days aforementioned; scientific presentations at universities and scientific meetings; publications in scientific journals or reports e) Public: surveys; farmers' markets Changes/Problems:Two issues haveslowed down the project, butwhich we are addressing, so that the project can continue successfully: 1) The genotyping by DNA sequencing of the LIma bean collection and recombinant inbred populationswas contracted out to the Hudson Alpha Institute (Huntsville, AL). There was a delay in returning the expected sequencing data to us due to several reasons, including the sequencing coverage's unevenness and the approach's novelty. Through a dialog between Hudson Alpha and the Lima team, especially PI Dr. A. Farmer at NCGR, these issues have now been addressed and the sequencing data can be further analyzed and used in genetic analyses. 2) The widespread lack of adaptation of the Lima bean germplasm (~90%) is slowing down the phenotypic analysis because seed production is reduced. We are addressing this issue by increasing the number of greenhouse increases in winter (short-days) and developing a protocol for a winter field increase in southern California with the assistance of PI P. Roberts at UC Riverside. What opportunities for training and professional development has the project provided?1. Dr. C. Diepenbrock (UC Davis) has mentored Dr.J. Adaskaveg as a postdoc across a broad range of plant science activities, includingNIRS and wet chemistry analyses of lima bean seeds and field experiments to evaluate phenotypic diversity of the USDA lima bean collection. 2. Dr. J. Adaskaveg (UC Davis) has been mentoring two undergraduate students hired to work on this project. One of them is a member of the Multicultural Scholars Program through the UC Davis Plant Breeding Center. 3. Dr. J. Hershberger (Clemson U.)is mentoring Ph.D. student Sangita Subedi. Herdissertation title is "Genetic Control of Succulent Butter Bean Seed Quality," expected graduation 05/2027. 4. Dr. D. Winham is teaching her staff/students (Glick, Heer) about the theoretical development of surveys using lima consumption as a topic; She is also teaching them about survey methodology, data analysis, pilot testing surveys with a national panel service; and qualitative survey methods. 5. Dr. D. Winham (Iowa State U.) mentored Ms. Abigail A. Glick, BS Dietetics. Ms. Glick will start a MS program in Nutritional Sciences at Cornell U. in September 2024. 6. Dr. T. Parker (UC Davis) has trained a postdoctoral researcher in drone-based high-throughput phenotyping. 7.Dr. S. Dohle (USDA) trained two biological science technicians on lima bean research fieldmanagement and how to do crosses, and 5 Washington State University undergraduatestudents got experience with lima bean regenerations at the genebank in Pullman, WA. How have the results been disseminated to communities of interest?1. The status of the project was presented to the Outside Advisory Committee in an online meeting on February 23, 2024 (Mid-year 2 of the project). Prior to this meeting, the OAC members had received a written report of the project team. 2. Presentation at Plant and Animal Genome meeting by C. Diepenbrock, UC Davis (January 2024): Diepenbrock CH, Adaskaveg J, Murray C. Applying AI-Enabled Sensing, 3-D Biophysical Modeling, and Genomics to Improve Climate Resilience of Grain Legume Productivity and Quality Profiles. USDA-NIFA-SCRI funding acknowledged. 3.Diepenbrock (UC Davis) presented on this project (a general overview) as part of invited seminars at the Donald Danforth Plant Science Center (Dec. 2023) and at the University of Illinois (Feb. 2024).USDA-NIFA-SCRI funding acknowledged. 4. Diepenbrock presented on this project (a general overview) as part of her talks at the Kearney (CA) Field Crops, Alfalfa, and Forage Field Day (Sept. 29, 2023) and at the San Joaquin County and Delta (CA) Field Crops Meeting (Jan. 2024).USDA-NIFA-SCRI funding acknowledged. 5. Diepenbrock presented on this project (a general overview) as part of her talk to the Plant Breeding and Biotechnology Committee at the California Seed Association Convention (Mar. 2024).USDA-NIFA-SCRI funding acknowledged. 6. Diepenbrock presented on this project (preliminary NIRS data collected by Jaclyn Adaskaveg and Celaya Murray, an undergraduate student at Fort Valley State University) as part of her talk at the UC Davis Integrative Center for Alternative Meat and Protein launch event (Jan. 2024). 7. Diepenbrock presented on this project (a general overview) as part of her talk in the UC Davis Plant Sciences seminar series (Apr. 2024). 8. UC Davis Dry Bean Field Day (August 15, 2024): The project was presented by Paul Gepts, Christine Diepenbrock, Jaclyn Adaskaveg, Sarah Dohle, and Antonia Palkovic. Paul Gepts (PD) provided an overview of the project with an accompanying handout adapted by C. Diepenbrock (Co-PD; also Director of the UC Davis Bean Breeding Program)from the two-page Bean Improvement Cooperative report. Jaclyn Adaskaveg (Postdoc with C. Diepenbrock) and Sarah Dohle (Co-PI at the USDA-NPGS-Pullman, WA, Regional Plant Introduction Station).showed results from the diverse collection of limas obtained from the USDA with accompanying handouts. Various of these parties discussed the USDA material with growers in the field (with discussions regarding individual lines, traits, and agronomic considerations). 9. Invited seminar by J. Hershberger (Collaborator at Clemson Univ.) at UC Davis Dept. of Plant Sciences (02/14/2024). Sowing seedsfor a quality-focused vegetable breeding and genetics program. 10. Invited seminar: Hershberger JM. Sowing seeds for a quality-focused vegetable breeding and genetics program. Plant and Agroecosystem Sciences Department. 2024 February 9; University of Wisconsin-Madison, Madison, WI 11. Invited seminar: Hershberger JM. Sowing seeds for a quality-focused vegetable breeding and genetics program. Plant and Agroecosystem Sciences Department. 2024 February 9; University of Wisconsin-Madison, Madison, WI 12.Hershberger, J. (Clemson U.): Butter bean breeding at the PDREC, Oral presentation at the Clemson Extension Pea and Butterbean Production Meeting 2024. 13. Hershberger, J. (Clemson U.). Butter bean breeding at the PDREC, Demonstration at the South Carolina Women's Agricultural Network 2nd Annual Conference (2024). 14. P. Roberts (UC Riverside): The nematode resistance Activity 3.10 resultswere reported to the project Outside Advisory Committee (OAC) during a virtual online meeting on February 23, 2024. Results were also communicated to the Lima bean industry stakeholders at the Annual California Dry Bean Field Day held at UC Davis in August 15, 2024. What do you plan to do during the next reporting period to accomplish the goals?OBJECTIVE 1 A third meeting of the Outside Advisory Committee will be held online in February (Activity 1.1). Based on the preliminary results obtaine in Year 2, the Iowa State team will conduct a national-level consumer survey focused on Lima bean only. In parallel, a farmer survey will be administered in January 2025 (Activity 1.2). Sensory and culinary evaluations and identification of parents as donors (to add into crossing blocks) will be conducted with Prof. J.-X. Guinard (UC Davis), Row 7 seed company, and breeding programs at U. of Delaware, Clemson University, and UC Davis. A project web page (currently in development: https://lima.sf.ucdavis.edu/) will be finalized and updated with accomplishments and products of the project). Other educational materials about Lima bean will be developed and assembled to include the development of public-facing educational materials for this website and in-person events. Videos will be developed on crop genetic diversity, plant breeding, drone methods, and germplasm conservation(Activity 1.4). Results of the team will be further disseminated at field days (e.g., UC Dry Bean Field Day; USDA-ARS-NPGS germplasm diversity demonstration at Pullman, WA), grower meetings, and scientific meetings. (Activity 1.5). OBJECTIVE 2 The germplasm conversion strategy will be further validated by 1) continued crosses and application ofadaptation markers to F2 seeds of multiple populations involving crosses between unadapted (e.g., nematode resistance) and adapted lines;and 2) planting the selected F2 progenies and verifying their adaptedness (e.g., ability to flower under long days, bush growth habit, white seededness)at USDA-ARS-NPGS and UC Davis (Activities 2.2 -2.4). Flowering individuals will be integrated into the regular breeding programs (Activity 2.5). OBJECTIVE 3 Germplasm Acquisition A winter nursery in Southern California (in collaboration with UC Riverside) at the Coachella Valley Agricultural Research Station (CVARS) will be fine-tuned (based on 2023-2024 results) to produce seeds under short-day conditions for photoperiod-sensitive accessions. The UC Davis group will provide seed samples originating from the USDA ARS NPGS to the U. of Delaware group (Activity 3.1). Genotyping Having finally obtained a genotyping dataset of the USDA collection and other Lima bean materials, the team will finalize a SNP dataset to be used across the project (Activity 3.3). This set will be integrated into the Legume Information System (https://www.legumeinfo.org/) datastore and from there insertedinto user-facing applications such as genome browsers and other more specialized tools for genotype data access already used at other genus-focused offshoots of the LIS system (e.g. https://www.peanutbase.org/gigwa/). A new tool (https://github.com/IPK-BIT/divbrowse) for presentation of genotype data across many lines and capable of supporting diversity analysis on the fly is now being adapted for use at LIS and we will use the LIMA dataset as an opportunity for getting valuable feedback on usability of this tool from the project team before it is made broadly available(Activity 3.4). Phenotyping The possibility of adrone methods paper will be investigated if the originality of the data warrants it. A Youtube channel of drone applications developed at UC Davis by T. Parker will potentially be integrated into the project (Activities 3.5 - 3.6).The phenotyping activity for agronomic, seed composition/nutritional, and nematode resistance will be completed for the USDA-ARS-NPGS Lima bean collection and the recombinant inbred populations (Activities 3.7-3.10). This includes wrapping up the UC Davis Summer 2024 field evaluation of NPGS materials and RI populations and conducting asimilar field evaluation inSummer 2025. The root-knot nematode resistance phenotypingof the Lima germplasm diversity set of 400 lines and three biparental RIL