Association analysis of the amino acid contents in rice.
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 genotyped 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.
Zhao
Weiguo
W
Department of Applied Bioscience, Konkuk University, Seoul 143-701, Korea.
Park
Eun-Jin
EJ
Chung
Jong-Wook
JW
Park
Yong-Jin
YJ
Chung
Ill-Min
IM
Ahn
Joung-Kuk
JK
Kim
Gwang-Ho
GH
D000596:Amino Acids / Q000032:analysis*; D002874:Chromosome Mapping; D014644:Genetic Variation; D015810:Linkage Disequilibrium; D018895:Microsatellite Repeats; D012275:Oryza / Q000737:chemistry / Q000235:genetics*; D010641:Phenotype
D000596:Amino Acids