Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice.
A genome-wide association study (GWAS) can be a powerful tool for the identification of genes associated with agronomic traits in crop species, but it is often hindered by population structure and the large extent of linkage disequilibrium. In this study, we identified agronomically important genes in rice using GWAS based on whole-genome sequencing, followed by the screening of candidate genes based on the estimated effect of nucleotide polymorphisms. Using this approach, we identified four new genes associated with agronomic traits. Some genes were undetectable by standard SNP analysis, but we detected them using gene-based association analysis. This study provides fundamental insights relevant to the rapid identification of genes associated with agronomic traits using GWAS and will accelerate future efforts aimed at crop improvement.
Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan.
Kenji
K
Yano
NARO Institute of Vegetable and Tea Science, Tsu, Japan.
Eiji
E
Yamamoto
Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan.
Koichiro
K
Aya
Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan.
Hideyuki
H
Takeuchi
Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan.
Pei-Ching
PC
Lo
Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan.
Li
L
Hu
Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Kasai, Hyogo, Japan.
Masanori
M
Yamasaki
Hyogo Prefectural Research Center for Agriculture, Forestry and Fisheries, Kasai, Hyogo, Japan.
Shinya
S
Yoshida
Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan.
Hidemi
H
Kitano
Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan.
Ko
K
Hirano
Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan.
Makoto
M
Matsuoka
D032461:Chromosomes, Plant / Q000235:genetics; D018556:Crops, Agricultural / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics*; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D005838:Genotype; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics*