Source: CLEMSON UNIVERSITY submitted to NRP
BREEDING BIOFORTIFIED ORGANIC CHICKPEAS AS A WINTER CASH CROP FOR SOUTHEASTERN STATES
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
Reporting Frequency
Annual
Accession No.
1032751
Grant No.
2024-51300-43057
Cumulative Award Amt.
$2,000,000.00
Proposal No.
2024-03353
Multistate No.
(N/A)
Project Start Date
Sep 1, 2024
Project End Date
Aug 31, 2028
Grant Year
2024
Program Code
[113.A]- Organic Agriculture Research & Extension Initiative
Recipient Organization
CLEMSON UNIVERSITY
(N/A)
CLEMSON,SC 29634
Performing Department
(N/A)
Non Technical Summary
Chickpea (Cicer arietinum L.) is a versatile, climate-resilient, and salt-tolerant pulse crop that will become an excellent new winter cash crop for southeastern organic producers. Pulses provide soil health and nitrogen benefits to cropping systems and are a significant source of plant-based protein. Chickpeas can grow as a winter cash crop in the Southeast, from upstate to the coast, replacing acreage left fallow or planted with cover crops. Cultivars bred for conventional production are often unsuitable for organic production, and organically grown pulse crops have lower protein, making organic pulse proteins more expensive. Increasing crop production costs and decreasing commodity prices mean organic growers are exploring new crop options. Our long-term goal is to develop short-season chickpea cultivars for organic production with higher protein quality and superior milling properties, sensory qualities, and adaptability to organic rice/vegetable systems. This project is built on OREI, Good Food Institute (GFI), and SC Department of Agriculture-funded projects to establish a breeding pipeline for the public release of protein-biofortified organic chickpea cultivars for southeastern states. Project objectives are to (1) develop protein-enriched organic chickpea varieties using on-farm field trails (participatory breeding), (2) combine genomic information and trait discovery to enable the best genotype-to-phenotype mapping, and (3) develop on-farm educational and extension activities using the "Going Organic" platform. This project is aligned with the OREI goals to (1) develop and improve organic agriculture production, breeding, and processing methods; (2) determine desirable traits; (3) on-farm research; and (4) develop new and improved seed varieties for organic agriculture.
Animal Health Component
50%
Research Effort Categories
Basic
30%
Applied
50%
Developmental
20%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2021419108040%
2011412108140%
5021414101020%
Goals / Objectives
Long-term goal: To develop biofortified winter chickpea cultivars suitable for organic adaptation with high protein quality, good digestibility, improved flavor, and acceptable milling quality.Key objectives:Develop an organic breeding pipeline for chickpea varieties using on-farm field selection and participatory breeding to: (i) increase agronomic adaptation toward sustainable organic farming systems, (ii) improve nutritional quality (protein, SAA) balance, protein digestibility, starch, RS, flavor, and milling quality), and (iii) initiate an Accelerated Seed Delivery System (ASDS) with regional industry and state partners.Develop a genomic prediction pipeline for combining genomic information and trait mapping to enable the best genotype-to-phenotype mapping for trait discovery.Develop on-farm educational and extension activities using the Clemson University (CU) "Going Organic" platform, industry partners, eOrganic resources, consumers, and classroom courses for graduate and undergraduate students.
Project Methods
On-farm field design and selection: In years 1 and 2, the ~50 chickpea cultivars and advanced breeding lines will be planted in a complete α-lattice field design with commercial checks with three replicates at three on-farm locations in SC (n=450). Each incomplete block will be augmented with Sierra (check cultivar) at random positions to reduce spatial variability. These cultivars will also be blocked based on days to maturity to avoid known phenological variation. Before sowing, soil samples will be randomly taken at 0-15 cm depth to track soil N and other nutrient levels. Cultivars will be sown in 1.2 m × 6 m plots at a rate of 60-70 seeds/m2 and a seeding depth of 5-7 cm. Each plot will contain four rows spaced 30 cm apart. On-farm growers will participate in participatory selections. We will invite interested growers to the field and record their responses related to cultivar performance, suitability to their farms, and seed quality, and then will rank these cultivars based on their preference for inclusion in the breeding program.FT-MIR phenome platform: Single seeds will be analyzed for protein, SAA, RS, total starch, fats, and moisture content using FT-MIRBreeding Pipline: The breeding pipeline includes agronomic and nutritional trait discovery, population improvement, product development, introgression effects, seed commercialization, and dissemination. A market segment analysis for biofortified chickpeas will focus on the product traits valued by farmers and consumers . The breeding scheme consists of crossing, evaluation, and selection (CES) tasks and decisions for each trait across breeding stages.Genomic pipeline: We will generate and utilize genomic resources in four stages: 1) developing reproducible computational workflows that enable robust quality control of genomic and phenomic data; 2) applying GWAS to identify large-effect, environment-specific, and pleiotropic loci in chickpea diversity panel; 3) utilizing knowledge of associated loci, comparative genomics, and genomic prediction (GP) to identify high-potential crosses for elite breeding populations; and 4) uploading of phenomic and genomic data to Breedbase as a community resource.

Progress 09/01/24 to 08/31/25

Outputs
Target Audience:Target audience is the critical stakeholders approached for this project as follows: Specility crop growers was approached in South Carolina (SC) for their issues on organic winter pulse crop production in the southeast region include: (i) growers (cultivars adapted to winter production (90-100 days), adaptation to organic rice/vegetable cropping systems in coastal areas, seed quality, marketing, and public seed system), (ii) food processors (milling with reduced fat content (<5%), flour color, balancing amino acids for plant-based protein quality (methionine and cysteine), flavor, digestibility (proteins and raffinose family oligosaccharides (RFOs)) and sensory attributes), and (iii) consumers (nutritional issues: protein quality, digestibility, beany flavor, pesticide-, gluten-, and allergen-free). Key stakeholders involved with the project on-farm trials conducted at the WP Rawl Farm, Pelion, SC, Anoson Mills, Columbia, SC, and Rollen's RAW Grains, Hardeeville, SC. We approached food processors, seed growers, SC seed companies, and more than 100 young SC residents on consumer engagement. Further, research findings were presented to the science community at conferences, published in peer-reviewed publications, Organic Pulse Crop Field Day, and at an extension and outreach communication that included 117 direct contacts on organic pulse breeding. We shared our research findings with the SC community, American researchers, national and international organic plant breeders and researchers via an organic plant forum. Changes/Problems:Our three on-farm chickpea variety tests failed because pythium infection led to no seed germination, and trials were terminated. We are collaborating with Dr. Lyndon Porter from USDA-ARS to obtain the proper USDA-certified organic seed treatment to improve the germination, and we will test in only two on-farm locations instead of three in 2026. There are no other changes at the moment. We will also add a few greenhouse experiments to test the phythium resistance for the chickpea diversity panel. What opportunities for training and professional development has the project provided?Dr. Thavarajah The PI received the Jefferson Science Fellowship and worked on International Pulse Crop Development at the USAID on chickpea breeding projects from August 2024 to January 2025. IRB training on sensory panels and human research. Patent and commercialization training. Graduate Students: Computational research activities using the Palemeto computer cluster at Clemson University. A graduate student completed a doctoral thesis, 'Breeding Biofortified Protein-Rich Organic Pulses for Better Human Health'--Chickpea GBS data used in the chickpea chapter of the thesis. Graduate students attended several conferences, presented their data, and attended commercialization/patent meetings. Two graduate students who worked on the project received the Wade Stackhouse Graduate Fellowship from Clemson University. Two graduate students attended the Qualitative Genetics graduate course at the University of Minnisorta. Teaching opportunity for 4-H workshops, and SC commissioner school