populations will be completed. Depending on the quality of the results obtained from the current field screening with Meloidogyneincognita at CVARS, which will be assessed in November 2024, a further field screening may or may not be necessary. The finalrounds of greenhouse inoculationscreens of the germplasm set and RIL populations with M. javanica and M. incognitawill be completed. Genotypingof the three RIL populations segregatingfor nematoderesistance will be completed using the DNA and leaf tissue samples preparedin year 2. In year 3, GWAS and linkage mapping to identify genome locations of the nematode resistance determinants and to identifymarker haplotypes for breeding will be initiatedusing the combined phenotype and genotype data (Activity 3.10). Genetic analyses The genotypic (SNP)and phenotypic data will be combined to conduct genetic analyses, including GWAS and QTL analyses.As GWAS and QTL analyses are made using this set of SNPs, we will further incorporate the trait association data into the comparative GWAS viewer that is already available at LIS (https://zzbrowse.legumeinfo.org/) and incorporate the genetic data into our InterMine instance for Phaseolus species (https://mines.legumeinfo.org/phaseolusmine/). A contined collabroation between Clemson U. and UC Davis will seek to further develop a BreedBase for Lima bean. A manuscript on GWAS of NIRS and California and Washington state agronomic data for ~200 NPGS lines will be initiated(Activity3.11). The phenotypic data will be integrated into GRIN-Global and LIS by USDA-ARS-NPGS and NCGR.As phenotypic data for the accessions in the germplasm collection is integrated into the GRIN-global system, LIS will access this data through the Breeding API (BrAPI: https://brapi.org/) and make it available via our existing GIS-based tool for display of germplasm-related information (https://germplasm-map.legumeinfo.org/). It should be noted that the genotype access tools described above are also BrAPI-compliant and we will explore integration of these data into the context of this tool as well.(Activity 3.12). ___________________
Impacts
What was accomplished under these goals?
OBJECTIVE 1: Consumer Information Bottleneck: Activity 1.1 Project-wide: Weorganized an online meeting with the Outside Advisory Committee in May 2024, in which the activities and accomplishments of the project and feedback were requested from the committee. Before this meeting, the committee had received a 10-page (single-spaced) report with a more detailed account of our activities. Activity 1.2 D. Winham, M. Heer, and A. Glick, Iowa State: a) Consumer surveys: The ISU team conducted a pilot study of a national-level survey on lima and pulse consumption patterns and health belief model of food choice. Two other sets of survey questions were piloted on limas and pulses for 1) consumer preferences and cooking experiences; and (2) knowledge and awareness of limas and pulses as vegetables. These data gave us estimates of the proportion of the US population, which consumes different lima types, and regional differences. These data will inform a national level consumer survey focused on limas only to address Objective 1. b) Farmer survey: Formative evaluation interviews have been completed with 7 small-scale farmers (5 non-lima growers; 4 lima growers). Additional farmer interviews with lima growers will be conducted August 2024. Activity 1.3: C.H. Diepenbrock & J. Adaskaveg, UC Davis: To address the goal of investigating consumer views of lima varieties as dry beans and processed/fresh-market vegetables, a collaboration with Dr. J.-X. Guinard in UC Davis Food Science & Technology is being established to facilitate sensory evaluations. A collaboration with the Row 7 Seed Company is also being established to conduct culinary evaluations with chefs. Activity 1.4: NA; will be pursued in 3rd year Activity 1.5: Project-wide: - Diepenbrock, Adaskaveg, Murray (UC Davis, Fort Valley State University):Legume session at the Plant & Animal Genome (PAG) conference (Jan. 2024): Title: Applying AI-Enabled Sensing, 3-D Biophysical Modeling, and Genomics to Improve Climate Resilience of Grain Legume Productivity and Quality Profiles. - Diepenbrock: Invited seminars: Donald Danforth Plant Science Center (Dec. 2023), University of Illinois (Feb. 2024). - Diepenbrock: Kearney (CA) Field Crops, Alfalfa, and Forage Field Day (Sept. 29, 2023); San Joaquin County and Delta Field Crops Meeting (Jan. 2024). - Diepenbrock:Plant Breeding & Biotechnology Committee, California Seed Association Convention (Mar. 2024). - Diepenbrock, Adaskaveg, Murray: preliminary NIRS data in talk at UC Davis Integrative Center for Alternative Meat and Protein launch event (Jan. 2024). - Diepenbrock:UC Davis Plant Sciences seminar series (Apr. 2024). - Two presentations on this project at the UC Dry Bean Field Day in Aug. 2024 (a general overview talk by Paul Gepts (UC Davis) and a joint talk on seed/culinary traits and the USDA NPGS collection by Jaclyn Adaskaveg (UC Davis) and Sarah Dohle (USDA-ARS-NPGS) -T. Parker (UC Davis); Bean Improvement Cooperative Biennial Meeting, November 2023, Greenville, SC:Putative adaptation mutations in Lima beans OBJECTIVE 2 Marker-based germplasm conversion program Activity 2.1 A. Farmer (NCGR), T. Parker (UC Davis),J. Hershberger (Clemson): See Objective 3, Activities 3.2 and 3.3 Activity 2.2V. Penmetsa & T. Parker, UC Davis: Sequence variants identified among reference genomes at candidate recessive core adaptation genes (PhyA: photoperiod sensitivity ; TFL1y, determinate habit ) were targeted for development into PACE genotyping. Field observations in summer 2024 strongly suggest that our proposed germplasm conversion strategy will be useful to introduce genetic diversity from unadapted germplasm in breeding programs. Activity 2.3 E. Ernest (U. Delaware) J. Hershberger (Clemson U.), A. Palkovic, V. Penmetsa, & C. Diepenbrock (UC Davis): Crosses between unadapted (recipient) and adapted (donor) varieties. UC DAVIS, USDA-ARS-NPGSS, U. Delaware, and Clemson U each each initiated or continued the development of recombinant inbred line (RIL) populations (20, 13, 4, and 14, cross-combinations, respectively). These progenies are being genotyped and phenotyped in conjunction with the USDA-ARS-NPGS germplasm collection (see OBJECTIVE 3). Activity 2.4 UC Davis: For Years 3 and 4. Activity 2.5 UC Davis, U. Delaware, Clemson U.: For Year 3. OBJECTIVE 3: Genotyping and phenotyping of the USDA lima bean collection Activity 3.1 S. Dohle & M. Warburton (USDA-ARS-NPGS): The USDA genebank continued its main objective of regenerating and characterizing the lima bean collection to make germplasm and data publicly available to breeders and researchers. They have also been testing field conditions and planting dates for growing lima beans at their Pullman, WA, farm location. Genotyping Activity 3.2 T. Parker (UC Davis) and J. Hershberger (Clemson U.): The sequencing of the lima bean collection and recombinant inbred line populations were contracted out to the Hudson-Alpha Institute in Huntsville, AL. The sequencing process suffered delays, but the data were eventually returned to the project and are now being analyzed. Activity 3.3 A. Farmer (NCGR), T. Parker (UC Davis): The primary focus of activities for the group at NCGR over the past project year has been validating and attempting to improve the quality of sequence-based genotyping results delivered to the project team by Hudson Alpha based on their Khufu genotyping pipeline. Several discussions between project members and Hudson-Alpha staff resulted in qualitative and quantitative improvements in the sequencing data,with a final delivery in late July 2024. A finalized SNP set is under discussion among project team members, and we plan to share it with all project members to have a common basis for downstream analyses. Activity 3.4 A. Farmer (NCGR): To be pursued in the 3rd and 4th year. Phenotyping Activities 3.5 and 3.6 T. Parker (UC Davis): In the Summer of 2024, Co-PD Parker conducted drone flights over the main drone field at three-week intervals since planting. These flights have been conducted at 20m high with a DJI Matrice 100 drone carrying a Zenmuse X3 RGB camera and a Micasense RedEdge-M multispectral camera. Similar drone flights were also carried outat the USDA Central Ferry, WA field planting.The data will be used to model growth parameters in the populations. A postdoctoral researcher was also trained in these methods. Activity 3.7 J. Adaskaveg, C.H. Diepenbroci (UC Davis): Genotyping and comprehensive field and laboratory-based phenotyping of the USDA NPGS lima collection are being conducted for agronomic (including essential adaptation) and grain nutritional quality (e.g., protein, fiber, starch, fat) and anti-nutritional (cyanogenic glucoside) traits. Activities 3.8 and 3.9 J. Adaskaveg, C.H. Diepenbroci (UC Davis): We have been characterizing the composition of Lima bean seeds for macronutrients--fiber, protein, starch, fat, moisture, and ash (total mineral content)-- with a benchtop near-infrared spectroscopy (NIRS). We are creating a calibration that will enable high-throughput analysis of beans with high accuracy at low cost to enable routine monitoring and selection of nutritional quality traits in breeding programs. Activity 3.10 P. Roberts, Bao-Lam Huynh (UC Riverside): Multiple sources of resistance were identified among more than 400 Lima germplasm entries in greenhouse and field screens under nematode infection. Next year's field and greenhouse trials will validate the data generated from these trials. Genetic Analyses Activity 3.11 Project-wide: To be pursued in 3rd and 4th year Activity 3.12 Project-wide: To be pursued in 3rd and 4th year
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Adaskaveg, J.A., Penmetsa, R.V., Hershberger, J., Wallace, L., Subedi, S., Heer, M., Hanifin, R., Warburton, M.L., Hokin, S., Farmer, A., Winham, D., Roberts, P., Ernest, E., Dohle, S., Palkovic, A., Parker, T., Gepts, P., and Diepenbrock, C. (2024). A collaboration towards the comprehensive improvement of lima beans: Addressing consumer information, pre-breeding, and germplasm information/utilization bottlenecks. Annual Report of the Bean Improvement Cooperative 67, 3-4.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Adaskaveg, J.A., Murray, C., Wallace, L., Subedi, S., Hershberger, J., Ernest, E., Palkovic, A., Gepts, P., and Diepenbrock, C. (2024). Utilizing benchtop near-infrared spectroscopy to predict lima bean (Phaseolus lunatus l.) nutritional composition. Annual Report of the Bean Improvement Cooperative 67, 29-30.
- Type:
Journal Articles
Status:
Published
Year Published:
2024
Citation:
Glick, A.A., Winham, D.M., Heer, M.M., Shelley, M.C., and Hutchins, A.M. (2024). Health belief model predicts likelihood of eating nutrient-rich foods among U.S. adults. Nutrients 16, 2335. doi: 10.3390/nu16142335
- Type:
Journal Articles
Status:
Other
Year Published:
2023
Citation:
Gepts, P. (2023). Biocultural diversity and crop improvement. Emerging Topics in Life Sciences 7, 151-196. URL: https://portlandpress.com/emergtoplifesci/article/7/2/151/233819/Biocultural-diversity-and-crop-improvement
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Progress 09/15/22 to 09/14/23
Outputs
Target Audience:In this report, 'Activities' refers to the Activities included in the funded proposal. The first number following the word Activity is the Objective under which this activity is conducted; the second number is the consecutive number of the activity under that objective. The following extension/outreach events or activities took place during this first year: 1) Activity 1.1: Establishment of an Activity 1.1. Establishment of an Outside Stakeholder Advisory Committee (OAC) The OAC for this project was established and met for the first time on December 15, 2022. Members of the OAC represent a broad range of geographies (Eastern and Western seaboards), from growers to food and seed companies.During the two-hour meeting, we presented the general objectives of the overall project (see .pdf of the slides attached to this report. We discussed how to interact between the OAC and research project members and decided to have one meeting per year (in October). In addition, we will have one-on-one ad hoc interactions as needed (see further). The following are members of the OAC: Luke McConnell, Crop Consultant, Owner of McConnell Agronomics; Andrew Wiersma, Bean breeder,Archer Daniels Midland (ADM);Sean Brock, Sprout House Agency; Will Lytle, USA Pulses; Devin Cornia, Northeast Organic Farming Association - New Jersey; Scott Morgan,Morganics Family Farm, NJ; Jim Wallace, Colusa Produce, Meridian, CA; Teddy Moynihan,Plowshare Farms, PA; Justin Prystajko, Hanover Foods Corporation; Steven Cannon, USDA-ARS; Charlotte Douglas & Patch Troffer, Row 7 Seeds, Dobbs Ferry, NY; Ken Bezilla,Southern Exposure Seed Exchange. In Mid-April 2023, we distributed a report to the AOC with the accomplishments available at that time. 2) Activity 1.3. Conduct demonstrations of lima bean In the Summer of 2023, the following activities took place in the U.S. Northeast: Plowshare Farms, Bucks County, PA: A biodiverse farm with a penchant for education and community building. Two events were hosted by farmer TEDDY MOYNIHAN, member of the OAC. They took place on May 20, 2023 (Planting Demonstration: "Get your hands dirty with Limas"; and on September 16, 2023 (Growing and Cooking Demonstration: Harvest and tasting, enjoy butter beans prepared by Chefs April McGreger and Valerie Erwin). LIMA! Project participants included eight members of the OAC and project researchers. Morganics Family Farm, Hillsborough Township, NJ: An organic grain and dry bean farm with direct farm-to-market sales. The event took place on August 26, 2023 and was hosted by farmer SCOTT MORGAN (member of the OAC) and focused on "Dry bean production education promoted by NOFA-NJ." These combined events had over 80 attendees. They generated satellite lima bean plantings at two community gardens in Philadelphia, a lima bean 'zine, an article in the Philadelphia Inquirer Newspaper by Jenn Ladd July 24, 2023 "Can lima beans become the new Brussels sprouts? Philly-area farmers hope to reform their image", an in-progress radio story by Lindsey Lazarski for WHYY, and lots of social media attention for lima beans and the important challenges of broadening the genetic base from farm to fork. In October 2022, MELISS WRIGHT and SUSAN TESTANI attended the day-long Lima Bean Festival in Cape May, NJ. The day-long event included about 80 vendors, 20% offering Lima bean products ranging from raw lima beans to value-added foods and even lima-themed clothing. While Lima beans did not appear at every booth, this event would surely be one to include as an educational outreach opportunity in October 2023. At the national level, the UC Davis team hosted Ms. Nicola Twilley and Cynthia Graber, co-hosts of Gastropod, a podcast devoted to the science and history of eating. A bean episode was released on October 24, 2023: https://gastropod.com/beans-beans-the-magical-fruit/, including information on Lima bean by PAUL GEPTS. Further information on the breeding work at UC Davis, including conversations with TRAVIS PARKER and CHRISTINE DIEPENBROCK, will appear in their newsletter. 3) Activity 1.4 Development of educational materials about lima beans Nothing to report. 4) Activity 1.5. Organization of institutional field days and grower meetings C. Diepenbrock and A. Palkovic (UC Davis) presented on the lima breeding program at the UC Intermountain Research & Extension Center field day (July 27) and at the UC dry bean field day (Aug. 15). The latter also included dedicated presentations by PI Gepts (UC Davis) giving an overview of this project and by J. Adaskaveg (UC Davis) on the nutritional quality results obtained thus far in this project. A. Palkovic presented on her and the team's work in Limas at the UC Davis Student Collaborative Organic Plant Breeding Education (SCOPE) field day (Sept. 7). C. Diepenbrock presented on the lima breeding program and this project at the UC Kearney Field Crops, Alfalfa, and Forage field day (Sept. 29). Diepenbrock also discussed this project with the California Dry Bean Advisory Board in Stockton, CA (Aug. 16). University of Delaware: The LIMA! project goals and activities were shared with participants in the Crops Field Day at Carvel Research & Education Center on August 9, 2023. ?Andrew Wiersma, LIMA! OAC member, visited Central Ferry with his assistant breeder to inform their decisions on what new accessions to integrate into the ADM lima bean breeding program. All are welcome to tour the USDA genebank fields. Changes/Problems:a) The project involved initially a participation of Delaware Valley University, a teaching institution in PA, with Dr. Meliss Wright and Ms. Susan Testani. Both collaborators have decided to sever their link to Delval U. and this project for personal reasons. In response, Dr. Donna Winham of Iowa State University has graciously accepted to expand her contributions to the project from Year 2 on, to include three surveys, the development of a three-class nutrition education module for shared use, and a layperson evaluation of Lima bean products. These modifications will strengthen the LIMA! Project's ability to increase awareness of Lima beans across multiple sectors beyond consumers. b) Most of the genetic resources of Lima bean show pronounced photoperiod sensitivity. While the UC Davis group is aware of this issue (and, indeed, this project is justified in part because of this issue), the group has struggled to produce enough seeds for our experiments despite measures taken, like fall or winter planting in the greenhouse. The UC Davis group plans to repeat plantings in the winter but in an alternative environment, i.e., a winter nursery at the Coachella Valley station operated by UC Riverside. c) Dr. Lyle Wallace (USDA-NPGS-Western Regional Plant Introduction Station) has been hired as a faculty at the Tennessee State University in Nashville, CA. He will continue research on Lima beans at his new institution, including his protein and dietary protein analyses on photoperiod-insensitive Lima bean germplasm in concert with the UC Davis group. What opportunities for training and professional development has the project provided?The project has hired a selected number of personnel to assist us. These include: UC Davis, with Dr. Christine Diepenbrock: Dr. Jaclyn Adaskaveg, postdoc for Lima phenotyping and genetic analyses; An undergraduate summer research scholar - Ms. Celaya Murray - from Fort Valley State University as part of the Plant Agricultural Biology Graduate Admissions Pathways Program (PABGAP) at UC Davis (poster presentation:Summer Scholar Mentoring and Research Program a Pathway for Diverse Students College of Agricultural and Environmental Sciences (ucdavis.edu) UC Davis, with MSc Antonia Palkovic:Kianna Benitez and Bradley Moore, undergraduate students; field trial preparation Udel: Mr. Robert Hanifin, technician in the Lima bean breeding program, with Dr. Emmalea Ernest Iowa State: Ms. Abigail Glick, a dietetics undergraduate student, and Ms. Michelle Heer (RD, LD) with Dr. Donna Winham How have the results been disseminated to communities of interest?In this first year, the limited results have been disseminated to: 1)the Outside Advisory Committee through a Zoom meeting and a mid-year report 2) farmers through field days in CA and DE. 3) the public through a farm event (PA), a festival (NJ), and an Instagram account (EatLimas). What do you plan to do during the next reporting period to accomplish the goals?Objective 1. Interactions & outreach among stakeholders, the public & this project Activity 1.1 Outside Advisory Committee (OAC) We will continue the yearly meeting and half-yearly report for the OAC, as well as the engagement with individual OAC members. Activity 1.2 Develop a survey of consumers about lima beans The survey(s) of Lima bean culinary and consumer traits will be initiated at Iowa State U. Activity 1.3 Conduct public taste testing and small-scale demonstration for novel lima beans. The public taste sessions will be initiated at Iowa State U., and small-scale demonstrations will be continued at various institutions, OAC-related locations, and festivals. Activity 1.4 Development of educational materials about lima beans We will further develop educational materials and seed to deploy these. Activity 1.5 Organization and participation in institutional field days, grower meetings, and scientific meetings, as well as public events These will continue as initiated in Year 1, but we will seek to expand them at other institutions and scientific meetings. Objective 2. Marker-based germplasm conversion program Activity 2.1 Targeted sequencing of adaptation genes in lima bean Now that HudsonAlpha data have been obtained at UC Davis, mapping the major adaptation loci in LIMA bean will proceed through GWAS. Mutations will be the basis for KASP or other genetic assays for screening for adaptation to production in temperate regions, such as the U.S. Activity 2.2 Development and validation of markers linked to adaptation alleles UC Davis will develop easy-to-use molecular markers (such as PACE, KASP, CAPS) for validation among segregating populations developed in Activity 2.3 and among the broader germplasm collection. Activities 2.3 & 2.4 Crosses between unadapted (recipient) varieties and adapted (donor) varieties; marker-assisted selection of adaptation alleles Further crosses will be made at UC Davis, UDel, and USDA-WRPIS; F2 generations will be selected for progenies that are homozygous recessive for adaptation alleles at UC Davis. Activity 2.5 Generation advance and field testing of converted populations None is expected yet. Objective 3. Genotyping and phenotyping of the USDA lima bean collection, biparental populations, and integration into the Legume Information System Activity 3.1. Acquisition of plant materials and greenhouse cultivation The various seed increases at UC Davis, USDA-WRPIS, and Clemson will be completed in the field and greenhouse. Activity 3.2. DNA Extraction, Library Preparation, and Genotyping-By-Sequencing We will continue with DNA sequencing at HudsonAlpha, notably for the UC Riverside, Clemson, and UDel projects. Activities 3.3 and 3.4 Bioinformatic analyses for SNP identification and genetic diversity and Integration of genotypic data into LIS This will continue the activities initiated in Year 1, adding the new sequence data obtained in Year 2 (see Activity 3.2). Activities 3.5 and 3.6. Design and use of a UAV (drone) protocol to phenotype field experiments with Lima bean T. Parker (UC Davis) and colleaguesare compiling a list of parties interested in discussing unoccupied aerial vehicle (UAV)-based data collection protocols-namely, those who have relevant experience and/or plan to fly their field trials that are taking place as part of this project to form a working group on that topic. They includeC. Diepenbrock and group, A. Palkovic (UC Davis), J. Hershberger and T. Rife (Clemson U.), E. Ernest (UDel), and S. Dohle (USDA-ARS Lima genebank).The team plans to draft and publish a manuscript on open-source and affordable drone-based methods in crops, including lima beans. Activity 3.7 Field evaluation of recombinant inbred line populations The recombinant inbred populations developed by Dr. Emmalea Ernest (UDel) will be assayed for the first time in the field in 2024. Activity 3.8. Measure nutritional traits in lima bean seeds Christine Diepenbrock (UC Davis), Lyle Wallace (Tennessee State University), and teams will conduct near-infrared spectroscopy (NIRS) for grain macronutrients (protein, total dietary fiber, total phenolics; also starch, fat, moisture %), both on the 2023 samples harvested in their respective location and 2023 samples harvested in the opposite location. In this manner, we will start to build instrument calibrations for the traits of interest on both NIRS platforms (which can vary in terms of the range of wavelengths that they assay and the resolution at which they do so, among other specifications) and start to examine the effects of Genotype, Environment, and the interaction of Genotype and Environment on grain macronutrient content. The developed calibrations will be used to predict trait values in thousands of samples (from various Genotype, Year, Location-and if applicable, Treatment-combinations) with medium to high throughput. The NIRS spectra data collected from the 2023 field trials will be integrated with trait data from the respective field trials to perform phenomic predictions. This will allow predicting performance for agronomic traits, such as yield or hundred-seed-weight, in individuals across and within environments and years. J. Adaskaveg (UC Davis) started testing phenomic predictions using the NIRS spectra obtained from materials collected before the Fall 2023 harvest. Activities 3.11 and 3.12 J. HERSHBERGER (CLEMSON U.) will continue developing a Breedbase instance for the Lima bean community. The first step in this process is the development of a Lima bean ontology or controlled, standardized vocabulary of Lima bean phenotypes that the community at large has agreed upon. A subset of LIMA! project members have joined together to form a data management working group that meets every other week to work on developing this ontology.
Impacts
What was accomplished under these goals?
Objective 1 See Stakeholder interactions under Target Audience Objective 2 Activity 2.1 T. Parker (UC Davis) has begun the exploration of sequence diversity across five lima bean lines to identify variations that might be related to core adaptation genes, including domestication-related loci. This analysis uses two genome assemblies from UC Davis (UC 92,UC Haskell), two from the University of Delaware (B2C,G25393,E. Ernest, U. of Delaware), and the lima bean reference genome. Activity 2.2 V. Penmetsa & T. Parker(UC Davis) Sequence variants in core adaptation genes (e.g., the determinate growth habit gene TFL1y, photoperiod sensitivity gene PHYA, etc.; activity 2.1) identified among reference genomes are being targeted for development into easy-to-use molecular markers (e.g., KASP) for validation among segregating populations (Activity 2.3) and among the broader germplasm collection. Activity 2.3 USDA GENEBANK: We attempted 30-some crosses between these exotic photoperiod-sensitive vining types and common market lima varieties. We have 21 putative F1 hybrids currently growing in Fall2023. UC DAVIS: During greenhouse grow-out in spring 2023 at UC Davis, crosses were performed on a subset of the greenhouse-grown USDA accessions (see Activity 3.1). Twenty different combinations of crosses were successful and yielded 36 putatively F1 seed from crosses between photoperiod sensitive and day-neutral accessions (16 cross-combinations) and involved an elite US cultivar or breeding line as one of the parents (14 cross-combinations). UNIVERSITY OF DELAWARE: Seed was obtained from 14 crosses between diverse and adapted germplasm were made in the greenhouse in winter 2021/2022. Andean diverse parents were crossed with a green-seeded UDel Fordhook DE1102103Cor with the Big Lima variety Dr. Martin. Diverse Mesoamerican parents were crossed with a green-seeded UDEL baby lima inbred line (DE100202C). Additional crosses between diverse and adapted germplasm were made in the greenhouse in winter 2022/2023 to introduce resistance to root-knot nematode or white mold. Activity 2.4 Nothing to report. Activity 2.5 C. DIEPENBROCK (UC DAVIS)is establishing a speed breeding setup to test two lima cultivars, then six upon scaling up. 4 recombinant inbred line (RIL) populations