Research Project: Conservation, Characterization, Evaluation, and Distribution of Grain, Oilseed, Vegetable, Subtropical and Tropical Legume, and Warm Season Grass Genetic Resources and Associated Information

Location: Plant Genetic Resources Conservation Unit

2020 Annual Report

Objectives
1. Efficiently and effectively acquire, distribute, and maintain the safety, genetic integrity, health, and viability of priority grain, oilseed, vegetable, subtropical and tropical legume, and warm season grass genetic resources and associated information. 1.A. Acquire genetic resources to expand the diversity of priority crops and crop wild relatives (CWR) available from the genebank via collection, exchange or other appropriate means. 1.B. Conserve and maintain over 94,000 accessions of priority genetic resources and their associated information, periodically assess these priority genetic resources for viability, trueness to type, and health, and distribute accessions upon request. 1.C. Conduct field and greenhouse regenerations of priority crops and CWR to replenish and safeguard high quality genetic resources in state-of-the-art genebank. 2. Develop more effective genetic resource maintenance, evaluation, or characterization methods and apply them to priority grain, oilseed, vegetable, subtropical and tropical legume, and warm season grass genetic resources. Record and disseminate evaluation and characterization data via GRIN-Global and other data sources. 2.A. Using phenotypic descriptors, evaluate priority crops and CWR for agronomic and horticultural traits and incorporate this data into GRIN-Global. 2.B. Develop and apply nuclear magnetic resonance (NMR), rapid N exceed [nitrogen/protein] analyzer (RNEA), high performance liquid chromatography (HPLC), gas chromatography (GC), and gas chromatography-mass spectrometry (GC/MS) procedures to evaluate variation in oil, protein, sugar content, amino acid composition, fatty acid composition, flavonoids, flavors, and other key phytochemicals in priority crops and CWR and incorporate this data into GRIN-Global. 2.C. Develop and apply DNA markers to assess phylogenetic relationships, genetic diversity, population structure, and association with phenotypic traits of priority crops and CWR. Enter DNA genetic marker characterization data into GRIN-Global or other databases (such as GenBank). 3. With other NPGS genebanks and Crop Germplasm Committees, develop, update, document, and implement best management practices and Crop Vulnerability Statements for priority grain, oilseed, vegetable, subtropical and tropical legume, and warm season grass genetic resource and information management.

Approach
Curators will acquire plant genetic resources from collection trips, donations, and exchanges with other gene banks and state universities to adequately conserve the range of crop genetic diversity. Seed from each accession maintained in the collection will be preserved in cold storage to optimize long-term seed viability and reduce the frequency of regeneration. Efforts will continue to conduct standard germination tests on the entire range of crop and crop wild relative accessions in the germplasm collection with emphasis on testing new material and retesting select inventories at ten year intervals. Plant genetic resources (seeds, in-vitro cultures, plants, cuttings, corms, and rhizomes) and associated information will be sent to users worldwide in response to requests received by email, internet, phone, and U.S. mail. Accessions with low seed viability, low seed numbers, original seed only, and age of seed will be targeted for regeneration. Curators will observe and collect phenotypic data using descriptors for each of the accessions/crops grown for regeneration or evaluation. Additional descriptors on classification, local adaptability, and other traits of agricultural importance will be recorded as opportunity permits. Valuable biochemical traits such as oil/fatty acid and protein/amino acid content in oil seed crops; flavonoids and anthocyanins in legumes; flavor and resveratrol in peanuts; protein content in Vigna; protein and mineral content in pearl millet seeds; and fruit color and flavor components in pepper (Capsicum spp.) will be collected, analyzed and made available on the Germplasm Resources Information Network (GRIN-Global). Genetic characterization and evaluation of plant germplasm will be conducted. For genetic characterization of little bluestem, sweet potato and pepper, previously published simple sequence repeat (SSR) markers are available and will be utilized as the focus of the research is not on marker development but rather characterization. For peanut and sorghum, where advanced genomic tools are available, single nucleotide polymorphism (SNP) markers will be used for characterization, association analysis, and design of functional DNA markers. Curators will consult with Crop Germplasm Committees (CGCs) to develop, update, document, and implement Best Management Practices (BMPs) and Crop Vulnerability Statements (CVS) for crops conserved in the genebank. All data including passport, regeneration, and characterization data will be submitted electronically to the Information Technology Specialist or Seed Storage Manager and their designated staff for local storage and uploading to the GRIN-Global database.

