Source: CLEMSON UNIVERSITY submitted to NRP
PLANT GENETIC RESOURCES CONSERVATION AND UTILIZATION
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
1016646
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
S-OLD 9
Project Start Date
Oct 1, 2018
Project End Date
Sep 30, 2023
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
CLEMSON UNIVERSITY
(N/A)
CLEMSON,SC 29634
Performing Department
Plant & Environmental Sciences
Non Technical Summary
Natural genetic variation of plants grown around the world has provided the mechanism to allow them to adapt and grow in various ecosystems and under various environmental and stress conditions. Hence, this biodiversity provides a wealth of traits for numerous plants of value. Modern crop varieties have been bred for a limited number of traits, which has resulted in relatively narrow gene pools being utilized. As environmental changes and stress situations create new pressures on plant growth and productivity, the genetic diversity available from plant accessions worldwide offers a wealth of traits that could be utilized by breeders, growers and plant scientists. Molecular and quantitative methods linking breeding, genetics, genomics, biochemistry and physiology will be used to discover new and useful variation in crop plants of importance to the southeastern U.S. This variation will be isolated, characterized and integrated into breeding programs.
Animal Health Component
50%
Research Effort Categories
Basic
50%
Applied
50%
Developmental
0%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2021599108034%
2011520108133%
2011542108133%
Knowledge Area
202 - Plant Genetic Resources; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1520 - Grain sorghum; 1542 - Soft red wheat; 1599 - Grain crops, general/other;

Field Of Science
1081 - Breeding; 1080 - Genetics;
Goals / Objectives
Conduct genetic characterizations and phenotypic evaluations of the conserved crops and related wild species for commercially important genetic and agronomic traits Distribute genetic resources and associated information to researchers, educators, and plant breeders in the Southern Region and worldwide S-009 was established in 1949 to enable federal and state cooperators to participate in coordinated efforts to acquire, regenerate, maintain, characterize, evaluate, document, distribute, and utilize plant genetic resources of value to agriculture. Plant genetic resources are the building blocks of genetic variability upon which scientists conduct research and develop improved cultivars and products. S-009 germplasm has been utilized in research resulting in hundreds of publications and numerous crop cultivars. This project has grown from 811 accessions of 41 genera in 1949 to one of the largest collection of the four NPGS regional multistate projects with 99,414 accessions of 263 genera and 1601 species in 2018. Over 84% of S-009 accessions are available for distribution and over 95% are safely backed up at Ft. Collins, CO (Appendix 1, Table 1). Intervals between seed regenerations are maximized to reduce loss of valuable genetic variability by storing 88% of the accessions in -18oC rather than 4oC (Appendix 1, Table 2). Requestors each year use these genetic resources in plant breeding, plant pathology, entomology, molecular biology, genomics, archaeology, anthropology, crop management, ecology, medical, and alternative uses. This project has had numerous impacts on research progress, agricultural productivity, and public benefits. For example, a peanut accession (PI 203396) collected in 1952 from a Porto Alegre, Brazil, market has resistance to a major peanut disease, tomato spotted wilt virus. Resistance from this single accession has been bred into 24 peanut cultivars including the five cultivars currently dominating the Southeastern U.S. peanut acreage for an estimated economic return of $200 million per year. The new project will continue to provide plant genetic resources and information to scientists for research, education, and extension programs in the region, the nation, and the world. The conservation of plant genetic resources is essential to safely preserve and have available for research the genetic diversity vital for global food security. Plant genetic diversity provides breeders the material to develop and select cultivars for increased production, improved quality, and resistance to biotic and abiotic stresses. Global food security depends on the extent to which genetic improvement of crops can meet the challenges of population increases, climate change, sustainability, increasing crop production, and reduced environmental resources (Ronald, 2011; Upadhyaya et al., 2011; Pautasso, 2012). The Plant Genetic Resources Conservation Unit (PGRCU)/S-009 Multistate Project at Griffin is one of 29 seed and clonal germplasm repositories in the NPGS. The National Laboratory for Genetic Resources Preservation stores reserve seed of accessions for the other repositories. The NPGS repositories, as well as germplasm repositories in other countries and international centers, have long preserved plant genetic resources for use by present and future researchers throughout the world (Fowler and Hodgkin, 2004). Presently, the NPGS preserves almost 587,229 accessions (USDA, ARS, 2018). Plant genetic resource collections worldwide consist of a wide range of material with no selection or different levels of selection or development. These collections may include crop wild relatives (CWR), primitive landraces, farmer selections, breeding lines, heirloom varieties, pure lines, germplasm, genetic stocks, and current cultivars. The goal of germplasm collections is to preserve the genetic diversity found in all species (Nelson, 2011). The S-009 Multistate project strives to conserve the range of genetic variation and diversity located within each plant species maintained at this location. This project is one of four regionally-based multistate projects, cooperating with USDA, ARS Units at each location, charged with the acquisition, characterization, maintenance, evaluation, documentation, and distribution of agronomic and horticultural crops in the U.S. Crops are divided among the four projects to prevent duplication of effort. These projects include NE-009 at Geneva, NY; NC-007 at Ames, IA; and W-006 at Pullman, WA. Techniques and procedures for plant genetic resource conservation and collection backup are coordinated with ARS projects at the National Laboratory for Genetic Resources Preservation, Ft. Collins, CO. Acquisition of new accessions and documentation efforts are coordinated with ARS projects at Beltsville, MD. Regeneration of sorghum and other photoperiod-sensitive crops is cooperative with ARS projects at Mayagÿ¼ez, PR. Being a collaborative project, both the USDA and the S-009 Regional Project provide funding for scientific, technical and administrative staff. Both entities also provide funding for supplies related to germplasm preservation, maintenance, distribution, regeneration, and characterization. PGRCU is located on the University of Georgia-Griffin Campus and is housed in both federal and state owned buildings.