are being developed at the University of Delaware. The F5 generation of three populations was seeded in the greenhouse on August 25, 2023. The fourth population has one photoperiod-sensitive parent and was planted inAugust2023. Objective 3 Activity 3.1. The USDA Western Regional Plant Introduction Station (WRPIS)planted 100photoperiod-sensitive, older accessions for regeneration in January 2023.We collected leaf tissue from 92 accessions for DNA extraction, seeds from single plants associated with that DNA, and seeds for distribution and backup at the genebank. In Summer 2023, the entire available day-neutral lima bean collection was field-grownat Central Ferry, WA, by the USDA-WRPIS.This seed production will be used for calibrating a Near Infrared (NIR) curve for protein and dietary fiber in lima beans to be used in genetic mapping (Activity 3.8). In addition to the ~130 diverse genebank accessions, the USDA-WRPISalso grew ~50 breeding and commercial lines from U. of Delaware, UC Davis, and Clemson U. A large set of accessions provided by the USDA Genebank at Pullman, WA, has also been planted at UC Davis. Although these were planted in the Fall season (2022) under short-day conditions, seed production was limited.Further rounds of seed increase will have to be conducted. DR. JENNA HERSHBERGER (CLEMSON U.) is starting a fresh market-focused Lima breeding program focused on bean quality and heat tolerance. Jenna's team is performing a seed increase on ~300 PI accessions this winter in the greenhouse. A field trial of these lines was planted in April at the Pee Dee Research and Education Center in Florence, South Carolina. Activity 3.2. This activity has been contracted out to the HudsonAlpha Institute for Biotechnology (Huntsville, AL) on behalf of the UC Davis, Clemson, UDEL, USDA-Phaseolus Gene Bank, and UCR groups. Hudson-Alpha expects a considerable number (approximately 900 K SNPs per genotype) and will be able to "match" a SNP set in future add-on populations. Sequencing results have recently been provided to the UC Davis group. Activities 3.3 and 3.4 Activities at NCGR have been focused on datarelevant to the LIMA project and currently available, notably as yet unpublished Phaseolus genomes assembled from PacBio HiFi data, further scaffolded using BioNano optical maps (four P. lunatus genomes contributed by the UC Davis and UDel groups as well as genomes from other cultivated and wild Phaseolus species). We have worked closely with Co-PD PARKER (UC DAVIS) to begin aligning the genomes to one another,to populate initial instances of genome browsers with this data, and to assess large-scale rearrangements and local structural variation. We have also begun annotating the genomes to pursue gene-based pangenomic analyses. Initial annotation of repetitive content has been performed to define structural variations described above and masking the genomes prior toab initio gene-finding approaches. Currently, annotation is focused on previously published data to inform annotation of the new genomes. Some of these results have helped inform plans for generating RNA-seq data. Previously published diversity data for Lima Bean is used to populate a GIGWA genotype management tool, which has been developed to conform to the Breeder's API (BrAPI) standard and will be used to introduce other BrAPI-compliant tools into lima bean breeding programs by DR. JENNA HERSHBERGER (CLEMSON U.). Initial GBS-derived SNP genotyping has just recently been delivered on a subset of samples along with raw sequence fastqs from Hudson Alpha and we have begun downstream analysis of their results. The initial analysis hasestablished that the overall patterns of diversity estimated from this data are as expected. These data will soon be added to the GIGWA instance for distribution to the community via a similar set-up hosted through the Legume Information System. Activities 3.5 and 3.6. Nothing to report. Activity 3.7 Nothing to report. Activity 3.8. The UC Davis postdoctoral fellow, Dr. Jaclyn Adaskaveg, has started to build an instrument calibration for the NIRS and conducting an initial characterization of natural variation for grain macronutrients in mid- to late-generation breeding material and relevant parents, before the Fall 2023 harvest. C. Diepenbrock (UC Davis) and S. Dohle and L. Wallace (Tennessee State University) met with Dr. Brennan Smith (USDA-ARS), who is interested in assaying protein profiles in ~30 lima bean cultivars (including traits relevant for processing potential). Brennan and his team have a quantitative method that they have developed for this profiling in grain legumes. A. Palkovic (UC Davis) sent seed of 30+ cultivars to Brennan to be profiled. Activity 3.9 Nothing to report Activity 3.10 Field sites with root-knot nematode infestations have been prepared at the UC Kearney and UC Riverside Coachella Valley Research Stations. The first site, planted in May 2023, has a high soil population density of Meloidogyne javanica and was planted with 400 Lima bean germplasm entries received from the USDA Pullman, Washington, germplasm repository. The second site, also planted with the same accessions, will be harvested in the coming 10 days. Existing phenotyping data from greenhouse-screened plants of UC 92 x UC Haskell and Henderson x L136 RIL populations have been prepared for genetic analyses with the genotyping data to be generated by HudsonAlpha. Cultures of M. javanica and M. incognita have been increased to provide inoculum for greenhouse screening of the 400-entry germplasm set and a RIL population of PI256874 x L136 in Year 2. Genetic Analyses Activities 3.11 and 3.12 Nothing to report.
Publications
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