Rapid identification of a new gene influencing low amylose content in rice landraces (Oryza sativa L.) using genome-wide association study with specific-locus amplified fragment sequencing.
Starch is the major component of milled rice, and amylose content (AC) affects eating quality. In this study, a genome-wide association study (GWAS) with specific-locus amplified fragment sequencing (SLAF-seq) data was performed for AC on a core collection of 419 rice landraces. Using the compressed mixed linear method based on the Q+K model, we identified a new gene, LAC6 (Chr6: 5.65-6.04 Mb), associated with AC in the low amylose content panel. The LAC6 candidate gene was detected by qRT-PCR in rice panicles. Results indicate that LOC_Os06g11130 was up-regulated, and LOC_Os06g11340 was significantly down-regulated, making it most likely a key candidate gene of LAC6. In conclusion, the findings provide a certain theoretiacal basis of molecular biology for genetic improvement of AC in rice and rice quality variety breeding.
Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning 530007, China.|Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning 530007, China.
Xinghai
X
Yang
Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning 530007, China.|Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning 530007, China.
Baoxuan
B
Nong
Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning 530007, China.|Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning 530007, China.
Xiuzhong
X
Xia
Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning 530007, China.|Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning 530007, China.
Zongqiong
Z
Zhang
Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning 530007, China.|Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning 530007, China.
Yu
Y
Zeng
Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning 530007, China.|Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning 530007, China.
Kaiqiang
K
Liu
Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning 530007, China.|Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning 530007, China.
Guofu
G
Deng
Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning 530007, China.|Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning 530007, China.
Danting
D
Li
D000688:Amylose / Q000235:genetics*; D015536:Down-Regulation / Q000235:genetics; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D056426:Genetic Loci / Q000235:genetics*; D055106:Genome-Wide Association Study / Q000379:methods; D012275:Oryza / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D015854:Up-Regulation / Q000235:genetics
D010940:Plant Proteins; D000688:Amylose
GWAS; SLAF-Seq; SLAF-seq; candidate gene; gène candidat; rice landraces; très faible teneur en amylose; variétés de pays du riz; very low amylose content