workshops Field Day engagement with the stakeholders and engagement in research communication. Drone training and obtained a pilot's licence to fly a drone in SC. Attended several leadership and teaching workshops. Undergraduate Students Computational training - cloud-based web application High-throughput platform testing with spectroscopy and drones Food processing technology hands-on learning opportunity Leadership and writing skills improvement via writing peer-reviewed manuscripts Presenting posters at the research conference. ?Project staff members: The bioinformatician (PDF) of this project gained training in pulse breeding and genomic research and numerous opportunities for professional development. PDF has had the opportunity to manage large phenotype datasets and high-density genotypic data, skills directly applicable to genomic-assisted breeding. She has conducted advanced data analyses, including genome-wide association studies (GWAS), which enhanced my genetics and trait mapping expertise. The research findings were presented at the 3rd Clemson Postdoctoral Symposium on April 22, 2025, allowing one to share key findings with a broader scientific audience, engage with peers, and receive constructive feedback. Furthermore, active participation in the pulses field day, such as the event held in Pelion, SC, on April 09, 2025, facilitated engagement with local growers, breeders, and students, enhancing my communication and collaboration skills. Additionally, participation in journal clubs, lab meetings, and fieldwork over the past six months has contributed significantly to my professional growth. How have the results been disseminated to communities of interest?On-farm results were disseminated directly to stakeholders (food processing, consumers, and marketing) using multiple social media outlets. As such, Dr. Attaway (Communications Lead) coordinatedsocial media releases and publications and updates social media networks at Clemson University. The first year results will be presented at the 2025 North American Pulse Improvement Association meeting in Nebraska to update the pulse research community, communicated to national and local stakeholders, published in peer-reviewed publications, and presented at conference papers to share results. Also, we shared our research findings via the "Going Organic" platform, including webinars, seminars, and other extension activities. What do you plan to do during the next reporting period to accomplish the goals?We plan to continue all three objectives for the second year, which include breeding activities, field and greenhouse activities, on-farm breeding activities, computational/genomic analysis, developing populations, high-throughput phenotyping platform, sensory analysis, and extension and education activities, as in the first year.

Impacts
What was accomplished under these goals? Major activities completed This project aims to adapt organic biofortified chickpea as a winter cash crop to the southeastern regions. To achieve this goal, the first year of the project activites include, (1) on-farm variety trials were conducted in three USDA-certified organic farms in Pelion, Hopkins, and Hardeeville, SC; (2) established the breeding pipeline by collecting diverse germplasm and seed increase in the field and the greenhouse; (3) genotyping data pipeline for the USDA chickpea diversity panel evaluted by Dr. Goerge Vandemark for fatty acids and mineral traits; (4) setting up the breedbase for chickpea breeding with the matrials obtained from USDA-ARS, ICARDA, and UC-Davis; and (5) conducted extension and out reach activities via "Going organic" platform. On-farm variety testing trials: 23 cultivars were obtained from the USDA-WSU, UC-Davis, and Meridian Seeds. These cultivars were planted at three USDA-certified organic on-farm locations in SC. The field design was a randomized complete block design (RCBD) with three replications per cultivar, one control per replication, and a border to minimize edge effects. Plots were 4.65 m² (50 ft²), consisting of seven rows spaced 7.5 inches (19 cm) apart, and were sown using an Almaco Light Duty Grain Drill at a seeding rate of 50 seeds/m². Fields were monitored weekly, and poor/no germination was observed across all entries and all three locations. To assess seed viability, a germination test was conducted under controlled greenhouse conditions, where all entries exhibited near-complete germination, confirming seed viability and suggesting that environmental factors in the field affected germination at the on-farm trials. As a result of the Phytophthora infestation in the soil, poor germination and trials were terminated. Breeding Pipeline: 12 parents of six commercial varieties and six Plant Introduction (PI) accessions from the Chickpea Single Plant (CSP) collection were grown in the Clemson University greenhouse. Fourteen crosses were made from the above parents. Four identical crossing blocks were planted at two-week intervals. Hybridization data was recorded using the PhenoApp 'Intercross'. Hybridized flowers were labeled using a barcode system to provide each cross with a unique 'cross ID'. At maturity, hybridized pods were hand-harvested and shelled to obtain F1 seed. 69 F1 seeds from nine crosses were planted in pots to produce the maximum number of F2 seeds. Then the F2 seeds were advanced using the Single