Research Project: An Integrated Approach for Plant Genetic Resources Conservation, Characterization, Evaluation, Documentation, and Distribution

Location: Plant Genetic Resources Conservation Unit

2024 Annual Report

Objectives
Objective 1. Optimize and implement best management practices to conserve, maintain, and distribute plant genetic resources and associated descriptive information. Sub-objective 1.A. Optimize and implement best management practices based on the NPGS plan to conserve and maintain more than 100,000 accessions of priority plant genetic resources and their associated information. Sub-objective 1.B. Distribute plant genetic resources and associated information to stakeholders, scientists, plant breeders, and educators. Objective 2. Ensure accessibility, quality, and integrity of plant genetic resources through regeneration and conservation practices. Sub-objective 2.A. Monitor and assess plant genetic resources for viability, trueness to type, vigor, and overall health. Sub-objective 2.B. Conduct field and greenhouse regenerations of priority crops and their wild relatives based on low viability and low seed numbers to replenish and safeguard high quality plant genetic resources. Objective 3. Conduct research to characterize and evaluate plant genetic resources for priority genetic, agronomic, nutritional, and health related traits. Sub-objective 3.A. Characterize plant genetic resources using basic descriptors and other phenotypic data to describe useful agronomic and horticultural traits. Sub-objective 3.B. Evaluate plant genetic resources using physiological, biochemical, and genetic techniques to determine seed quality, tolerances to biotic and abiotic stresses, and variations in nutritional and health related traits.

Approach
This project is part of a comprehensive nationwide program, the National Plant Germplasm System (NPGS), that conserves plant genetic resources for present and future crop improvement and related research activities. The project acquires, conserves, documents, distributes, characterizes, and evaluates the genetic resources of agronomic and horticultural crops including sorghum, peanut, peppers, watermelon, squash, eggplant, okra, sweetpotato, subtropical and tropical legumes, warm-season grasses, cowpeas, annual clovers, various industrial crops, other crops, and their wild relatives. All objectives and sub-objectives are non-hypothesis driven research as the mission is predominantly service oriented providing plant genetic resources and associated information to plant breeders and researchers for use in their scientific efforts. This project focuses on providing high quality, well-documented plant genetic resources and associated information to ARS, university, industry, and other research and education programs worldwide. The project investigators work closely with domestic and international scientists in helping them obtain the appropriate germplasm and information to achieve their research goals. Scientists remain current in all areas of research and education on each specific crop and their wild relatives through involvement with crop-specific Crop Germplasm Committees (CGC) and direct contact with scientists and educators who request plant genetic resources and information.

Progress Report
A large and highly diverse set of plant germplasm was preserved and distributed to scientists and plant breeders. A total of 104,831 accessions of 1,596 plant species representing 269 genera were maintained in the Griffin, Georgia collection. Over 88% of these accessions were available for distribution to users and over 94% were backed up securely at a second location. A total of 39,731 seed and clonal accessions were distributed upon request to scientists and educators worldwide in CY2023. Sorghum, millets, pepper, 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. Regeneration and evaluation activities are listed in detail below. These activities ensure that the crop genetic resources at the Griffin, Georgia location are safeguarded for future use to develop new cultivars and identify novel traits and uses in our food and fiber crops. Regenerations and Acquisitions: A total of 80 okra accessions were regenerated in collaboration with HM Clause; 340 pepper accessions were regenerated in collaboration with Curry Seed and Chile; 100 Citrullus accessions were regenerated in collaboration with Limagrain. A total of 382 cultivated peanut accessions were regenerated in the field and 52 accessions were regenerated in the greenhouse; 48 wild peanut accessions of 19 species were recently regenerated and 250 accessions were planted in the screenhouse and greenhouse for seed increase this year. A total of 96 newly regenerated cowpea accessions and 16 Bambara groundnut were submitted to the seed storage unit for processing; 60 cowpea accessions were sent to St. Croix for seed regeneration; 30 cowpea accessions are being regenerated in collaboration with Texas A&M AgriLife Research and 80 cowpea accessions with the University of Florida. Six new sweet potato accessions were introduced to our collection from Japan A total of 597 sweet potato accessions were maintained clonally; due to mold mite infestation, over 350 accessions have been regenerated from in vivo to in vitro; nine accessions of Ipomoea wild species were regenerated in ARS, St. Croix. Clover, Basella alba, and grass accessions with low seed numbers or low viabilities were successfully rescued and regenerated in a tower hydroponic system. Since castor beans are wind pollinated, they were successfully regenerated using sunn hemp as a buffer. An ARS scientist from USDA-ARS in Lubbock, Texas donated 252 accessions of the ARS Sorghum EMS population to the collection. A total of 988 millets were sent to ARS, St. Croix for regeneration in the fall of 2023, of which 259 were finger millet to be grown under quarantine.

