title: Genome-wide association study of eating and cooking qualities in different subpopulations of rice (Oryza sativa L.).
abstract: Starch 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.
  
  
  
  Population 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.
  
  
  
  This 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.
authors.affiliation: Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439, Republic of Korea.|Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Huajiachi Campus, Hangzhou, 310029, China.
authors.forename: Feifei
authors.initials: F
authors.lastname: Xu
authors.affiliation: Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439, Republic of Korea.|Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Huajiachi Campus, Hangzhou, 310029, China.
authors.forename: Jinsong
authors.initials: J
authors.lastname: Bao
authors.affiliation: Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439, Republic of Korea.
authors.forename: Qiang
authors.initials: Q
authors.lastname: He
authors.affiliation: Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439, Republic of Korea. yjpark@kongju.ac.kr.|Center for crop genetic resource and breeding (CCGRB), Kongju National University, Cheonan, 31080, Republic of Korea. yjpark@kongju.ac.kr.
authors.forename: Yong-Jin
authors.identifier: 0000-0001-9843-850X
authors.initials: YJ
authors.lastname: Park
mesh_terms: D000688:Amylose / Q000378:metabolism; D002874:Chromosome Mapping / Q000379:methods*; D032461:Chromosomes, Plant / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D055106:Genome-Wide Association Study / Q000379:methods*; D012275:Oryza / Q000145:classification* / Q000235:genetics; D010641:Phenotype; D010940:Plant Proteins / Q000235:genetics; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA
chemical_list: D010940:Plant Proteins; D000688:Amylose
keywords: Eating and cooking quality; GWAS; Rice; Subpopulations