The main objective of the present study was to identify simple sequence repeat （SSR） markers associated with the amino acid content of rice （Oryza sativa L.）. SSR markers were selected by prescreening for the rela...The main objective of the present study was to identify simple sequence repeat （SSR） markers associated with the amino acid content of rice （Oryza sativa L.）. SSR markers were selected by prescreening for the relationship to amino acid content. Eighty-four rice landrace accessions from Korea were evaluated for 16 kinds of amino acids in brown rice and ganotyped with 25 SSR markers. Analysis of population structure revealed four subgroups in the population. Linkage disequilibrium （LD） patterns and distributions are of fundamental importance for genome-wide mapping associations. The mean r^2 value for all intrachromosomal loci pairs was 0.033. LD between linked markers decreased with distance. Marker-trait associations were investigated using the unified mixed-model approach, considering both population structure （Q） and kinship （K）. A total of 42 marker-trait associations with amino acids （P 〈 0.05） were identified using 15 different SSR markers covering three chromosomes and explaining more than 40% of the total variation. These results suggest that association analysis in rice is a viable alternative to quantitative trait loci mapping and should help rice breeders develop strategies for improving rice quality.展开更多
基金Supported by the Biogreen 21 project (#20080401034058) of the Rural Development Administration (RDA), KoreaDr Zhao Weiguo was supported by the 2008 KU Brain Pool grant from Konkuk University, Korea
文摘The main objective of the present study was to identify simple sequence repeat （SSR） markers associated with the amino acid content of rice （Oryza sativa L.）. SSR markers were selected by prescreening for the relationship to amino acid content. Eighty-four rice landrace accessions from Korea were evaluated for 16 kinds of amino acids in brown rice and ganotyped with 25 SSR markers. Analysis of population structure revealed four subgroups in the population. Linkage disequilibrium （LD） patterns and distributions are of fundamental importance for genome-wide mapping associations. The mean r^2 value for all intrachromosomal loci pairs was 0.033. LD between linked markers decreased with distance. Marker-trait associations were investigated using the unified mixed-model approach, considering both population structure （Q） and kinship （K）. A total of 42 marker-trait associations with amino acids （P 〈 0.05） were identified using 15 different SSR markers covering three chromosomes and explaining more than 40% of the total variation. These results suggest that association analysis in rice is a viable alternative to quantitative trait loci mapping and should help rice breeders develop strategies for improving rice quality.