Seed Descent (SSD) method. F4 seeds will be harvested, and a single seed from each plant will advance to the field nursery in January 2026. Chickpea advanced breeding lines from ICARDA: A set of 36 chickpea lines was obtained from the International Center for Agricultural Research in the Dry Areas (ICARDA), Egypt. The collection included kabuli and desi types, selected based on key agronomic traits such as early maturity, seed size, plant architecture, and yield potential. Each accession was grown in a greenhouse with three replicates to facilitate seed increase. The resulting seed stock will be used for field evaluation in the 2026 growing season, and selected lines will be used as parents in the chickpea breeding pipeline. High-throughput phenotyping platform: Fourier transform mid-infrared (FT-MIR) spectroscopy with Cary 630 and 4300 hand-held spectrometers is used in this platform. The FT-MIR technology was further advanced into a web application. This online platform utilizes pre-trained Chemometric models with k-fold cross-validation to predict all the nutritional traits studied in the chickpea breeding pipeline. The UAV pipeline for field phenotyping is in progress. Genomic analysis: To initiate genomic prediction and genome-wide association studies, the chickpea germplasm collection was planted for seed increase and evaluated for the first time at a certified organic location in Pelion, South Carolina. The collection consisted of 251 accessions from the Mini-core collection from the USDA-ARS GRIN germplasm in Pullman, Washington, and 13 breeding lines from the USDA-WSU. The germplasm collection was planted in a randomized complete block design (RCBD) with one replicate per entry, 24 check entries, and encompassed by border plots. The trial was planted using an Almaco Light Duty Grain Drill, sown into 4.65 m2 (50 ft2) plots with four rows spaced 15 inches (38.1 cm) apart at a seeding rate of 22 seeds/m2. Accessions on agronomic adaptability and performance were evaluated using the Pheno App 'Field Book' to record quantitative and visual assessment data. The collection was hand-harvested at maturity. The seed obtained will be sampled and ground for nutritional analysis, and the remaining seed will be planted in 2026 for genomic studies and developing a new diversity panel with 400 PI accessions to develop the genomic prediction pipeline. Data analysis is in progress for the first year. Genome-wide association (GWAS): The chickpea diversity panel, composed of 256 accessions, was used to evaluate fatty acids and mineral composition. Dr. Vandemark conducted this field study, and the Thavarajah program performed nutritional composition and the GWAS analysis to identify the trait variations to incorporate into the breeding program. The phenotypic data were collected for four fatty acids (Palmitic acid: PA; linoleic acid: LA; alpha-linolenic acid: ALA; and oleic acid: OA) and minerals (Calcium: Ca, potassium: K; magnesium: Mg; phosphorus: P; copper: Cu; iron: Fe; manganese: Mn; selenium: Se and zinc: Zn). Genotyping-by-Sequencing (GBS) technology generated the sequencing data for the diversity panel. GBS data was processed using standard tools, including Burrow-Wheeler aligner, Genome Analysis Toolkit, VCFtools, etc., to obtain 15,947 high-quality single-nucleotide polymorphism (SNP) markers. Phenotypic data for fatty acids and minerals were used with SNP data to conduct genome-wide association analysis (GWAS) to identify significant SNPs and candidate genes associated with the study traits. GWAS identified five significant SNPs for only PA, while 14 were identified for five minerals (Ca, Mg, P, Mn, and Zn). Several SNPs were associated with candidate genes governing physiological pathways related to the study traits. Extension and education activities: For (i) Growers: Organic Pulse Field Day (60 participants); (ii) High school students: summer day camps for underrepresented students [4-H, Minority Youth Groups (two workshops-75 participents), SC Commissioner School (15 participents)]; (iii) For undergraduate and graduate students: (i) a three-credit spring course (12-15 partcipents); (ii) research internships: University Professional Internship and Co-op (UPIC) course (2 interns); and (iv) Two organic plant breeding doctoral student enrolled into the virtual quantitative genetics course offered by the University of Minnesota (Dr. Rex Bernardo). Outcomes: >60 growers attended the field day, and 3-10 growers requested organic chickpea seeds for on-farm trials. Fatty acid and mineral genes were discovered. A bioinformatician, a full-time technician, and a research scientist were hired. Four undergraduates (two from computer science and two from plant sciences) were trained, a doctoral student partially worked on analysing chickpea genomic data (completed the doctorate), and another doctoral student developed an FT-MIR platform for chickpea. Output: 7 peer-reviewed publications (3 published; 4 submitted); 14 conference papers, 6 other publications, one patent, signed commercialization agreement with an SC company, 12 educational products, 3 high-school workshops, 7 speakers for organic webinar series, and 117 in-person contacts on organic pulse breeding activities. 314 attendees for the Going Organic webinar series to engage with organic pulse breeding. 434 YouTube views on our "Going Organic " series.

