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

2021 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
ARS Griffin, Georgia preserved and distributed a large and highly diverse set of plant germplasm to scientists, educators, and plant breeders. A total of 102,245 accessions of 1602 plant species representing 25 genera were maintained in the ARS Griffin, Georgia plant genetic resources collection. Over 86% of these accessions were available for distribution to users and over 94.5% were backed up for security at a second location. A total of 16,275 seed and clonal accessions were distributed by ARS Griffin, Georgia upon request to scientists and educators worldwide between October 1, 2020 and July 14, 2021. Sorghum, cowpea, watermelon, and sesame 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. Fifteen accessions of sweet potato were sent to USDA-ARS, Fort Collins, Colorado for cryopreservation. These activities ensure that the crop genetic resources at the ARS Griffin, Georgia location are safeguarded for future use to develop new cultivars and identify novel traits and uses in our food and fiber crops. Although on site regeneration were greatly reduced at the beginning of 2020, late season plantings and collaborator regenerations led to successful regeneration of many crops including wild peanut (Griffin, Georgia), sorghum and millet (USDA-ARS, Puerto Rico) and vegetable crops (USDA-ARS, Parlier, California; Rijk Zwaan; Vilmoran; HM Clause; Curry Seed and Chile Company and the World Vegetable Center). This season, regenerations planted by ARS scientists at Griffin, Georgia include vegetables (605), peanut (639), miscellaneous crops (11), industrial crops (52), legumes (47), clover (26), grasses (39) and okra (70). Of these, 86 wild peanuts (35 different species) were planted in the greenhouses for replenishment of fresh seeds while 435 cultivated peanuts and 154 cowpeas were planted in field plots for regenerations in Georgia. Another 50 cowpeas were sent for regeneration in St. Croix. A collaborative research project with ARS Griffin, Georgia, Texas A&M University and Texas Tech University on drought tolerance in peanut was completed. Over two crop seasons, twelve interspecific hybrid derived germplasm lines from the national peanut collection along with three peanut cultivars as controls were evaluated under a rainout shelter for drought in Griffin. None of them performed better than the cultivated control peanuts for overall drought tolerance. New funding was obtained from the National Plant Disease Recovery System for a collaborative project between ARS Griffin, Georgia,and the University of Georgia-Tifton to develop molecular diagnostic tools for the detection of peanut clump virus and the Indian peanut clump virus. These diagnostic tools are needed to screen new peanut germplasm entering the country. With partial support from the National Peanut Board, a new collaborative research project was initiated with ARS Griffin, Georgia, USDA, ARS, Stoneville, Mississippi, bioinformatics laboratory and the Hudson Alpha Institute, Huntsville, Alabama, to analyze the wild peanut genome. Increased knowledge of the wild peanut genome will enable peanut breeders to more efficiently cross wild peanut with cultivated peanut. This allows new peanut varieties to be developed with desirable traits originally found in the wild peanut. Collaboration continues between ARS Griffin, Georgia and USDA-ARS, Charleston, South Carolina, to cross wild species related to watermelon with cultivated watermelon species. Wild species provide a unique source of important traits for introduction into cultivated crop species. Large portions of the pepper collection were screened for the presence of Tobamoviruses (ToBRFV) and pospiviroids. The presence of viruses or the lack of knowledge concerning the presence or absence of viruses in germplasm hinders the ability to distribute germplasm and can result in the unintentional distribution of plant pathogens. Collaborative studies continue with Griffin, Georgia and Baylor College of Medicine to use Next Genome Sequencing to define genetic relationships in pepper and to examine evolution in wild pepper species. Information gained will help plant breeders more efficiently make crosses between cultivated and wild pepper with hopes of bringing new traits into the crop. Collaborative efforts to identify and characterize novel uses of capsinoids in pepper are on-going. Capsinoids, the substance that gives peppers their hot pungent flavor, has been shown to be an important nutraceutical compound with many potential health benefits. A nutraceutical and health forage evaluation of several Desmodium species was completed by ARS scientists at Griffin, Georgia in collaboration with Fort. Valley State University. Crude protein levels averaged 23% in two Desmodium species and all Desmodium species had in vitro true digestibility ranging from 80-87%. There were species differences in flavonoid content and high protein precipitable phenolics as well as high total phenolics in one of the species. This encourages the potential use of these Desmoidum species for nutraceutical livestock forages. ARS Griffin, Georgia in collaboration with Tuskegee University, 580 individual peanut seeds were analyzed for fatty acid composition. The overall project goal is to develop genetic tools for peanut breeders to increase the level of the healthy fat, oleic acid, in peanut seeds. ARS scientists at Griffin, Georgia with University of Florida collaborators, measured six peanut lines for protein content as the first step to identify genes for nitrogen-fixation by peanut root nodulation. ARS scientists at Griffin, Georgia in collaboration with USDA-ARS, Tifton, Georgia, 23 breeding lines were analyzed for fatty acid composition. The aim of the project is to develop new peanut cultivars with both improved disease resistance and seed nutrition quality. A total of 50 peanut samples were measured by ARS scientists at Griffin, Georgia for protein content, oil content, fatty acid composition, and sugar content as part of a joint seed sprout project with the University of Georgia. The goal of the project is to develop peanut varieties with improved nutritional properties in sprouted product used for human consumption. Additionally, 18 germplasm accessions (3 accessions x 6 botanical varieties) were planted for two years (2019 and 2020) with two replicates. Protein content, oil content and fatty acid composition were measured in these samples. There are very limited genetic resources for improvement of peanut seed flavors. The goal is to detect genetic variation in flavors among the botanical varieties and provide useful genetic materials to breeders for development of peanut varieties with enhanced flavors.

