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Registration of the Rice Diversity Panel 1 for Genomewide Association Studies

Georgia C. Eizenga, Md. Liakat Ali, Rolfe J. Bryant, Kathleen M. Yeater, Anna M. McClung, Susan R. McCouch
Journal of plant registrations 2014 v.8 no.1 pp. 109-116
Oryza sativa, alkali spreading value, amylose, ancestry, chromosome mapping, cultivars, digital images, discriminant analysis, gelatinization temperature, genetic variation, grain quality, homozygosity, inflorescences, landraces, loci, protein content, rice, single nucleotide polymorphism
The Rice Diversity Panel 1 (Reg. No. MP-6, NSL 500357 MAP) (RDP1) is a collection of 421 purified, homozygous rice (Oryza sativa L.) accessions (GSOR 301001 through GSOR 301421; GSOR 312001 through 312020) representing the broad range of genetic variation within O. sativa. The accessions include both landraces and elite rice cultivars, which were classified into five subpopulation groups, including indica (95 accessions) and aus (60), which belong to the Indica varietal group, and tropical japonica (106), temperate japonica (111), and aromatic (Group V) (16) which comprise the Japonica varietal group. Thirty-three accessions are classified as admixtures because they shared <60% ancestry with a single group. The seed, with and without the hull, and panicle morphology of each accession were documented with digital images, and the RDP1 was phenotyped for morphological, developmental, and physiological traits. Genotypes for 36,901 SNP loci are publicly available for additional genomewide association mapping studies. In this report, we evaluate three grain quality traits on the RDP1: apparent amylose content (AC), gelatinization temperature as measured by alkali spreading value (ASV), and protein content. Canonical discriminant analysis revealed AC was the quality trait most closely correlated with subpopulation structure, followed by ASV. These traits indicate that temperate japonica was the most distinct group, whereas aus and indica could not be differentiated, and the aromatic accessions were closest to tropical japonica.