Project Methods
A variety of different approaches will be taken, depending on the specific goal of each project.1. Individual accessions or multiple accessions (such as diversity panels) may be grown in the field for various phenotypic measurements, such as height, seed yield, biomass yield, chemical composition, biotic and abiotic stress resistance.2. Tissue culture or in vitro approaches may be taken to develop propagation methods for recalcitrant genotypes or to mass propagate specific genotypes, and/or to develop genetic engineering protocols. The development of tissue culture protocols is based on surveys of the current literature for input on the types of growth media, plant growth regulators, culture conditions and plant explant sources to be used.3. Molecular and genetic analyses to assess gene transcripts, genetic variation and protein variants may utilize a variety of techniques for RNA and DNA isolations, protein extractions, cDNA library syntheses, probe production and hybridizations, whole genome sequencing and genotyping-by-sequencing. In addition, equipment and the associated use protocols for specialized process such as protein electrophoresis, real time PCR, DNA sequencing and polymorphism analysis are available, and are used as the basis for further modifications in protocols as required.4. Chemical analyses to assess specific metabolite profiles or compositional phenotypes may utilize analytical methods such as NIR, GC/MS and LC/MS methodologies.5. Molecular and chemical analyses may utilize computational and/or bioinformatics resources to compare/contrast big data signatures across different genotypes, developmental and growth time points.

Progress 10/01/19 to 09/30/20

Outputs
Target Audience:Agricultural researchers, plant scientists, professional breeders, backyard breeders, agricultural stakeholders, educators and their students, government officials, and the general public. Changes/Problems:Changes Dr. Richard Boyles: While the ramifications of the COVID-19 pandemic has undoubtedly alteredoperations of the research program, essential breeding and other applied research activities have been maintained. Dr. Sachin Rustgi: Unavailability of funds for traveling making it challenging to attend the annual project meeting and also to present the results in national/international conferences. What opportunities for training and professional development has the project provided?Training and professional development opportunities Dr. Sachin Rustgi: This project allowed the training of an undergraduate student, Ms. Rachael Kerr of Francis Marion University in Florence, SC, and four graduate students - Mr. Tariq Alam, Mr. Salman Naveed, Mr. Samneet Kashyap, and Mr. Jonathan Windham of Clemson University. We provided updates at the 4th CRISPR AgBio Congress and the Annual Meeting of the Crop Science Society of America. We also spoke to the students and interested researchers via delivering lectures at the Newman Seminar and Lecture Series in Natural Resources Engineering in the Clemson University Department of Agricultural Sciences, Recent Trends in Biological Sciences lecture series of the Post Graduate Department of Botany at Vimala College, and Plant Breeding (PES 4050/6050) and Agricultural Biotechnology (PES 3350) courses at Clemson University, and to the producers via delivering a talk at the Pee Dee Res. and Edu. Center Field Day. How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals?Dr. Sachin Rustgi: We will continue to analyze the wheat landraces for their gluten content and composition and identify genotypes with reduced content of immunogenic gliadins, and screen peanut genotypes for the high- and low-expression alleles of the Fatty acid desaturase (FAD) genes as a surrogate for heat-tolerance.