Progress Report
A large and highly diverse set of plant germplasm was preserved and distributed to scientists, educators, and plant breeders. A total of 100,081 accessions of 1602 plant species representing 286 genera were maintained in the Griffin, Georgia, plant genetic resources collection. Over 86% of these accessions were available for distribution to users and over 97% were backed up for security at a second location. A total of 16,275 seed and clonal accessions were distributed upon request to scientists and educators worldwide between October 1, 2019 and August 4, 2020. Sorghum, cowpea, peanut and pepper were the most distributed crops. Clonal collections were continually maintained and distributed to stakeholders. Clonal collections include warm-season grasses, bamboo, Chinese water chestnut, perennial peanut, and sweet potato. Preservation methods include tissue culture, field plots, greenhouse plants, and hydroponics. All of these activities ensure that the crop genetic resources at the Griffin, Georgia, location are safeguarded for future use in developing new cultivars and identifying novel traits and uses in our food and fiber crops. Newly increased seed from a variety of crops in the collection were harvested, cleaned, and added to the collection by ARS researchers at Griffin, Georgia, to ensure high quality, viable seed samples continue to be available for distribution for scientific studies and breeding. During this process, valuable characterization data was collected in the field and greenhouse. Vegetable crops were regenerated in collaboration with ARS researchers at Parlier, California, HM Clause, Bayer, and the World Vegetable Center (Taiwan and Thailand). Peanut and cowpea were regenerated on site and digital images of peanut pods and seeds were captured. Numerous legume species, industrial crops, and warm-season grasses were regenerated on site as well. Sorghum was regenerated by ARS scientists in Puerto Rico and received for cleaning and processing on site. Several sweet potato wild species were regenerated in greenhouses. Collaboration continues with ARS Charleston, South Carolina,regarding evaluation of Citrullus and Cucurbita germplasm. Portions of the pepper collection are being screened for the presence of Pospiviroids and Tobamoviruses. Collaborative studies continue with Baylor College of Medicine,in an effort to examine genetic evolution in pepper by examining genome structure. Loofah fruit are edible and provide the well-known loofah sponge. Collaborative efforts have identified disease-resistant loofah and work is underway to examine genetic diversity in a loofah germplasm collection. First year multi-location analysis of jute and basella for flavonol, cyanidin, and protein variability was completed by ARS researchers at Griffin, Goergia. Significant location and accession effects were observed for quercetin and protein concentrations while only significant accession effects were found for kaempferol and cyanidin concentrations. Quercetin was negatively correlated with kaempferol and kaempferol was also negatively correlated with protein. Analysis of flower color, % germination, 100 seed weight, total seed weight, seed number, and origin for 26 butterfly pea accessions was completed. Flower color and origin were shown to be correlated. Butterfly pea germplasm was divided into five seed production groups. The information from these studies will provide plant breeders and scientists valuable biochemical variability in jute and basella as well as morphological and seed trait variation in butterfly pea for variety development. Biochemical characterization of a wide variety of germplasm was conducted. In peanut, protein was measured to verify the role of location grown on this trait. The variation of oil content and fatty acid composition among six botanical varieties of peanut was measured to determine variation among botanical varieties. Flavonoids were measured in peanut root nodules to determine if flavonoids play a role in the development of root nodules in peanut as has been shown previously in soybean. Sugar content and flavonoids were measured in peanut sprouts to assess nutritive values. Protein content and flavonoid content of jute were measured to assess nutritive value in different germplasm populations. Genetic markers for the high oleic acid trait were used to determine if the high oleic trait is correlated with germination rate in peanut. In total, the molecular lab measured 172 samples for protein content, 700 samples for oil content, 740 samples for fatty acid composition, 60 samples for sugars, and 90 samples for flavonoids. DNA were extracted from 350 samples and genotyping was performed on 500 samples.

Accomplishments
1. Watermelon root traits. Root morphology has an immediate effect on water uptake and thus stress tolerance. The root systems of over 300 germplasm accessions of watermelon were characterized ARS researchers at Griffin, Georgia, for various morphological traits likely to affect water uptake. Great variability was observed. The information gained will be utilized in future crop improvement efforts that aim to take advantage of this diversity in the development of stress tolerant watermelon varieties.

2. Root morphology in sorghum. Root morphology can significantly affect sorghum stress tolerance such as drought tolerance and affect sorghum yield and production. ARS researchers at Griffin, Georgia, tested different methods to measure and characterize root morphology. The researchers identified the most efficient and reliable method to use in sorghum root morphology studies. This discovery allows for easier testing of roots traits in sorghum and to aid in identification of drought tolerant germplasm for use in variety development.

3. Fatty acid profiles in peanut. Oleic acid is a healthy fat found in peanut. Oleic acid is controlled by genetics, but environment such as temperature during seed development can have an effect. Peanuts were in different field environments and oleic acid content measured by ARS reseachers at Griffin, Gerogia. Seeds produced in areas with higher temperatures during the growing season had higher oleic acid content than seeds from areas with cooler temperatures. Peanut breeders and farmers can use this research to manipulate peanut seed oil composition.

