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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

Title: Use of the RDP1 to map traits important for rice improvement

Authors
item Eizenga, Georgia
item McClung, Anna
item McClung, Anna
item Wright, Mark -
item Greenberg, Anthony -
item Singh, Namrata -
item Agosto-Perez, Francisco -
item Declerck, Genevieve -
item Mezey, Jason -
item Mccouch, Susan -

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: January 2, 2014
Publication Date: N/A

Technical Abstract: The ‘Rice Diversity Panel 1’ (RDP1) is composed of 421 diverse Oryza sativa accessions from 79 countries, including indica and aus which belong to the Indica varietal group, and tropical japonica, temperate japonica, and aromatic (Group V) which comprise the Japonica varietal group. This panel was previously genotyped with 36 SSR (simple sequence repeat) markers, an Illumina 1536-SNP OPA with 1,311 high-quality single nucleotide polymorphisms (SNPs), and an Affymetrix custom-designed genotyping array with 36,901 high quality SNP genotypes. Currently, the SNP genotypes from a second Affymetrix custom-designed array identified as HDRA (high density rice array) are being finalized that will result in about 470,000 high quality SNPs useful for genotyping the O. sativa accessions. It is estimated that the number of useful SNPs will range from approximately 143,000 SNPs for temperate japonica accessions to 359,000 SNPs for indica accessions. The ‘Rice Diversity Panel 2’ (RDP2) composed of an additional 1,411 accessions, developed at the International Rice Research Institute, is currently being introduced into the USA and genotyped with the HDRA. The RDP1 was characterized for several agronomic, morphological, developmental, and physiological traits and has been used in genome-wide association studies (GWAS) conducted using the initial Affymetrix SNP array. Currently, these analyses are being re-evaluated using the HDRA genotypes to discover additional marker-trait associations. Seed of all accessions is available from the Genetic Stocks-Oryza (GSOR) collection and all SNP genotypes can be downloaded from the web site (www.ricediversity.org). Digital images of the seed can be viewed in the Seed Photo Library (www.ricediversity.org) and an individual panicle of each accession, as well as, means of the phenotypic traits, and SSR marker data including those for blast and grain quality, can be downloaded from the GSOR website. These RDP1 resources will allow interested rice researchers to (a) conduct GWAS on a trait(s) of interest, (b) verify seed identify, and (c) develop mapping populations to validate GWAS results for the trait(s) of interest. The RDP1 was characterized for three grain quality traits: apparent amylose content (AC), gelatinization temperature as measured by alkali spreading value (ASV), and protein content. Canonical discriminant analysis (CDA) revealed AC was the quality trait most closely correlated with subpopulation structure, followed by ASV. The CDA of these grain quality traits and the previously analyzed 18 agro-morphological traits, confirmed that although there is significant variability within each of the five rice subpopulations, they can be differentiated on the basis of numerous traits, including plant height, number of panicles per plant, panicle length, and seed shape, as well as on cooking and eating qualities.

Last Modified: 12/19/2014
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