Impacts
What was accomplished under these goals? Characterization of Fusarium grain mold resistance within the Sorghum Association Panel The sorghum association panel (SAP), a collection of 400 accessions representing global sorghum diversity, was evaluated for grain mold resistance in a replicated field design under inoculated conditionsfor two years at the Pee Dee Research and Education Center in Florence, SC. Measurement of fumonisin content, the toxin produced by Fusarium verticillioides, for each accession is near completion using established ELISA protocols. Sources of resistance has been either confirmed or identified across the panel. Metabolomics analysis has identified secondary metabolites with differential concentration between the resistant and susceptible check in the study. Identification of sorghum hybrids that thrive in organic cropping systems Funded by USDA NIFA OREI project 2018-51300-28431, two-year certified organic on-farm data from multiple locations reveal that sugarcane aphid tolerant sorghum hybrids significantly outyield susceptible hybrids and inbreds. There were significant grain nutritional quality differences across the 150 genotypes included in the field study. Sources of aphid tolerance that were well adapted to organic, low input management practices are currently being increased for final evaluation and release for commercial use and marketing. The S-009 Multistate Hatch project has enabled reliable seed sources from genetically diverse sorghum germplasm provided by the Plant Genetic Resources Conservation Unit. Targeting sorghum traits associated with the drought stress response This 2-yr research project screened more than 700 sorghum hybrids and 400 inbred lines in the field in year 1 to identify genotype extremes for water-use efficiency under natural intermittent drought conditions. In year 2, we measured grain yield performance of the 46 extreme genotypes (34 high WUE and 14 low WUE) selected in year 1 under both irrigated and dryland conditions to compare yield change across water input. A subset of 16 of these 46 genotypes were also grown under controlled greenhouse conditions to measure individual yield components and other fitness traits such as pollen volume between water treatments (intermittent drought and well-watered). Determining the genetic underpinnings of heterosis in grain sorghum A project funded by the DOE ARPA-e TERRA program has agoal of establishing integrated, real-time phenotyping and analysis of above- and below-ground plant architecture and total carbon partitioning and allocation to predict heterosis and develop superior crop hybrids by fully leveraging the sorghum gene pool. A total of 700 unique hybrids were developed from crossing 350 male parents (~300 lines within the SAP) to two elite female lines. Again, more than 300 accessions were requested from the S-009 Plant Genetic Resources Conservation Unit to serve as the germplasm base for this study. Quantitative/Qualitative differences in protein profiles of wheat landraces This study's objective was to identify reduced-immunogenicity genotypes among the wheat landraces collected from different high-altitude regions of the word. For this purpose, the seeds of these landraces were procured from the National Small Grains Collection (NSGC).Thirty-four wheat landraces were tested for their protein profiles using SDS-PAGE-based densitometric analysis. Gluten-banding patterns from the genotypes of a landrace or across landraces were compared, and the mutant types were identified. Mutants with different missing gluten proteins were selected for the genetic crossing to stack their effects on gluten content in a single genotype. The differences in the banding pattern observed in these genotypes were divided into two categories: qualitative differences and quantitative differences. The deficiency of a protein subunit (qualitative differences) was determined by comparing the protein profile of different genotypes of a landrace (analyzed three to four half-seeds per landrace). Different seeds analyzed from a landrace exhibited differences in the quantities of corresponding protein bands. Not to our surprise, some genotypes showed reduced accumulation of one gluten protein subfamily and over-accumulation of another subfamily upon loading equal amounts of gliadins/glutenins from different genotypes onto a gel. Altogether, eight (23.5%) out of 34 landraces showed differential accumulation of proteins when three-four seeds of each landrace were tested. It suggested the presence of different gluten genotypes in such landraces. In some instances, up to three different genotypes (based on protein profiles) were observed out of the four seeds tested for a landrace. Among these eight landraces, three landraces have genotypes that specifically showed a reduction in the content of gliadins, two in glutenins, and three in both gliadins and glutenins. When comparisons were made across landraces using an arbitrary meta-reference (a gliadin/glutenin profile with all bands observed in studied landraces), 16 (47%) out of 34 landraces showed a deficiency of one or more protein bands. Among the 16 landraces, seven landraces have genotypes that specifically show missing glutenin bands, four showed missing gliadins bands, and the remaining five landraces showed missing glutenin and gliadin bands. Precisely, out of these 16 landraces, ten showed deficiency in one or more of the ω-gliadins (including D-type ω-gliadins), four in LMW-glutenin subunits, three each in a/b- and g-gliadins, and two in HMW glutenin subunits. Protein and expression profiles of the soybean varieties, breeding lines and fatty acid desaturase (FAD) mutants An attempt was made to examine the seed protein content and compositions ofsoybean genotypes (soybean varieties, breeding lines, and fatty acid desaturase mutants) with variable response to heat stress, and some with known differences in lipid content and compositions. For this purpose, thetotal protein extracted from the seed of wild type soybean genotype 'Williams 82' (PI 518671), other contemporary soybean varieties, such as 'Osage' and 'Dare,' a heat-tolerant (DS25-1) and a heat susceptible (DT97-4290) soybean genotype, three soybean breeding liens NO-7432, S11-21092, and M92-220, fast neutron mutations, and the double, triple and quadruple soybeanFADgene mutants. Interestingly, a triple FAD gene mutant (FAD2-1A,FAD2-1B, andFAD3Anull), S17CR-180 MO, showed a distinct protein profile than the wild type 'Williams 82.' Total RNA was also extracted from the leaf samples collected from the wild type 'Williams 82' (PI 518671) and M92-220, and the double, triple and quadruple soybeanFADmutants exposed to heat stress (for 15 days after 15 days of growth in optimal conditions) and the plants that were kept at optimal day/night growth temperature all through. Samples for RNA extraction were collected at two-time points, on the 7th day of heat stress treatment and the 15th day of heat stress treatment. Leafsamples from five plants of each genotype were collected to serve as biological replicates in this experiment. RNA was extractedwhich is currently being used to perform the quantitative RT-PCR with the soybean FAD genes inFAD3A,FAD3B,FAD3C,FAD2-1A,andFAD2-1Bmutants. Expression profiles of the peanut mini-core collection for high- and low-expression alleles of the FAD genes 104 genotypes of the peanut mini-core collection were used. Six seeds per genotype were germinated. After 7 d at 30/25ºC (day/night) temperature and 16/8 hr (day/night) photoperiod (optimal growth conditions), half of the plants will be exposed to heat stress 38/28ºC for two weeks. On the 11th day of the heat stress, the two leaflets from each plant will be collected for expression analysis with the peanutFAD2-1,FAD2-2,FAD6,FAD3-1,FAD3-2,FAD7-1, andFAD7-2gene-specific primers.

