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ARS Home » Pacific West Area » Davis, California » Crops Pathology and Genetics Research » Research » Research Project #424579

Research Project: Generation and Characterization of Novel Genetic Variation in Rice for the Enhancement of Grain Quality and Agronomic Performance

Location: Crops Pathology and Genetics Research

Project Number: 2032-21000-021-00-D
Project Type: In-House Appropriated

Start Date: Apr 17, 2013
End Date: Apr 16, 2018

Objective 1: Evaluate and apply chemical and physical agents to generate populations of rice mutants for forward and reverse genetic analyses. Sub-objective 1A: Evaluate chemical and gamma-irradiation protocols for seed mutagenesis. Sub-objective 1B: Identify alternative seed mutagenesis approaches to increasing mutation density. Sub-objective 1C: Determine the GECN in rice by reduced representation sequencing. Objective 2: Develop rice induced mutant resources (genotypic and phenotypic data, seeds) as a public resource for functional genomics research and as novel germplasm for rice breeding. Sub-objective 2A: Phenotype M2 individuals and their corresponding self progeny (M3 generation) using a standard panel of traits/descriptors and established rice mutant ontology. Sub-objective 2B: Sequence the exome and catalog mutations of M2 individuals. Sub-objective 2C: Produce fixed mutant lines for quantitative trait phenotyping (e.g., field sites, multiple locations, replications, and users, destructive phenotyping/selective screening). Objective 3: Identify, characterize, and make available mutant phenotypes/mutations that affect rice grain quality and agronomic traits as tools for functional studies and/or varietal improvement. Sub-objective 3A: Identify grain quality and agronomic mutants using phenotypic evaluation. Sub-objective 3B: Identify useful mutant phenotypes by screening populations for mutations in genes involved in biosynthesis and/or accumulation of cooking, eating, and nutritional quality components (i.e. reverse genetics). Sub-objective 3C: Simultaneous mapping of mutations and germplasm enhancement.

Goal 1A: The mutation density of ~4 mutants per Mb using seed mutagenesis will be improved through modification of current protocols. Goal 1B: Two approaches will be taken: 1) mutagenesis of tetraploid rice; and 2) seed mutagenesis at mutagen doses that elicit high or complete pollen sterility followed by crossing with wild-type pollen. Goal 1C: The GECN in rice will vary depending on the mutagen, the dose, and the inflorescence (primary vs. secondary tillers). Goal 2A: Phenotypic data from a systematic evaluation of M2 and M3 mutants will add value to the mutant resource and provide users with additional criteria for selecting mutant lines for further characterization and/or incorporation into variety development programs. Goal 2B: Generate in silico mutation profiles of 1,500 to 2,000 independent M2 rice mutants by exome sequencing existing and newly created mutant populations. Goal 2C: Many valuable mutations/mutant phenotypes may be missed in early generations (i.e. M2 or M3). Fixed lines (=M6 generation) will provide researchers a long-term resource for evaluation of traits under field conditions, that require multiple replications (e.g. locations and years), or that are destructive in nature. Goal 3A: Mutations that improve grain quality (milling, cooking, eating, and nutritional) or agronomic performance of rice or that result in novel phenotypes of commercial value may be identified through phenotypic evaluation (i.e. forward genetics). Goal 3B: Through a combination of TILLING and targeted exome sequencing, mutations in genes of interest will be identified and the corresponding mutants will be characterized. Goal 3C: Develop a functional genomics/variety development pipeline by applying next-gen sequencing-based methods in combination with accelerated mapping population development to identify mutant phenotypes, map and clone the underlying genes, and generate enhanced germplasm for breeding programs.