Genome-wide association study of eating and cooking qualities in different subpopulations of rice (Oryza sativa L.)

BMC Genomics

Research Article

Qiang He¹  Yong-Jin Park²  Feifei Xu³  Jinsong Bao³ 

[1] Department of Plant Resources, College of Industrial Science, Kongju National University, 32439, Yesan, Republic of Korea;Department of Plant Resources, College of Industrial Science, Kongju National University, 32439, Yesan, Republic of Korea;Center for crop genetic resource and breeding (CCGRB), Kongju National University, 31080, Cheonan, Republic of Korea;Department of Plant Resources, College of Industrial Science, Kongju National University, 32439, Yesan, Republic of Korea;Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Huajiachi Campus, 310029, Hangzhou, China;

关键词: Rice;    Eating and cooking quality;    Subpopulations;    GWAS;   

DOI  :  10.1186/s12864-016-3000-z

 received in 2016-01-23, accepted in 2016-08-05,  发布年份 2016

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© The Author(s). 2016