Publications

  • Type: Journal Articles Status: Accepted Year Published: 2021 Citation: Disharoon A, Boyles R, Jordan K, Kresovich S (2020) Exploring diverse sorghum sorghum [Sorghum bicolor (L.) Moench] accessions for malt amylase activity. J Inst Brewing. Accepted.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2020 Citation: Shields L, Gang Y, Jordan K, Sapkota S, Boatwright J, Jiang X, Kresovich S, Boyles R*. (2020), Genome?wide association studies of antimicrobial activity in global sorghum [Sorghum bicolor (L.) Moench]. Crop Sci. In press. doi:10.1002/csc2.20348
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2020 Citation: Ibrahim A, Sutton R, Johnson J, Mergoum M, Simoneaux B, Harrison S, Murphy J, Mason R, Babar A, Neely C, Opena G, Jin Y, Kolmer J, Boyles R, Cambron S, Baik B-K, Brown-Guedira G, Marshall D, Fountain M. (2020) Registration of GA06343-13E2 (TX-EL2) soft red winter wheat. J Plant Registr. In press.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Sapkota S, Boyles R, Cooper E, Brenton Z, Myers M, Kresovich S (2020) Multi-trait regressor stacking increased genomic prediction accuracy of sorghum grain composition. Agronomy 10:1221. doi:10.3390/agronomy10091221
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Brenton Z, Cooper E, Myers M, Jordan K, Glaubitz J, Boyles R, Kresovich S (2020) Identification of sorghum-specific duplication event controlling sugar accumulation. G3: Genes | Genomes | Genetics. doi:10.1534/g3.119.400921
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Sapkota S, Boatwright J, Jordan K, Boyles R, Kresovich S (2020) Impact of sorghum racial structure and diversity on genomic prediction of grain yield components. Crop Sci 60:132-148. doi:10.2135/cropsci2019.04.0221.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2020 Citation: Lwe ZSZ, Welti R, Anco D, Naveed S, Rustgi S, Narayanan S (2020) Heat stress elicits remodeling in the anther lipidome of peanut. Scientific Reports (in press)
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Yang MM, Wang X, Dong J, Zhao W, Alam T, Thomashow LS, Weller DM, Gao X, Rustgi S, Wen S (2020) Proteomics reveals the changes that contribute to Fusarium head blight resistance in wheat. Phytopathology https://doi.org/10.1094/PHYTO-05-20-0171-R
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Rustgi S, Brouwer B, von Wettstein D, Reisenauer PE, Lyon S, Ankrah N, Jones S, Guy SO, Chen X (2020) Registration of Fritz, a two-row spring barley. Journal of Plant Registrations 14:242-249.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Alam T, Rustgi S (2020) Organic management of bacterial wilt of tomato and potato caused by Ralstonia solanacearum. eOrganic https://eorganic.org/node/34193
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Alam T, Anco DJ, Rustgi S (2020) Management of aflatoxins in peanuts. Clemson University Land-Grant Press LGP 1073. https://doi.org/10.34068/report7
  • Type: Books Status: Awaiting Publication Year Published: 2020 Citation: Windham J, Sharma S, Kashyap MK, Rustgi S (2020) CRISPR/Cas12a (Cpf1) and its role in plant genome editing. In: G. Tang, S. Teotia, X. Tang, D. Singh (Eds.), RNA-based technologies for functional genomics in plants. Springer Nature (in press)
  • Type: Books Status: Awaiting Publication Year Published: 2020 Citation: Rustgi S, Kashyap S, Deleu LJ, Delcour J (2020) Reduced-immunogenicity wheat now coming to age. In: Wani SH, Mohan A, Singh GP (eds) Physiological, Molecular, and Genetic perspectives of Wheat Improvement. Springer Nature (in press)
  • Type: Book Chapters Status: Accepted Year Published: 2020 Citation: Rustgi S, Kashyap S, Ankrah N, von Wettstein D (2020) Use of microspore-derived calli as explants for biolistic transformation of common wheat. In: S. Rustgi, H. Luo (Eds.), Biolistic DNA delivery in plants. Springer Nature, New York, NY. pp 263-279.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Narayanan S, Zoong-Lwe ZS, Gandhi N, Welti R, Fallen B, Smith JR, Rustgi S (2020) Comparative lipidomic analysis reveals heat stress responses of two soybean genotypes differing in temperature sensitivity. Plants 9:457.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Osorio CE, Wen N, Mejias JH, Mitchell S, von Wettstein D, Rustgi S (2020) Directed-mutagenesis of Flavobacterium meningosepticum prolyl-oligopeptidase and a glutamine-specific endopeptidase from barley. Frontiers in Nutrition 7:11.
