Genome-wide Association Analysis Of Quality Traits In Indica Rice Based On NC? Design

High-yielding and high-quality hybrid rice has always been the goal of the breeders.With the development of rice breeding technology,the overall quality of rice has been continuously improved,but there are still many problems.Under North Carolina design ?,113 elite rice varieties?male parent?,including 84 three-way wild-abortive hybrid restorer lines and 29 mini-core collection lines,crossed with four two-way restorer lines and one three-way male sterile line?female parent?to produce 565 testcrosses.We analyzed the genetic basis of quantitative trait phenotypes,general combining ability,and heterosis of indica rice at the level of classical quantitative genetics and high-throughput sequencing based on whole genomes.We also analyzed the quality genes and sources of rice in order to provide reference for rice quality improvement direction and strategy.Classical Genetic Analysis:the results were as follows:?1?Both general combining ability?Gca?and specific combining ability?Sca?were highly significant in all 12 characters,which indicated that all traits were determined by additive and non-additive effect.The genetic additive effects dominated amylose content,grain length-width radio,grain length,grain width,chalky grain and chalkiness degree;while the non-additive effects were greater than additive effects in protein content,brown rice rate,milled rice rate,head rice rate,transparent degree and alkali spreading value.?2?The Sca of different combinations with one same parent or of the same combination for different traits had significant difference and the combinations with top Sca?or bottom Sca?could be derived from different parental Gca groups,which showed that there is no constant relation between Sca and parental Gca.?3?The Gca variance contribution of the female parent for traits ranged from 0.76%to27.08%,and of the male parent ranged from 17.47%to 81.94%.The contribution rate of Gca variance to each quality characters of female parent was lower than that of male parent.This results showed all 12 characters were influenced less by female parent?sterile lines?.?4?Amylose content,grain length-width radio,grain length,grain width,chalky grain percent and chalkiness degree had higher narrow heritability?50%?and these characters may be selected in early breeding generation.Genome-wide association study:We further analyzed the genome-wide associations of four datasets:parental phenotype,parental general combining ability,hybrid F₁ phenotype,and hybrid F₁ mid-parent heterosis,using GLM,MLM,CMLM,and FarmCPU four algorithms.Keep the best results of each data in the four algorithms.?1?A total of 56significant SNP loci associated with traits were mapped and distributed on 12 chromosomes,of which the most significant loci detected on chromosome 5 were 9.According to the classification of traits,8 significant SNPs were detected in grain length,7 significant SNPs were detected in grain width,and 14 SNP loci were detected in grain length to width ratio.A total of 4 significant SNP loci about chalkiness were detected.,5 significant SNPs were detected in the chalkiness rate,7 significant SNPs were detected in transparency,and 11significant SNPs were detected in the amylose content.?2?A total of 11 significant SNP loci were detected in gene region,and these genes were not reported by the investigators.We guess these genes likely to be newly discovered genes associated with quality traits.?3?A total of 12"multiple-effect"SNP loci were detected,seven of which were near the cloned genes.Such as the chr03₁6720836 locus was not only detected to be significantly associated with the general combining ability of grain length and the hybrid F₁ phenotype,but also detected with general combining ability of the grain length to width ratio.Meanwhile,chr03₁6720836 is near the major gene GS3 that controls grain length and grain weight.?4?We analyzed the degree of dominance and found that the phenotype of the variety was mainly controlled by additive and partially dominant,while the mid-parent heterosis was mainly controlled by overdominance.?5?we also found that the parental phenotype,general combining ability,phenotypic value of F₁ hybrids,and mid-parent heterosis all increased with the increase in the number of superior alleles.This finding indicates that the superior alleles have aggregation effect is not only reflected in the heterosis,but also in the complex traits such as phenotypic traits,general combining ability,and phenotypic value of cultivated rice.There are abundant natural variations in the quality traits of rice.Understanding its genetic mechanism and excavating excellent alleles can provide great help for breeding excellent varieties.