ARS | Publication request: EVALUATION OF LINKAGE DISEQUILIBRIUM IN RICE AND ITS WILD RELATIVES

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Proceedings
Publication Acceptance Date: December 1, 2005
Publication Date: January 14, 2006
Citation: Agrama, H.A., Eizenga, G.C. 2006. Evaluation of linkage disequilibrium in rice and its wild relatives [abstract]. In: Proceedings of the XIV Annual International Plant & Animal Genome Conference, January 14-18, 2006, San Diego, California. p. 14.

Technical Abstract: The linkage disequilibrium (LD) background level in 172 accessions of rice (Oryza sativa L.) and rice wild relative (Oryza spp.) was analyzed using 120 SSR markers. The accessions were divided into three germplasm sets. One set consisted of 53 rice accessions introduced from seven countries, including five regions of China. A second set was made up of 60 Oryza spp. accessions represented by 10 different species. The third set included 59 US varieties released in the past 25 years and selected ancestral cultivars in US rice breeding programs. Population structure was conducted using the model-based program Structure. Pattern and distribution of LD in the three genetic backgrounds were compared. TASSEL software was used to assess linkage disequilibrium for pair-wise combinations of markers for each germplasm set. The extent of LD among marker loci was estimated by r2 and D’ measures. SSR markers were highly polymorphic across all accessions. There is significant evidence for LD extending over a 15 cM range. LD between adjacent loci is strong enough to be useful in association mapping of important agronomic trait loci via genome-wide scans.