  • Type: Book Chapters Status: Published Year Published: 2020 Citation: M, Liu Y, Dong J, Zhao W, Kashyap S, Gao X, Rustgi S, Wen S (2020) Probing early wheat grain development via transcriptomic and proteomic approaches. Functional & Integrative Genomics 20:63-74.
  • Type: Book Chapters Status: Published Year Published: 2020 Citation: Rustgi S, Luo H (2020) Biolistic DNA delivery in plants. Springer Nature, New York, NY. Pp. 334.
  • Type: Books Status: Awaiting Publication Year Published: 2020 Citation: Rustgi S, Naveed S, Prasanna S (2020) Advances in understanding the genetics of the nutritional properties of cereals particularly maize and oat proteins. In: T. Beta (Ed.), Improving the nutritional and nutraceutical properties of wheat and other cereals. Burleigh Dodds Science Publishing (in press)
  • Type: Book Chapters Status: Published Year Published: 2020 Citation: Rustgi S, Skadhauge B (2020) Diter von Wettstein, Professor of genetics and master of translating science into applications. In: S. Rustgi, H. Luo (Eds.), Biolistic DNA delivery in plants. Springer Nature, New York, NY. pp 3-18.
  • Type: Book Chapters Status: Published Year Published: 2020 Citation: Rustgi S, Shewry P, Brouns F (2020) Health hazards associated with gluten consumption in susceptible individuals and current status of research on the dietary therapies, In: Igrejas G, Ikeda TM, Guzm�n C (Eds.), Wheat Quality for Improving Processing and Human Health, Springer, Cham. pp. 471-515.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Boyles R. Improving grain production of sorghum. Pee Dee REC 2020 Virtual Field Day (September 3, 2020). www.clemson.edu/cafls/research/fieldday/ (www.youtube.com/watch?v=oBkOX34Z62Q)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Boyles R. Targeting sorghum traits underlying water use efficiency to mitigate intermittent drought on marginal soils. US Department of Energy Sorghum Annual Meeting, Colorado State University, Fort Collins, CO (January 27, 2020).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Boyles R. Targeting traits associated with the drought stress response to breed grain crops with increased water use efficiency and productivity for SC growers. PSA Water Research Symposium, Clemson Public Service and Agriculture, Clemson McKissick Center, Clemson, SC (January 13, 2020).
  • Type: Conference Papers and Presentations Status: Awaiting Publication Year Published: 2021 Citation: Rustgi S (2021) "Developing genome editing reagents and fungal management strategies for peach," Peach Educational Sessions at the Southeast Regional Fruit and Vegetable Conference, Savannah, GA (January 8-9, 2021).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Rustgi S (2020) "Next-generation plant breeding and management strategies to develop safe and surplus crops," Workshop B, How to Establish a Presence in the CRISPR Space, 4th CRISPR AgBio Congress, online event (December 1-3, 2020).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Rustgi S (2020) "Next-generation management and breeding practices for sustainable crop production." Newman Seminar and Lecture Series in Natural Resources Engineering, Department of Agricultural Sciences, Clemson University (October 30, 2020).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Zoong-Lwe ZS, Narayanan S, Welti R, Rustgi S (2020) Peanut plants adjust their anther lipid biosynthesis pathway in response to heat stress. Annual meeting of the Crop Science Society of America, online event (November 8-11, 2020).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Rustgi S, Alam T, Kashyap S, Naveed S, Jones Z, Kerr R (2020) Crafting of reduced-immunogenicity wheat and peanut lines to ensure safe food supply to people suffering from foodborne disorders. Annual meeting of the Crop Science Society of America, online event (November 8-11, 2020).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Rustgi S (2020) 'Applying new-breeding technologies towards the goal of attaining sustainable agriculture' Guest lecture in the PES 3350, "Agricultural Biotechnology," Clemson University, Clemson SC (November 24, 2020).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Rustgi S (2020) "Novel strategies to develop crops and management strategies to meet the growing demand for food and fiber," Recent Trends in Biological Sciences lecture series of the Post Graduate Department of Botany, Vimala College, Kerala, India (September 29, 2020).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Rustgi S (2020) "New-breeding technologies (NBTs)-assisted development of non-immunogenic crops with sustained yields and environment-friendly pesticides," Pee Dee Research & Education Center Field Day, Florence SC (September 3, 2020).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Rustgi S (2020) "Contemporary Plant Breeding;" Guest lecture in the PES 4050/6050 Plant Breeding course, Clemson University, Clemson SC (April 9, 2020).
