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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #287590
Title: Registration of the "Rice Diversity Panel I' Genome-Wide Association Mapping Studies

Author
item Eizenga, Georgia
item ALI, LIAKAT - University Of Arkansas
item Bryant, Rolfe
item Yeater, Kathleen
item McClung, Anna
item MCCOUCH, SUSAN - Cornell University

Submitted to: Journal of Plant Registrations
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/3/2013
Publication Date: 10/4/2013
Citation: Eizenga, G.C., Ali, L.M., Bryant, R.J., Yeater, K.M., McClung, A.M., McCouch, S. 2013. Registration of the Rice Diversity Panel I for genomewide association mapping studies. Journal of Plant Registrations. 8(1):109-116.

Interpretive Summary: Cultivated Asian rice is extremely diverse, in fact the two different types of rice, Indica and Japonica, have been recognized since ancient times. With the advent of DNA markers, it is now possible to further subdivide the different types of rice into additional subgroups. Indica rice is now divided into aus and indica, and Japonica rice into temperate and tropical japonica. The aromatic subgroup of rice also is recognized. A collection of 409 rice cultivars identified as the “Rice Diversity Panel I” was assembled to represent the rice growing areas of the world and begin to unravel the tremendous amount of variation present in these five rice subgroups. In this study, we describe the variation present for the three grain quality traits that affect the cooking, eating, and nutritional quality of cultivated rice. The results indicate that amylose (or starch) content which affects cooking quality, is the quality trait that most strongly distinguishes the different subgroups. This Rice Diversity Panel was genotyped with DNA markers and the results of this genotyping will ultimately make it possible to identify the genes that are unique to the rice subgroups. This information will make it possible to breed the desired traits into new rice cultivars being developed for particular environments and markets. The Rice Diversity Panel is freely available to anyone requesting the seed, enabling the panel to be evaluated for countless traits of interest. A large amount of genotypic data is also freely available, so the location of any trait evaluated can be quickly mapped to chromosomal location, providing a starting point for additional studies of the selected trait.

Technical Abstract: The Rice Diversity Panel (RDP) is a collection of 409 O. sativa accessions (GSOR301001 through GSOR301422) representing the five subpopulations: aromatic (Group V) composed of 15 accessions; aus (59) and indica (90) which compose the Indica subspecies; tropical (104) and temperate (108) japonica which compose the Japonica subspecies and 33 accessions being admixtures of either the Indica or Japonica subpopulations. The accessions are documented with digital images of seed with and without the hull (lemma and palea) and individual panicles. The RDP was phenotyped by several groups for a number of morphological traits and genotyped with 36,901 SNPs for association mapping. In this report we evaluate the diversity for three grain quality traits: apparent amylose content, gelatinization temperature as measured by alkali spreading value (ASV), and percent protein. Canonical discriminate analysis of the quality traits revealed apparent amylose was the major quality trait deciding subpopulation structure followed by ASV. Accessions classified as temperate japonica had low amylose content (15.93%), whereas aus (25.11%) and indica (22.90%) accessions had the highest amylose content. Temperate japonica was the most distinct group based on these three quality traits, followed by the tropical japonica subpopulation. The aus and indica subpopulations could not be separated based on the quality traits and the aromatic accessions were closest to tropical japonica accessions.