20946420
not annotated - annotated - LINNAEUS only
Association between nonsynonymous mutations of starch synthase IIa and starch quality in rice (Oryza sativa).
Starch quality is one of the most important agronomic traits in Asian rice, Oryza sativa. Starch synthase IIa (SsIIa) is a major candidate gene for starch quality variation. Within SsIIa, three nonsynonymous mutations in exon 8 have been shown to affect enzyme activity when expressed in Escherichia coli. To search for the variation in SsIIa that is responsible for starch quality variation in rice, we sequenced the SsIIa exon 8 region and measured starch quality as starch disintegration in alkali for 289 accessions of cultivated rice and 57 accessions of its wild ancestor, Oryza rufipogon. A general linear model and nested clade analysis were used to identify the associations between the three nonsynonymous single nucleotide polymorphisms (SNPs) and starch quality. Among the three nonsynonymous SNPs, we found strong evidence of association at one nucleotide site ('SNP 3'), corresponding to a Leu/Phe replacement at codon 781. A second SNP, corresponding to a Val/Met replacement at codon 737, could potentially show an association with increased sample sizes. Variation in SsIIa enzyme activity is associated with the cohesiveness of rice grains when cooked, and our findings are consistent with selection for more cohesive grains during the domestication of tropical japonica rice.
Ann file
T1 Species 89 93 rice
N1 Reference T1 Taxonomy:4530
T2 Species 95 107 Oryza sativa
N2 Reference T2 Taxonomy:4530
T3 Species 182 186 rice
N3 Reference T3 Taxonomy:4530
T4 Species 188 200 Oryza sativa
N4 Reference T4 Taxonomy:4530
T5 Species 400 416 Escherichia coli
N5 Reference T5 Taxonomy:562
T6 Species 507 511 rice
N6 Reference T6 Taxonomy:4530
T7 Species 646 650 rice
N7 Reference T7 Taxonomy:4530
T8 Species 691 706 Oryza rufipogon
N8 Reference T8 Taxonomy:4529
T9 Species 1258 1262 rice
N9 Reference T9 Taxonomy:4530
T10 Species 1392 1405 japonica rice
N10 Reference T10 Taxonomy:4529
N11 Reference T10 Taxonomy:39947 Oryza sativa Japonica Group