  • Type: Websites Status: Published Year Published: 2020 Citation: Boyles R. Cereal Grains Breeding and Genetics Program. https://www.clemson.edu/cafls/research/peedee/breeding_genetic.html
  • Type: Websites Status: Published Year Published: 2020 Citation: Lawrence T, Boyles R, Thavarajah D. USDA OREI Project Website. https://www.clemson.edu/cafls/organic-breeding/orei/index.html
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Sapkota S, Boatwright JL, Boyles R, Kresovich S. Genome-wide prediction, association, and gene network analysis of grain composition in sorghum. Plant and Animal Genome Conference XXVIII, Scherago International, Town and Country Hotel, San Diego, CA (January 13, 2020).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Park W, Boyles R, Ye R, Chong J, Martin S (12 Nov 2019) Developing canola germplasm in the Southeast region. ASA, CSSA, and SSSA annual meetings, San Antonio, TX.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Park W, Chong J, Riddle J, Ye R, Boyles R, Stancil B, Campbell B, Ro K, Dant L, Martin S, Ray C, Smith M (12 Nov 2019) Characterization of oilseed rape varieties for cool season germplasm development in the Southeast region. ASA, CSSA, and SSSA annual meetings, San Antonio, TX.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Zoong-Lwe ZS, Narayanan S, Welti R, Rustgi S (2020) Peanut plants adjust their anther lipid biosynthesis pathway in response to heat stress. Annual meeting of the Crop Science Society of America, November 8-11, 2020, Phenix, Arizona.
  • Type: Conference Papers and Presentations Status: Awaiting Publication Year Published: 2021 Citation: Alam T, Kerr R, Gandhi N, and Rustgi S (2020) Crafting reduced-immunogenicity peanut genotypes for peanut-allergic individuals. 3rd International Conference on Food Bioactives & Health, June 16-19, 2020, Parma, Italy. (now, postponed until restrictions lift)


Progress 10/01/18 to 09/30/19

Outputs
Target Audience:Agricultural researchers, plant scientists, professional breeders, backyard breeders, agricultural stakeholders, educators and their students, government officials, and the general public. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project allowed training of an undergraduate student, Ms. Rachael Kerr of Francis Marion University in Florence, SC, and three graduate students - Mr. Gregory Hoover, Mr. Salman Naveed, and Mr. Samneet Kashyap of Clemson University. How have the results been disseminated to communities of interest?We provide updates at the Plant and Animal Genome annual meeting, the Crop Science of America annual meeting, and the Sorghum Improvement Conference of North America. We also speak to relevant commodity groups interested in southeastern feed grains as well as the National Sorghum Producers/The United Sorghum Check-off Program (Lubbock). We also gavepresentations to the South Carolina Department of Agriculture for sorghum production and the development of heirloom crops for niche markets. What do you plan to do during the next reporting period to accomplish the goals?We will analyze the wheat landraces collected from different parts of the world for their gluten composition and identify genotypes with reduced content of immunogenic gliadin proteins. The genotypes characterized to carry reduced-immunogenicity will be used in genetic crossing to pyramid the effect by genetic crossing. We would screen the peanut germplasm for the high- and low-expression alleles of the Fatty acid desaturase (FAD) genes as a surrogate for heat-tolerance.

Impacts
What was accomplished under these goals? Scientific Accomplishments by Scientist Dr. Sachin Rustgi Analysis of total seed-storage protein from the ICRISAT mini-core collection.In addition to the U.S. peanut mini-core collection, a set of 93 non-redundant genotypes of the ICRISAT (International Crops Research Institute for the Semi-Arid Tropics) mini-core collection was procured and analyzed for the seed storage protein content and composition. For this purpose, the total seed storage protein from each accession was extracted and quantified using Bradford assay and resolved on the polyacrylamide gels. Ten of 93 genotypes showed reduced arachin content, especially in the atomic mass range of the major immunogenic arachin proteins (Ara h1, Ara h2, Ara h3, and Ara h6). The selected peanut genotypes also exhibited variations in their grain morphologies. The seed storage proteins from two selected reduced-arachin peanut genotypes (A. diogoi'GK10602' andA. hypogaea'PI664994'), and a large-seeded Virginia-type peanut cultivar 'Gregory' were analyzed using HPLC. Both GK10602 and PI664994 showed significant reductions in their arachin contents in comparison to 'Gregory.' Genetic analysis of the reduced arachin peanut genotypes using DNA sequencing.Genomic DNA from the selected genotypes of the USDA mini-core collection with reduced-arachin content (PI 152146, PI 157542, PI 196622, PI 259658, PI 259836, and PI 496401) and wild type protein profile (PI 196635) was amplified using theAra h1,Ara h2,Ara h3, andAra h6specific primers. The PCR products amplified using these primers were sequenced via Sanger sequencing to determine if the absence of a specific arachin protein in selected genotypes is due to a sequence variation within the structural genes encoding specific arachins. Interestingly, in genotypes PI 259658, PI 259836, and PI 496401, the sequence variations corresponded with the lack of the specific arachin proteins. Additionally, we obtained detailed genomic information (13,527 DNA markers) on 106 peanut genotypes of the USDA mini-core collection. This information will be used to map the reduced allergenicity trait to the peanut chromosomes with an expectation to identify master