| Rice(Oryza sativa L.)is one of the most important subsistence food resources for the world’s population.With the improvement of rice yield and living standards,people’s requirements for rice quality have reached a new height.The cultivation of new highquality rice varieties has become one of the critical goals of breeders.At present,identification and application of quality genes is one of the effective ways to improve rice quality,and it is a common method to mine beneficial natural variations of plant quantitative traits by using short-cycle and high-efficiency genome-wide association study.In this study,561 rice core germplasm resources were used as research materials to investigate a total of 14 phenotypic traits,including appearance quality(grain length,grain width,ratio of length to width,1000-grain weight,grain thickness,chalkiness,transparency),cooking and eating quality(gel consistency,gelatinization temperature,amylose)and nutritional quality(four storage proteins).Furthermore,the genome-wide association analysis was carried out to identify the key loci controlling rice quality traits through combined with the genotypic data from sequencing,so as to laying the foundation for fine mapping and cloning of quality genes.The main conclusions are as follows:1.The results of quality phenotype detection and distribution of germplasm population showed below: the distribution of grain length from 5.62～10.88 mm,grain width from1.82～3.70 mm,ratio of length to width from 1.93～5.23,1000-grain weight from15.78～42.81 g,chalkiness from 0.25%～49.63%,transparency grade from 1～5,grain thickness from 1.57～2.40 mm,alkali elimination value from 1～7,gel consistency from14.50～100 mm,amylose content from 1.16%～37.24%,albumin content from 0.8～10.92mg/g,globulin content from 2～6.14 mg/g,prolamin content from 0.11～9.84 mg/g and glutenin content from 20.06～68.42 mg/g,respectively.2.The results of correlation analysis among different rice quality traits showed as follows: grain length was negatively correlated with grain width and chalkiness,respectively;grain width was positively correlated with chalkiness;gel consistency was significantly negatively correlated with transparency and amylose content,respectively;there was no significant correlation among the four storage proteins in nutritional quality.3.The results of genome-wide association analysis showed that a total of 49 QTL related to quality traits were located.Among them,the LOD value of QTL q AC6 controlling amylose content was the highest at 16.45,and the phenotypic contribution rate of QTL q GT11.3 controlling grain thickness was the highest at 49.49%.Based on the bioinformatics analysis of the identified candidate genes,the interval of grain type QTL q GL3.2 and q LWR3 coincided with the cloned grain length gene GS3,and the interval of cooking and eating quality QTL q GC6 and q AC6 coincided with the cloned amylose content gene Wx.Among the located QTL of storage proteins,the total protein QTL q AP4 was located in the same interval as the glutenin QTL q GTC4.2.In addition,some cloned genes(GS2,GL3.2,GW5,TRBF3,WTG1,Os TPS1,ALK)have been repeatedly identified in this study,indicating that the phenotypic data and the mapping results of association analysis are true and reliable.Besides,our work also identified some new QTL,such as q AC11 controlling amylose content with a LOD value of 13.0 and explaining 5.16% of phenotypic variation,q GDC11 and q GDC10.1 for prolamin,and q ABC1.2 for albumin.These QTL are believed to serve as key genes for regulating related traits.In conclusion,this research can quickly mine and locate rice quality-related QTL through phenotypic identification,re-sequencing of rice natural population,and genomewide association study.In the follow-up,the target genes will be determined by multiple linkage analysis of NAM population,expression detection of candidate genes and genetic transformation,and ultimately reveal the molecular mechanisms of candidate genes involved in rice quality. |
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