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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT AND CHARACTERIZATION OF GENETIC RESOURCES FOR AGRONOMIC AND QUALITY TRAITS USING GENOMIC TOOLS Title: Association mapping of straighthead disorder induced by arsenic in rice

Authors
item Agrama, Hesham - UNIV. OF AR RREC
item Yan, Wengui

Submitted to: Plant Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 11, 2008
Publication Date: June 1, 2009
Citation: Agrama, H.A., Yan, W. 2009. Association mapping of straighthead disorder induced by arsenic in rice. Plant Breeding. 128:551-558.

Interpretive Summary: Straighthead is a physiological disorder in rice resulting in sterile florets, poorly developed panicles, and significant yield loss. Its sporadic nature of occurrence and environmental concern of evaluation method applying arsenic in soil demand an indirect and accurate strategy for breeding straighthead resistant cultivar, marker-assisted selection. Using 547 accessions of germplasm from the USDA rice core collection and 75 molecular markers covering the entire rice genome about every 35 cM, six single sequence repeat (SSR) markers were found to be highly and significantly associated with straighthead with a mixed-linear model approach combining the principal component assignments with kinship estimates. The six markers explained 35% of the total phenotypic variation and two markers, RM413 and RM277, on chromosome 5 and 12, respectively, had a significant association with low rating indicating straighthead resistance. Confirmation with segregating populations, i.e., F2 or recombinant inbred lines, is necessary before marker-assisted selection can be applied.

Technical Abstract: Straighthead is a physiological disorder in rice resulting in sterile florets, poorly developed panicles, and yield loss. Because of its sporadic nature and unidentified causes for the disorder, molecular marker assisted selection is essential for resistance improvement in breeding programs. To take advantage of recent advances in gene-mapping technology, we executed a genome-wide association mapping to identify genetic markers associated with straighthead disorder using 547 accessions of germplasm from the USDA rice core collection. Straighthead was evaluated in arsenic treated soil and genotyping was conducted with 75 molecular markers covering the entire rice genome about every 35 cM. A mixed-linear model approach combining the principal component assignments with kinship estimates proved to be particularly promising for association mapping. The extent of linkage disequilibrium was described among the markers. Six markers were found to be highly and significantly associated with straighthead, explaining ~35% of the total phenotypic variation. However, only two SSR markers, RM413 and RM277 on chromosome 5 and 12, respectively have a significant association with low rating indicating straighthead resistance. Confirmation with segregating populations, i.e., F2 or recombinant inbred lines, is necessary before marker-assisted selection can be applied.

Last Modified: 12/22/2014
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