regulator(s) of the arachin genes and to breed non-immunogenic peanut genotypes. The former approach (sequencing of gene-fragments) will allow mapping of theciseffects, i.e., the structural defects in the arachins genes or associated promoters. Whereas, the second approach will map thetranseffects (away from the arachin gene), which are responsible for the lack of arachins in peanut seeds. Transfer of reduced allergenicity trait to elite peanut germplasm.A. diogoiaccession GK 10602 bears an impressive protein profile lacking several of the immunogenic arachins. Therefore, to transfer this trait from wild to cultivated peanuts, crosses were made betweenA. hypogaeacv. Gregory and GK 10602 (courtesy Dr. S. Tallury). The interspecific hybrid population derived from this genetic cross was later screened for phenotypic attributes and the seed protein composition. A few progeny plants resemblingA. hypogaeain phenotypic characteristics and their protein composition to GK 10602 were identified. And these selected progeny plants will be used to cross with other reduced-arachin peanut genotypes earlier identified by us. Screening of peanut germplasm for mutations in theFAD2AandFAD2Bgenes.The peanut genotypes of the USDA mini-core collection were also screened for alleles at theFatty Acid Desaturation 2(FAD2) loci.A. hypogaeapossess two copies of theFAD2gene, one each on A and B subgenomes. Mutations in theFAD2genes result in high oleic acid to linoleic acid ratio. Natural mutations in theFAD2BandFAD2Agenes were identified in 18 of 66 (27.3%), and 44 of 102 (43.1%) analyzed peanut genotypes, respectively. Six genotypes carried mutations in bothFAD2AandFAD2Bgenes. Among the genotypes exclusively carrying mutations in theFAD2AandFAD2Bgene, 13 and 1 genotypes, respectively, also exhibited reduced-arachin content. Interestingly, two peanut genotypes carried mutations in bothFAD2AandFAD2Bgene and also showed a deficiency in the arachin content. Dr. Richard Boyles Characterization of Fusarium grain mold resistance within the Sorghum Association Panel The entire SAP, consisting of approximately 400 accessions representing global sorghum diversity, is has been evaluated under inoculated field conditions in two years (2017 and 2019) at the Pee Dee Research and Education Center in Florence, SC. Host plant resistance is being measured for individual accessions using panicle grain mold severity ratings and grain toxin levels with established ELISA protocols. Sources of resistance has been either confirmed or identified across the panel. Genetic mapping is underway to identify quantitative trait loci and candidate genes associated with Fusarium grain mold resistance. Metabolomics analysis is also in progress to target individual secondary metabolites underlying the physiological plant defense mechanisms. Evaluating sorghum as a potential value-added crop in organic cropping systems The project will address critical SC agriculture stakeholder needs including (1) production system issues, (2) nutritional quality and grading, (3) marketing and trade, and (4) current public research availability. Development of nutritionally enhanced, sustainable crop varieties/hybrids optimized for organic cropping systems will provide economic benefits to suppliers, producers, processors, end-users, and consumers as well as offer more sustainable food and feed production to reduce statewide degradation to valuable farmland. While this work is predominantly funded by USDA NIFA OREI project 2018-51300-28431, support has come from the S-009 Multistate Hatch project in the form of previously increased seed of sorghum accessions initially provided by the Plant Genetic Resources Conservation Unit. Targeting sorghum traits associated with the drought stress response This research project aims to identify genetic variation that influences water use efficiency (WUE) and drought tolerance to breed and develop new grain crops with enhanced productivity under both high and low water inputs. In the study, we are using sorghum as a model grain crop to characterize the morphological and physiological traits that are critical for water use and managing drought stress among cereals. Genotypes with highest observed WUE in the field will be further validated in the greenhouse are being evaluated under dryland and irrigated field environments to measure differences in overall yield and individual yield components including tiller number, grain number, and grain weight. Deliverables include (1) multiyear field-based phenotypic data for WUE, agronomic, and yield traits within a diverse mapping panel of 400 inbred lines and 300 diverse hybrids; (2) greenhouse validation of WUE and drought response traits for 50 genotypes; (3) yield data of top 15 WUE hybrids under both dryland and irrigated conditions; and (4) candidate genes associated with sorghum and corn WUE. Determining the genetic underpinnings of heterosis in grain sorghum Led by PI Stephen Kresovich, this interdisciplinary project funded by the DOE ARPA-e TERRA program is aimed to transform the current methodology of sorghum crop improvement by incorporating genomic and advanced phenomics tools. The goal of the proposed research and development program is to establish integrated, real-time phenotyping and analysis of above- and below-ground plant architecture and total carbon partitioning and allocation to predict heterosis and develop superior crop hybrids by fully leveraging the sorghum gene pool. A total of 700 unique hybrids were developed from crossing 350 male parents (~300 lines within the SAP) to two elite female lines. Again, more than 300 accessions were requested from the S-009 Plant Genetic Resources Conservation Unit to serve as the germplasm base for this study.