Review Publications
Branch, W.D., Tallury, S.P., Clevenger, J.P., Schwartz, B.M., Hanna, W.W. 2020. Inheritance of a novel heterozygous peanut mutant, 5-small leaflet. Peanut Science. 47:33-37. https://doi.org/10.3146/PS19-11.1.
Harrison, M.L., Bradley, V.L., Casler, M.D. 2019. Native grass species for forage and turf. In: Greene, S.L., Williams, K.A., Khoury, C.K., Kantar, M.B., Marek, L.F., editors. North American Crop Wild Relatives. New York, NY: Springer, Cham. Volume 2, p. 579-605.
Khoury, C.K., Carver Jr, D.P., Barboza, G., Jarret, R.L., Van Zonneveld, M., et. al. 2019. Modeled distributions and conservation status of the wild relatives of chile peppers (Capsicum L). Diversity and Distributions. 26(2):209-225. https://doi.org/10.1111/ddi.13008.
Khoury, C.K., Kates, H.R., Carver Jr, D.P., Achicanoy, H.A., van Zonneweld, M., Thomas, E., Heinitz, C.C., Jarret, R.L., Labate, J.A., Reitsma, K., Nabhan, G.P., Greene, S.L. 2019. Distributions, conservation status, and abiotic stress tolerance potential of wild cucurbits (Cucurbita L.). Plants, People, Planet. 2(3):269-283. https://doi.org//10.1002/ppp3.10085.
Guo, S., Zhao, S., Sun, H., Wang, X., Wu, S., Lin, T., Ren, Y., Deng, Y., Zhang, J., Lu, X., Zhang, H., Shang, J., Gong, G., Wen, C., He, N., Li, M., Liu, J., Wang, Y., Zhu, Y., Tian, S., Jarret, R.L., Levi, A., Huang, S., Fei, Z., Liu, W., Xu, Y. 2019. Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits. Nature Genetics. 51:1616–1623. https://doi.org/10.1038/s41588-019-0518-4.
Quispe-Huamanquispe, D., Gheysen, G., Yang, J., Jarret, R.L., Rossel, G., Kreruze, J. 2019. The horizontal gene transfer of Agrobacterium T-DNAs into the series Batatas (Genus Ipomoea) genome is not confined to hexaploid sweetpotato. Scientific Reports. 9:12584. https://doi.org/10.1038/s41598-019-48691-3.
Jackson, M., Harrison Jr, H.F., Jarret, R.L., Wadl, P.A. 2020. Phenotypic variation in leaf morphology of the USDA, ARS sweetpotato (Ipomoea batatas) germplasm collection. HortScience. 55(4):465-475. https://doi.org/10.21273/HORTSCI14703-19.
Hanson, E., Zhou, H., Tallury, S.P., Yang, X., Paudel, D., Tillman, B., Wang, J. 2020. Identifying chromosomal introgressions from a wild species Arachis diogoi into interspecific peanut hybrids. Plant Breeding. https://doi.org/10.1111/pbr.12828.
Tishchenko, V., Wang, M.L., Xin, Z., Harrison, M.L. 2020. Development of root phenotyping platforms for identification of root architecture mutations in EMS-induced and Low-path-sequenced Sorghum mutant population. American Journal of Plant Sciences. 11:838-850. https://doi.org/10.4236/ajps.2020.116060.
Zhang, H., Chu, Y., Dang, P.M., Tang, Y., Jiang, T., Clevenger, J.P., Ozias-Akins, P., Holbrook Jr, C.C., Wang, M.L., Campbell, H., Hagan, A., Chen, C. 2020. Identification of QTLs for resistance to leaf spots in cultivated peanut (Arachis hypogaea L.) through GWAS analysis. Theoretical and Applied Genetics. 133:2051-2061. https://doi.org/10.1007/s00122-020-03576-2.
Morris, J.B., Tonnis, B.D., Wang, M.L. 2020. Protein content and seed trait analysis in a subset of the USDA, ARS, PGRCU cowpea [Vigna unguiculata (L.) Walp.] core collection. Legume Research. 43(4):495-500.
Tonnis, B.D., Wang, M.L., Li, X., Wang, J., Puppala, N., Tallury, S.P., Yu, J. 2020. Peanut FAD2 genotype and growing location interactions significantly affect the level of Oleic acid in seeds. Journal of the American Oil Chemists' Society. 97. https://doi.org/10.1002/aocs.12401.
Zhang, H., Wang, M.L., Schaefer, R., Dang, P.M., Jiang, T., Chen, C. 2019. GWAS and co-expression network reveal ionomic variation in cultivated peanut. Journal of Agricultural and Food Chemistry. 63(43)12026-12036. https://doi.org/10.1021/acs.jafc.9b04939.
Dhillon, N., Abu Taher Masud, M., Pruangwitayakun, S., Natheung, M., Lertlam, S., Jarret, R.L. 2020. Evaluation of loofah lines for resistance to Tomato leaf curl New Delhi virus, downy mildew, and key horticultural traits. Agriculture. 10(7):298. https://doi.org/10.3390/agriculture10070298.
Katuuramu, D.N., Wechter, W.P., Washington, M., Horry, M.I., Cutulle, M.A., Jarret, R.L., Levi, A. 2020. Phenotypic diversity for root traits andiIdentification of superior germplasm for root breeding in watermelon. HortScience. 55(8):12-72-1279. https://doi.org/10.21273/HORTSCI15093-20.