Sequence variations in OsAGPase significantly associated with amylose content and viscosity properties in rice (Oryza sativa L.)

Sequence-based variations in starch synthesis-related genes (SSRGs) exert a basic influence on the determination of eating quality in rice (Oryza sativa L.). This study aimed to investigate the relationship between the sequence variations from parts of 10 SSRGs and the amylose content (AC) plus rapid viscosity analysis (RVA) profiles in a heuristic rice core set by association mapping (AM). In total, 86 sequence variations were found in 10 sequenced amplicons, including 79 single-nucleotide polymorphisms (SNPs), six insertion-deletions (InDels) and one polymorphic simple sequence repeat (SSR). Among them, 61 variations were exon-based, of which 41 should lead to amino acid changes. Four subpopulations were revealed by population structure analysis based on 170 genome-wide SSR genotypes. The final AM showed a sum of four significant associations between three phenotypic indices and three sequence variations. An ADP-glucose pyrophosphorylase small unit 1 (OsAGPS1) SNP (A-G) was significantly associated with increased AC (P<0.001, R-2=15.6%), while a 12-bp deletion of AGPase large unit 4 (OsAGPL4) was significantly related to the decreased breakdown viscosity (BDV) (P<0.001, R-2=16.6%) in both general linear model (GLM) and mixed linear model (MLM). This study provides a new perspective of allele mining for breeding strategies based on marker-assisted selection.