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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT AND CHARACTERIZATION OF GENETIC RESOURCES FOR AGRONOMIC AND QUALITY TRAITS USING GENOMIC TOOLS

Location: Dale Bumpers National Rice Research Center

Project Number: 6225-21000-009-00
Project Type: Appropriated

Start Date: Jul 10, 2008
End Date: Jul 09, 2013

Objective:
Objective 1: Phenotypically and genotypically characterize the rice National Small Grains Germplasm Collection (NSGC) and conserve genetic stocks, mutants, and mapping populations in the Genetic Stocks Oryza (GSOR) to promote greater use by the research community. Sub-objective 1.A. Characterize accessions in the NSGC rice collection for 27 descriptors and rejuvenate seed of low inventory genetic seedstocks. Sub-objective 1.B. Perform structure analysis following genotypic and phenotypic evaluation of the NSGC Core collection. Sub-objective 1.C. Expand the GSOR collection to 15,000 accessions and establish a web-based ordering and distribution system. Objective 2: Evaluate rice germplasm to identify genetic resources having enhanced nutritional properties and added-value for the food industry. Sub-objective 2.A. Identify genetic variability for antioxidant capacity and the content of main classes of polyphenols and carotenoids in rice germplasm. Sub-objective 2.B. Structurally identify and quantify major flavonoid and proanthocyanidin compounds in rice genotypes with different bran color. Sub-objective 2.C. Determine the effect of processing on rice bran phytochemicals. Sub-objective 2.D. Identify quantitative trait loci (QTL) associated with rice grain elemental content. Sub-objective 2.E. Measure genotype and environment interactions on starch structure and grain quality. Sub-objective 2.F. Determine the impact of non-conventional cultural management practices on rice grain quality. Objective 3: Map new resistance genes for blast disease and straighthead disease identified in germplasm accessions. Sub-objective 3.A. Mine novel blast resistance genes from indica rice germplasm for use in U.S. breeding programs. Sub-objective 3.B. Decipher genetic mechanism for resistance to straighthead, a physiological disease. Objective 4: Map genes associated with grain quality traits, including rice paste viscosity and grain chalk. Sub-objective 4.A. Genetically map starch paste viscosity variation as a predictor of rice processing quality. Sub-objective 4.B. Genetically map grain chalk formation which influences milling quality.

Approach:
Additional germplasm and data will be added to the NSGC rice collection for distribution to the public via GRIN. The Core collection will be characterized for sheath blight disease resistance, grain mineral accumulation, straighthead tolerance, protein content, and cold tolerance, and genetic markers will be identified that are associated with these traits. The Genetics Stocks Oryza (GSOR) collection will be expanded to 15,000 accessions that are curated and distributed to the research community through a searchable on-line database. Selected accessions from the NSGC collection will be evaluated for health beneficial compounds like polyphenols, flavonoids, and carotenoids and the influence of the environment and processing methods on levels of these compounds will be evaluated. Germplasm will be evaluated under flooded and aerobic conditions to understand the genetic mechanisms controlling nutrient uptake. Mapping populations will be developed, and rice gene microarray chips will be used to identify chromosomal regions associated with nutrient uptake. The genotype x environment interaction on key enzymes in the starch pathway will be studied to determine how they impact starch structure and processing quality. In an effort to understand how rice quality will be impacted by crop rotation systems, 5 to 10 rice cultivars will be grown using conventional tillage/no-till, permanent flood/intermittent-flushing, different fertilization rates, and different crop rotations, and agronomic and cooking quality traits will be evaluated to provide insight as to how changing cropping systems will impact rice milling and cooking quality. Novel genes for blast and straighthead disease resistance will be identified using mapping populations. Markers and germplasm will be released to breeders for developing improved cultivars. Sequence variation around a SNP in exon 10 of the rice Waxy gene will be evaluated to determine what impact it has on RVA paste viscosity characteristics. Genetic markers will be developed that can be used in breeding for elevated pasting profiles, which is desired for rice used in canning, instantizing, and other food preparation processes. We will fine map several QTL previously identified to be associated with grain chalk. Progeny from the selected recombinant lines will be grown in two environments and chalk amounts quantified with a Winseedle Image analysis system. Segregation of tightly linked SSR and SNP markers will be analyzed to pinpoint recombination points and candidate genes in the finely mapped region. Genetic markers developed from this research will be used by breeders to develop new cultivars that have greater translucency, higher milling yield, and consistent cooking quality.

Last Modified: 9/1/2014
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