Abstract
BackgroundStarch and protein are two major components of polished rice, and the amylose and protein contents affect eating and cooking qualities (ECQs). In the present study, genome-wide association study with high-quality re-sequencing data was performed for 10 ECQs in a panel of 227 non-glutinous rice accessions and four derived panels.ResultsPopulation structure accounted for high phenotypic variation in three routine panels and had minor effects on subspecies-based panels. Using the mixed linear model method based on the P + K model, we detected 29, 24, 16, 17, and 29 loci that were significant for ECQ parameters in each of the five panels. Some of these loci were close to starch synthesis-related genes. Two quantitative trait loci (QTLs) (chr.9: 15417525 ~ 15474876; 17538294 ~ 18443016) for several starch paste viscosity properties detected in four panels were close to the isoamylase 3 gene, one QTL (chr.1: 30627943 ~ 31668474) for consistency detected in three panels was close to the starch synthase IV-1 gene. The QTL (chr.7: 1118122 ~ 1967247) for breakdown (BD), detected in the whole panel and japonica panel, and one QTL (chr.7: 25312126 ~ 26540950) for BD and setback (SB), detected in the whole panel and indica panel, may be specific gene alleles in japonica or indica panels. One previously detected QTL (chr.11: 22240707 ~ 22563596) for protein content and one new QTL (chr.5: 7756614 ~ 8042699) for many ECQ traits detected in more than two panels, may represent valuable targets for future cloning of the underlying genes.ConclusionsThis study detected minor-effect QTLs affecting ECQs, and may increase our understanding of the genetic differences regulating the formation of ECQ between indica and japonica varieties.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3000-z) contains supplementary material, which is available to authorized users.
Highlights
Starch and protein are two major components of polished rice, and the amylose and protein contents affect eating and cooking qualities (ECQs)
Principal component analysis (PCA) plots of the first two components (Fig. 1) clearly differentiated rice accessions into different subpopulations, which corresponded with the population structure results (Fig. 1; Additional file 1: Figure S1)
Only two traits were significantly affected by population structure in the indica and japonica panels at significance level of P
Summary
Starch and protein are two major components of polished rice, and the amylose and protein contents affect eating and cooking qualities (ECQs). Apparent amylose content (AAC) is known to affect the eating and cooking quality (ECQ) of rice [1]. The rapid viscosity analyser (RVA) profile can distinguish eating quality rice varieties with similar AACs by evaluating the breakdown (BD), setback (SB), and consistency (CS) viscosities [2]. Starch paste viscosities play an essential role in estimating the eating, cooking, and processing qualities of rice, and have received more and more attention in rice breeding programs [4, 5]. The starch paste viscosity of glutinous rice differs from that of nonglutinous rice due to its lack of amylose [1]. Since GBSSI is inactive in glutinous varieties, the starch paste
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