Publications

  • Type: Other Journal Articles Status: Under Review Year Published: 2025 Citation: Adam Niemczura*, Ethan Marquez*, Amod Madurapperumage , Pushparajah Thavarajah, Leung Tang, Dil Thavarajah!, 2025. Nutri-Phenomics: A cloud computing platform for real-time phenotyping of nutritional quality traits in food crops. The Plant Phenome Journal, TPPJ-2025-07-0045-OA.
  • Type: Other Journal Articles Status: Under Review Year Published: 2025 Citation: Carolina Ball�n-Taborda�, Nathan Johnson�, Lucas Boatwright, Tristan Lawrence, Josua Kay, Nathan Windsor, Amod Madurapperumage, Pushparajah Thavarajah, Leong Tang, Emerson Shipe, Shiv Kumar, Dil Thavarajah!, 2025. Genome-wide association studies of nutritional traits in peas (Pisum sativum L.) for biofortification. The Plant Genome; TPG-2025-06-0159.
  • Type: Other Journal Articles Status: Under Review Year Published: 2025 Citation: Amod Madurapperumage , Pushparajah Thavarajah, Dil Thavarajah!, 2025. Flavor and texture-related compounds in raw dry pea (Pisum sativum L.) towards consumer acceptance. Legume Sciences. 3002798.
  • Type: Other Journal Articles Status: Under Review Year Published: 2025 Citation: Sonia Salaria , Lucas Boatwright, George Vandemark, Dil Thavarajah*, 2025. Genetic mapping of a chickpea diversity panel for mineral biofortification towards human nutrition. The Plant Genome, TPG-2025-05-0131,
  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2025 Citation: Sonia Salaria , Tristan Lawrence, Dil, Thavarajah!, 2025. Nutritional composition of chickpea (Cicer arietinum L.) grown in winter cropping systems: a new sustainable legume opportunity. Legume Science. https://doi.org/10.1002/leg3.70034
  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2025 Citation: Gamlath Senarathne , Dil, Thavarajah!, 2025. Interdisciplinary approaches to enhance sensory properties and consumer acceptance in pulse crops. Plants, People, Planet. 13 June 2025; https://doi.org/10.1002/ppp3.70048.
  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2025 Citation: Amod Madurapperumage , Pushparajah Thavarajah, Leung Tang, George Vandemark, Dil Thavarajah!, 2025. Fourier-transform mid-infrared (FT-MIR) spectroscopy for high-throughput phenotyping of total dietary fiber (TDF) in pulse crops. The Plant Phenome Journal, 8, e70022. https://doi.org/10.1002/ppj2.70022.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Adam Niemczura, Ethan Marquez, Amod Madurapperumage, Pushparajah Thavarajah, Leung Tang, Dil Thavarajah, 2025. High throughput phenotyping platform for nutritional traits in pulse crops: A cloud computing approach. 8th Annual Clemson Student Research Forum April 9 - 11, 2025, Clemson University.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Amod Madurapperumage, Dil Thavarajah 2025. High-throughput phenotyping platforms for pulse crop breeding. Clemson Fresh, Food, Packaging and Sustainability Summit, March 3-5, 2025.
