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United States Department of Agriculture

Agricultural Research Service

Research Project: Genomic Approaches and Genetic Resources for Improving Rice Yield and Grain Quality

Location: Dale Bumpers National Rice Research Center

Project Number: 6028-21000-010-00
Project Type: Appropriated

Start Date: Jul 10, 2013
End Date: Jul 09, 2018

Objective:
This project will explore existing genetic rice resources and develop new methods of evaluation to elucidate genetic and environmental factors that influence yield and grain quality. Phenotypic information will be combined with genomic scans to identify chromosomal regions and genes that control these traits. 1: Maintain, regenerate, back-up, characterize, and distribute rice genetic stocks and associated information, and genetically and phenotypically characterize accessions in the NSGC rice collection and elite breeding materials for agronomic and grain quality traits to provide new genetic resources for rice research 1A: Expand and phenotypically and genotypically characterize NSGC collection (Core, Mini-Core, GSOR subsets) for traits essential to rice research community and US rice industry 1B: Develop/characterize a tropical japonica Core collection (TRJ-Core) representing US and international tropical japonica rice germplasm for mining genes for US breeding programs 1C: Evaluate cultivars with divergent processing quality for differences in enzyme activity of starch metabolism genes in response to environmental temperature 1D: Evaluate germplasm with pigmented bran using in vitro cell assays for 1) influence of cooking on bioactivity of phenolics having potential health-beneficial properties against cancer, and 2) bioactivity of bran extracts against diabetes 1E: Assess accessions in rice diversity panels for health-beneficial starch fractions 1F: Assess accessions for bran components that impact storage stability of brown rice 2: Use genome wide association studies and QTL mapping techniques to identify alleles that control yield components and grain quality traits in response to environmental variables 2A: Determine location of QTL and allelic variability associated with yield components in bi-parental mapping populations 2B: Identify QTLs and alleles responsible for transgressive variation in selected yield components found in rice wild species using chromosome segment substitution lines 2C: Identify QTLs for rice grain chalkiness in bi-parental mapping populations, and validate the markers in diverse germplasm 2D: Characterize QTLs associated with rice milling yield 2E: Identify/fine-map/further characterize the mode of action of genomic regions affecting rice grain fissure resistance 2F: Identify/further characterize genes affecting grain mineral nutritional value 2G: Evaluate germplasm/RILs that differ for grain arsenic accumulation and resistance to straighthead disease to understand mechanisms of arsenic uptake from soil and association with staighthead 3: Use marker-assisted selection to introgress novel alleles and to stack genes associated with yield, disease resistance, and grain milling, cooking and nutritional quality into new cultivars and improved breeding stocks 3A: Develop marker analysis platform for marker-assisted transfer of traits from various rice germplasm backgrounds into targeted US cultivars 3B: Utilize genetic resources (RIL, genetic fingerprints, and markers linked to QTLs) to introgress improved alleles for agronomic performance, disease resistance, and stress tolerance into southern US adapted cultivars

Approach:
This project will explore genetic resources using phenotypic and genomic tools to identify novel traits that impact rice yield and grain quality. Chromosomal regions that control these traits will be determined though association mapping techniques using germplasm surveys and QTL mapping of bi-parental and backcross mapping populations. Genetic resources ranging from elite US breeding materials and commercial cultivars, to diverse global germplasm, and wild Oryza species accessions will serve as the basis for extensive phenotyping and genotyping studies. In addition, a new diversity panel based upon tropical japonica germplasm, which is the source of US cultivars, will be developed to mine for novel alleles for traits relevant to the US rice industry. Targeted traits will include yield, disease resistance, and agronomic traits, as well as milling, nutritional, and processing quality. Mapping populations will be developed for diverse tropical japonica parents and from crosses with wild species to identify alleles that are associated with yield components. Compounds in rice bran that have been identified in raw rice that reduce cancer cell growth and glucose uptake in in vitro studies will be isolated and evaluated for their health beneficial properties and their bio-activity following cooking. Global rice genetic resources that have high amylose content will be evaluated for resistant starch to identify germplasm that may be beneficial for reducing spikes in blood sugar associated with diabetes. Enzymes that control starch structure and rice parboiling quality will be evaluated in diverse rice germplasm grown under high temperature. Enzymes that are sensitive to temperature stress and negatively impact processing quality will be identified. These will be targets for genetic improvement to develop improved stability in processing quality. In an effort to increase market use for whole grain brown rice, which is more nutritious than milled rice, components in the rice bran that can reduce rancidity during storage will be identified. Mapping populations that are segregating for grain chalk, milling yield, and grain fissure resistance, factors that impact crop value, will be used to finely map QTL and identify candidate genes associated with these traits. In addition, segregating populations will be analyzed for grain mineral content in an effort to develop nutrient-dense germplasm. Grain arsenic accumulation can occur when rice is grown under flooded, anaerobic conditions. The interaction of diverse germplasm and water management techniques will be studied to identify how these two factors can minimize grain arsenic accumulation while sustaining economically viable yields. The long-term objective of this project is to seek a better understanding of the genetic control of yield and grain quality traits, and this information can be translated into superior rice cultivars that will strengthen domestic and export markets for USA rice.

Last Modified: 10/31/2014
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