Accomplishments
1. Guar Nutraceutical. Guar is an important food ingredient and has recently been shown to promote gut health due to its nutraceutical content such as guar gum. Some guar plants may contain lower amounts of guar gum in seeds than others, therefore a study was needed to determine the amount of guar gum in different varieties. Ten guar varieties were selected from the USDA, ARS unit's cold storage for evaluation of seed traits and nutraceutical content. Information for percent mannose, galactose, galactomannan, and the mannose to galactose ratio as well as seed and endosperm weight plus years in storage prior to planting were measured. Several guar plants showed higher amounts of guar gum in the seeds than others. These guar types can be used to develop varieties with higher amounts of guar gum in the seeds.

2. Cowpea Genetics and Traits. Cowpea is a dry-land legume used for food and forage in arid and semi-arid areas of the world. Knowledge on the genes and the traits they encode in cowpea are needed to facilitate breeding efforts and optimize germplasm preservation. Genetic tools including Single Nucleotide Polymorphism (SNP) markers and Genotyping by Sequencing (GBS) were used to identify genes associated with useful traits and to understand the genetic structure in cowpea germplasm. Genes responsible for flower color, root nutrients, and environmental stresses were found. This information is useful because it helps other scientists develop new cowpea varieties.

3. Pepper Genetics. Garden pepper is an important and valuable crop in the USA, and elsewhere in the world. Fundamental in efforts to improve this crop is a thorough knowledge and understanding of the genetic basis that accounts for the many traits that contribute to pepper productivity and fruit edibility and desirability such as yield, fruit shape and taste, resistance to diseases and insects. A new and higher quality DNA sequence of the entire pepper genome was published that provides a more detailed analysis of the total genome (genetic makeup) of pepper (several types) than has previously been obtained. This improved DNA sequence was used successfully to classify various types of peppers into distinct groups that permits their classification as an aid to the management of pepper genetic resources. Unique areas within this DNA sequence provided useful information on how the various pepper types evolved and identified areas that are associated with resistance characteristics. This improved DNA sequence, and the tools that will be developed from it, contribute to our ability to understand the basis for the diversity of pepper types and characteristics, thus our ability to develop improved varieties of this important crop.

4. Genome analysis of a native gourd species with potential to contribute to crop improvement. The Okeechobee gourd (Cucurbita okeechobeensis var. okeechobeensis), native to south Florida, is known to contain disease resistance genes that can be transferred to cultivated squash using conventional plant breeding techniques. This gourd species is currently endangered in its natural habitat and may well become extinct before science has an understanding of its genetic diversity and thus its full potential to contribute to crop improvement. This study was undertaken to examine the genome of Okeechobee gourd by sequencing and assembling a reference genome and acquiring related data in order to establish a genomic baseline that can be used in ongoing and future biodiversity and comparative genomic studies with members of this genus. The study resulted in a fully assembled 13-chromosome genome (total length ~ 303 x 106 bp) that is closely related to the genomes of cultivated squash species including summer squash/pumpkin (C. pepo), winter squash (C. maxima) and butternut squash (C. moschata). Approximate 51% of the genome is comprised of repetitive sequences including transposable elements. It is anticipated that the data provided by the current study will be used to estimate the extent of the loss of the genetic diversity of this species and the extent of remaining genetic diversity by examination of additional plant material. As a tool for use in comparative genomic studies, the reference genome will provide a basis for examining the evolution, expression and function of genes within members of this plant family (Cucurbitaceae) that contribute to disease resistance and other traits of agricultural importance.