Accomplishments
1. Pepper genome structure. ARS scientists at Griffin, Georgia, believe knowledge of the genetic relationships among genebank accessions and the genomic structure within the USDA vegetable collections is fundamental to effectively conserve resources and facilitate further utilization and investigation. The genome of Capsicum rhomboideum, an ancestral pepper species, was sequenced and assembled. The results indicate the occurrence of substantial genome reorganization when compared to modern peppers. The results will serve as a basis for further studies on gene and genome evolution in this important crop.

2. Pepper seed health. ARS scientists at Griffin, Georgia, found the provision of healthy seed is an important consideration in genebank operations to reduce or eliminate the unintentional dissemination of seed-borne pathogens. Seed samples of over 3000 genebank accessions of pepper were screened by ARS scientists at Griffin, Georgia, for pospiviroids. Infected seed lots were identified. The information gained will be used to modify current seed distribution policies and regeneration practices.

3. Seed dormancy trait in peanut. ARS scientists at Griffin, Georgia, found seed dormancy is important to prevent peanut seed from sprouting prematurely in their pods before harvest which can affect crop yield. ARS scientists screened a portion of the USDA peanut collection for variation in seed size, shelling percentage, seed quality, and seed dormancy. ARS scientists studied the genetics of the population and compared it to the trait variation to locate and identify genes that code for these traits. Using this powerful technique of trait association, ARS scientists were able to identify several possible candidate genes which may control seed dormancy. Knowledge of these genes help peanut breeders develop peanut varieties with improved seed quality and crop yield.

Review Publications
Dahlberg, J., Harrison, M.L., Upadhyaya, H.D. 2021. Global status of sorghum genetic resources conservation. Book Chapter. pp 43-64. https://doi.org/10.1007/978-981-15-8249-3_3.
Morris, J.B., Wang, M.L., Tonnis, B.D. 2021. Variability for oil, protein, lignan, tocopherol, and fatty acid concentrations in eight sesame (Sesamum indicum L.) genotypes. Industrial Crops and Products. 164:113355. https://doi.org/10.1016/j.indcrop.2021.113355.
Tate, T.M., Mccullough, P.E., Harrison, M.L., Chen, Z., Raymer, P.L. 2021. Characterization of Acetyl Coenzyme A inhibitor resistance in turfgrass and grassy weeds. Crop Science. Special Issue. https://doi.org/10.1002/csc2.20511.
Da Silva Ledo, A., Do Amaral, A., Jenderek, M.M., Harrison, M.L., Manter, D.K. 2020. Sterilization procedures and Plant Preservative Mixture on in vitro establishment of Miscanthus sinensis Anderson. Plant Cell Culture & Micropropagation. 15(2):27-32. https://doi.org//10.46526/pccm.2019.v15i2.139.
Bennett, R., Harting, A.D., Simpson, C.E., Tallury, S.P., Pickering, A.B., Wang, N., Dunne, J.C. 2021. A note on a Greenhouse evaluation of wild Arachis species for resistance to Athelia rolfsii. Peanut Science. 48(1):40-48. https://doi.org/10.3146/PS20-21.1.
Zhang, H., Wang, M.L., Dang, P.M., Jiang, T., Zhao, S., Lamb, M.C., Chen, C.Y. 2020. Identification of potential QTLs and genes associated with seed composition traits in peanut (Arachis hypogaea L.) using GWAS and RNA-Seq analysis. Gene. 769:145215. https://doi.org/10.1016/j.gene.2020.145215.
He, S., Tang, C., Wang, M.L., Li, S., Diallo, B., Xu, Y., Zhou, F., Sun, L., Shi, W., Xie, G. 2020. Combining ability of cytoplasmic male sterility on yield and agronomic traits of sorghum for grain and biomass dual-purpose use. Industrial Crops and Products. 157:112894. https://doi.org/10.1016/j.indcrop.2020.112894.
Zhang, H., Goettel, W., Song, Q., Jiang, H., Hu, Z., Wang, M.L., An, Y. 2020. Selection of GmSWEET39 for oil and protein improvement in soybean. PLoS Genetics. 16(11).e1009114. https://doi.org/10.1371/journal.pgen.1009114.
Lovell, J.T., MacQueen, A.H., Mamidi, S., Bonnette, J., Jenkins, J., Napier, J.D., Sreedasyam, A., Healey, A., Session, A., Shu, S., Barry, K., Bonos, S., Boston, L., Daum, C., Deshpande, S., Ewing, A., Grabowski, P., Haque, T., Harrison, M.L., Jiang, J., Kudrna, D., Lipzen, A., Pendergast IV, T.H., Plott, C., Qi, P., Saski, C.A., Shakirov, E., Sims, D., Sharma, M., Sharma, R., Stewart, A., Singan, V., Tang, Y., Thibivillier, S., Webber, J., Weng, X., Williams, M., Wu, A., Yoshinaga, Y., Zane, M., Zhang, L., Zhang, J., Behrman, K.D., Boe, A.R., Fay, P.A., Fritschi, F.B., Jastro, J.D., Lloyd-Reilley, J., Martinez-Reyna, J., Matamala, R., Mitchell, R., Rouquette Jr., F.M., Ronald, P., Saha, M., Tobias, C.M., Udvardi, M., Wing, R., Wu, Y., Bartley, L.E., Casler, M.D., Devos, K.M., Lowry, D.B., Rokhsar, D., Grimwood, J., Juenger, T.E., Schmutz, J. 2021. Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass. Nature Genetics. 590:438-444. https://doi.org/10.1038/s41586-020-03127-1.