SSR markers associated with straighthead resistance genes in rice

Authors: AGRAMA HESHAM, A - UNIV. OF AR RREC; Yan, Wengui

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 12/1/2007
Publication Date: 1/12/2008
Citation: Agrama Hesham, A., Yan, W. 2008. Ssr markers associated with straighthead resistance genes in rice. Plant and Animal Genome Conference Proceedings. P241 p. 179.

Interpretive Summary:

Technical Abstract: Straighthead, a physiological disease largely affected by environments, causes massive loss of yield and is costly to prevent. A collection of 268 rice accessions representing 52 countries was developed from the USDA rice core subset for this study. This collection was phenotyped with the aid of Arsenic and genotyped with 49 simple-sequence repeat (SSR) markers that completely cover the rice genome. Decay of linkage disequilibrium was estimated by calculating the squared correlation between pairs of marker loci. Two loci identified by SSR marker RM413 and RM277 on chromosome 5 and 12, respectively were found to be highly significantly associated with straighthead resistance. Two accessions (PI 596827 and 458488) with allele 105 at RM 413-ch5 and another two (PI 505386 and 596815) with allele 122 at RM277-ch12 were significantly resistant to straighthead than other accessions carrying other alleles. The mixed-model approach combining the principal component assignments or population structure matrix with kinship estimates was proved to be particularly promising for association mapping of straighthead. The results illustrate the potential of association mapping with phenotypic data in a diversified population and a modest number of SSR markers for identification of interesting associations by a relatively simple statistical analysis in rice.