Review Publications
Morris, J.B., Dierig, D., Heinitz, C.C., Hellier, B.C., Bradley, V., Marek, L. 2023. Vulnerability of U.S. new and industrial crop genetic resources. Industrial Crops and Products. 206. Article 117364. https://doi.org/10.1016/j.indcrop.2023.117364.
Wang, M.L., Tonnis, B.D., Li, X., Benke, R.L., Huang, E., Tallury, S.P., Pupplala, N., Peng, Z., Wang, J. 2024. Genotype, environment, and their interaction effects on peanut seed protein, oil, and fatty acid content variability. Crop Science. pgs. 1-15. https://doi.org/10.1002/agj2.21559.
Zhang, H., Yu, Y., Wang, M.L., Dang, P.M., Chen, C. 2023. Effect of Genotype-by-Environment interaction on oil and oleic fatty acid contents of cultivated peanuts. Horticulturae. 9(12):1242. https://doi.org/10.3390/horticulturae9121272.
Liu, F., Zhao, J., Sun, H., Xiong, C., Sun, X., Wang, X., Wang, Z., Jarret, R.L., Wang, J., Tang, B., Xu, H., Hu, B., Suo, H., Yang, B., Ou, L., Li, X., Zhou, S., Yang, S., Liu, Z., Yuan, F., Pei, Z., Ma, Y., Dai, X., Wu, S., Fei, Z., Zou, X. 2023. Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation. Nature Communications. 14(5487):1-14. https://doi.org/10.1038/s41467-023-41251-4.
Zhang, H., Dean, L.L., Wang, M.L., Dang, P.M., Lamb, M.C., Chen, C.Y. 2023. GWAS with principal component analysis identify QTLs associated with main peanut flavor-related traits. Frontiers in Plant Science. 14. Article 1204415. https://doi.org/10.3389/fpls.2023.1204415.
Wu, X., Vincent, M.N., Lopez-Hernandez, F., Cortes, A.J., Morris, J.B., Wang, M.L., Tallury, S.P., Miller II, M.C., Blair, M.W. 2024. Genetic Diversity and Genome-Wide Association in Cowpeas (Vigna unguiculata L.Walp). Agronomy. 14(5):961. https://doi.org/10.3390/agronomy14050961.
Morris, J.B., Tonnis, B.D., Wang, M.L. 2024. Evaluating galactomannan concentrations in ten Guar (Cyamopsis tetragonoloba (L.) Taub.) genotypes over 2 locations for potential use as a healthy nutraceutical source. Current Topics in Phytochemistry. 19:97-105.
Leal-Bertioli, S.C., De Blas, F., Chavarro, C.M., Simpson, C.E., Valls, J.F., Tallury, S.P., Moretzsohn, M.C., Custodio, A.R., Stalker, H.T., Seijo, G., Bertioli, D.J. 2024. Relationships of the wild peanut species, section Arachis: A resource for botanical classification, crop improvement, and germplasm management. American Journal of Botany. 111. Article e16357. https://doi.org/10.1002/ajb2.16357.
Chae, H., Cantrell, C.L., Khan, I.A., Jarret, R.L., Khan, S.I. 2023. Capsiate-rich fraction of Capsicum annuum induces muscular glucose uptake, ameliorates rosiglitazone-induced adipogenesis, and exhibits activation of NRs regulating multiple signaling pathways. Journal of Agricultural and Food Chemistry. https://doi.org/10.1021/acs.jafc.3c06148?urlappend=%3Fref%3DPDF&jav=VoR&rel=cite-as.
Massa, A.N., Sobolev, V., Faustinelli, P.C., Tallury, S.P., Stalker, T., Lamb, M.C., Arias De Ares, R.S. 2024. Genetic diversity, disease resistance, and environmental adaptation of arachis duranensis L.: new insights from landscape genomics. PLOS ONE. 19(4):Article e0299992. https://doi.org/10.1371/journal.pone.0299992.
George, J., Reddy, G.V., Wadl, P.A., Rutter, W.B., Culbreath, J.R., Lau, P.W., Rashid, T., Allan, M.C., Johanningsmeier, S.D., Nelson, A.M., Wang, M.L., Gubba, A., Ling, K., Meng, Y., Collins, D.J., Ponniah, S.K., Gowda, P.H. 2024. Sustainable Sweetpotato Production in the United States: Current Status, Challenges, and Opportunities. Agronomy Journal. 116(2):630-660. https://doi.org/10.1002/agj2.21539.
Chamberlin K, Tallury S., Volk GM. 2024. Peanut NPGS Germplasm – Smut Resistance. In: Volk GM, Chen K, Byrne P (Eds.) Plant Genetic Resources: Success Stories. Fort Collins, Colorado: Colorado State University. Available from https://colostate.pressbooks.pub/pgrsuccessstories/chapter/peanut-npgs-germplasm-smut-resistance/
Zhang, Y., Zhao, M., Tan, J., Huang, M., Chu, X., Li, Y., Han, X., Fang, T., Tian, Y., Jarret, R.L., Lu, D., Chen, Y., Xue, L., Li, X., Qin, G., Li, B., Sun, Y., Wang Deng, X., Deng, Y., Zhang, X., He, H. 2024. Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding. Nature Genetics. https://doi.org/10.1038/s41588-024-01823-6.
Morris, J.B. 2021. Review of antimicrobial and other health effects in 5 essential oil producing grass species. Journal of Dietary Supplement. pp 1-14. https://doi.org/10.1080/19390211.2021.1944422.
Chen, Y., Xiong, H., Ravelombola, W., Bhattarai, G., Barickman, C., Alatawi, I., Phiri, T.M., Chiwina, K., Mou, B., Tallury, S., Shi, A. 2023. A genome-wide association study reveals region associated with seed protein content in cowpea. Plants. 12(14). Article 2705. https://doi.org/10.3390/plants12142705.
Wang, D., Tian, J., Guan, J., Ding, Y., Wang, M.L., Tonnis, B.D., Liu, J., Huang, Q. 2022. Valorization of sugarcane bagasse for sugar extraction and residue as an adsorbent for pollutant removal. Frontiers in Bioengineering and Biotechnology. https://doi.org/10.3389/fbioe.2022.893941.
Chamberlin, K.D., Bennett, R., Baldessari, J., De La Barrera, G., Cordes, G., Grandon, N.G., Mamani, E., Rodriguez, A.V., Morichetti, S., Holbrook, C.C., Ozias-Akins, P., Chu, Y., Tallury, S.P., Clevenger, J.P., Korani, W., Scheffler, B.E., Youngblood, R., Simpson, S.A. 2024. Discovery of a resistance gene cluster associated with smut resistance in peanut. Peanut Science. 51(1):59-65. https://doi.org/10.3146/0095-3679-51-PS23-6.