  • Type: Other Status: Published Year Published: 2025 Citation: 2025: Rapid, Simple, and High-Throughput Nutritional Phenotyping of Pulse Crops. Agilent Technologies, https://gcms.labrulez.com/paper/29022
  • Type: Other Status: Published Year Published: 2025 Citation: 2025: The researcher aims to develop chickpeas as a winter cash crop in the Southeast. Market Bulletin, SC Department of Agriculture, Jan 16, 2025.
  • Type: Other Status: Published Year Published: 2024 Citation: 2024: Researcher Aims to Develop Chickpeas as Winter Cash Crop in Southeast. https://www.morningagclips.com/researcher-aims-to-develop-chickpeas-as-winter-cash-crop-in-southeast/
  • Type: Other Status: Published Year Published: 2024 Citation: 2024: Researcher Aims to Develop Chickpeas as Winter Cash Crop in Southeast. https://m.farms.com/news/researcher-aims-to-develop-chickpeas-as-winter-cash-crop-in-southeast-221188.aspx
  • Type: Other Status: Published Year Published: 2024 Citation: 2024: Clemson University researcher aims to develop chickpeas as a winter cash crop in the Southeast. https://www.seedquest.com/news.php?type=news&id_article=159725
  • Type: Other Status: Published Year Published: 2024 Citation: 2024: Clemson announces 2024-25 Going Organic webinar series. https://news.clemson.edu/clemson-announces-2024-25-going-organic-webinar-series/
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Thavarajah Dil, 2025. Organic pulses and healthy diet, Invited lecture, SC Commissioner School, Clemson, SC, July 21, 2025.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Thavarajah Dil, 2025. Organic Pulse Breeding, Invited lecture, Pinckney Leadership Conference, Clemson, SC, July 15, 2025.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Thavarajah Dil, 2025. Pulse Crops, Invited lecture, Pinckney Leadership Conference, Clemson, SC, June 10, 2025.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Thavarajah Dil, 2025. Organic Pulse Breeding for SC, Invited lecture, SC Department of Agriculture-ACRE Program, June 9, 2025.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Thavarajah Dil, 2025: Organic Pulse Breeding, PES 4050/6050 Plant Breeding, Invited lecture, April 13, 2025.
  • Type: Other Status: Published Year Published: 2025 Citation: Thavarajah Dil, 2025. Organic Pulse Breeding Program Update, Pulse Crop Field Day, Pelion, SC, April 9, 2025.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Thavarajah Dil, 2024. Invited Webinar, Pulse crops toward Middle Eastern food security, USAID, MERC program webinar, Oct 1, 2024.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Thavarajah Dil, 2025. Pulse Crops Towards Global Food Security, The International Legume Society webinar, May 29, 2025.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Thavarajah Dil, Leong Tang, Pushparajah Thavarajah, 2025. Unlocking Agricultural Potential: Fast, Cost-Effective and Non-destructive Analysis with FT-MIR Spectroscopy, Agilent and Separation Science Global Webinar, March 25 and 26, 2025.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Thavarajah Dil, 2024. Organic Pulse Breeding and Nutrition, Institute of Chemistry, Sri Lanka. Nov 30, 2024.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Adam Niemczura, Ethan Marquez, Amod Madurapperumage, Pushparajah Thavarajah, Leung Tang, Dil Thavarajah, 2025. High throughput phenotyping platform for nutritional traits in pulse crops: A cloud computing approach. Organic Pulse Field Day, April 9, 2025, Pelion, SC.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Charles Kresser, Chamodi Senarathne, Amod Madurapperumage, Scott Whiteside, Pushparajah Thavarajah, Dil Thavarajah, 2025. Canning quality of Organic Dry pea (Pisum sativum L.) advanced breeding lines adapted to South Carolina. Organic Pulse Field Day, April 9, 2025, Pelion, SC.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Amod Madurapperumage, Dil Thavarajah 2025. High-throughput phenotyping platforms for pulse crop breeding. Organic Pulse Field Day, April 9, 2025, Pelion, SC.