Publications

  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Sapkota S, Boyles R, Cooper E, Brenton Z, Myers M, Kresovich S (2019) Impact of sorghum racial structure and diversity on genomic prediction of grain yield components. Crop Science - First Look. doi: 10.2135/cropsci2019.04.0221
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Boyles R, Marshall D, Bockelman H (2019) Yield data from the Uniform Southern Soft Red Winter Wheat Nursery emphasize importance of selection location and environment for cultivar development. Crop Science 59: 1887-1898. doi: 10.2135/cropsci2018.11.0685
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Boyles R, Brenton Z, Kresovich S (2019) Genetic and genomic resources of sorghum to connect genotype with phenotype in contrasting environments. The Plant Journal 97:19-39. doi: 10.1111/tpj.14113
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Rustgi S, Shewry P, Brouns F, Deleu L, Delcour JA (2019) Wheat seed proteins - factors influencing their content, composition, and technological properties, and strategies to reduce adverse reactions. Comprehensive Reviews in Food Science and Food 18:1751-1769.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Cong X, Miao Y, Xu L, Zhang Y, Yuan C, Wang J, Zhuang T, Lin X, Jiang L, Wang N, Ma J, Sanguinet KA, Liu B, Rustgi S, Ou X (2019) Transgenerational memory of gene expression changes induced by heavy metal stress in rice (Oryza sativa L.). BMC Plant Biology 19:282.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Yang M, Liu Y, Dong J, Zhao W, Kashyap S, Gao X, Rustgi S, Wen S (2019) Probing early wheat grain development via transcriptomic and proteomic approaches. Functional & Integrative Genomics doi: 10.1007/s10142-019-00698-9.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Brouns F, Van Rooy G, Shewry P, Rustgi S, Jonkers D (2019) Adverse reactions to wheat or wheat components. Comprehensive Reviews in Food Science and Food Safety 18:1437-1452.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Pollmann S, Springer A, Rustgi S, von Wettstein D, Kang C, Reinbothe C, Reinbothe S (2019) Substrate channeling in oxylipin biosynthesis through a protein complex in the plastid envelope of Arabidopsis thaliana. Journal of Experimental Botany 70:1483-1495.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Osorio CE, Wen N, Mejias JH, Liu B, Reinbothe S, von Wettstein D, Rustgi S (2019) Development of wheat genotypes expressing a glutamine-specific endoprotease from barley and a prolyl endopeptidase from Flavobacterium meningosepticum or Pyrococcus furiosus as a potential remedy to celiac disease. Functional & Integrative Genomics 19:123-136.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2019 Citation: Rustgi S, Kashyap S, Deleu LJ, Delcour J (2019) Reduced-immunogenicity wheat now coming to age. In: Wani SH, Mohan A (eds) Physiological, Molecular, and Genetic perspectives of Wheat Improvement. Springer-Nature (in press)
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2019 Citation: Rustgi S, Shewry P, Brouns F (2019) "Health hazards associated with gluten consumption in susceptible individuals and current status of research on the dietary therapies," In: Igrejas G (Ed.), 'Wheat Quality for Improving Processing and Human Health', Springer (in press)
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2019 Citation: Osorio CE, Mej�as JH, Rustgi S (2019) Gluten detection methods and their critical role in assuring safe diets for celiac patients. Nutrients (in press)
  • Type: Journal Articles Status: Under Review Year Published: 2019 Citation: Osorio CE, Wen N, Mej�as JH, Mitchell S, von Wettstein D, Rustgi S (2019) Directed-mutagenesis of Flavobacterium meningosepticum prolyl-oligopeptidase and a glutamine-specific endopeptidase from barley to improve thermostability. Frontiers in Nutrition (under review)
  • Type: Journal Articles Status: Under Review Year Published: 2019 Citation: Narayanan S, Lwe ZSZ, Gandhi N, Welti R, Fallen B, Smith JR, Rustgi S (2019) Lipid metabolic changes contribute to heat tolerance in soybean. Scientific Reports (under review)
  • Type: Journal Articles Status: Under Review Year Published: 2019 Citation: Rustgi S, von Wettstein D, Reisenauer PE, Lyon S, Ankrah N, Brouwer B, Jones S, Guy SO, Chen X (2019). Registration of Fritz, a Two-Row, Spring Dual Purpose Barley. J. Plant Registr (under review).
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Rustgi S, Springer A, Kang C, von Wettstein D, Reinbothe C, Reinbothe S, Pollmann S (2019) Two non-canonical cytochrome P450s in Arabidopsis thaliana and their different roles in plant defense. International Journal of Molecular Sciences 20:3064.