Whole Genome Association Analysis Of Indica Rice Heading Stage Based On NCII Genetic Mating Design

Heading date is one of the most important agronomic traits that crop breeders pay attention to.It controls the distribution area and seasonal adaptability of different rice varieties.At the same time,a suitable heading period is conducive to the full use of light and temperature for crops and can increase rice yield.In this study,according to the two-factor cross genetic design（NCII）,115 indica rice were used as male parents and 5 male sterile lines were used as female parents,and 575 F1 hybrid populations were obtained.Genome-wide association study were performed for heading date of the parental lines and F₁ lines phenotypic value,general combining ability value,special combining ability value,and better-parental heterosis value,expect to discover more significant loci and candidate genes associated with heading date,and provide theoretical guidelines for rice breeding strategies and trait improvement.Using the mixed linear model in the GAPIT software package to perform genome-wide association analysis on the above five data sets.The results showed that:（1）At the level of P<1E-05,a total of 46 SNP sites that were significantly associated with traits were located on 10 chromosomes.Among them,26 SNP loci that were significantly associated with heading date were detected in the F₁representative value,and 20 significant SNP loci were detected in the better-parental heterosis value.However,the association analysis based on the mixed linear model failed to find significant locus in parent phenotype,special combining ability and parent general combining ability datasets.This may be because the heading period is controlled by minor effect multiple genes,and the single site does not contribute much to the phenotype,resulting in some marker sites not being detected.（2）By checking whether the significant SNP loci are located in the 200 kb region upstream and downstream of the gene as the selection criteria for candidate genes,finally,40and 12 candidate loci were located in the phenotypic value and the super-parental advantage value,respectively,and all gene were located and cloned.（3）Calculating the dominance of significant sites,it was found that the phenotype of the F₁ generation population was mainly controlled by partial dominance,while the better-parental heterosis value was mainly controlled by dominance.（4）Comparing the aggregation results of haplotypes and excellent haplotypes in different cloned genes,we found that in the parent variety population（V）,the yield average value in haplotype combination of Hd1＿（Hap.A）＿Hd17（Hap.C）＿Hd3a（Hap.C）＿HGW（Hap.B）＿Ghd2（Hap.C）is 35.41g,which is superior to the excellent haplotype of single gene（29.69-33.38g）;the heading date average value is 95.77 d in Hap.C,which is longer than the excellent haplotype of single gene（91.52-94.83d）.These results suggest pyramiding excellent haplotype of genes related to heading date will improve the grain yield per plant of rice and extended the heading period for rice varieties.Thus,in order to obtain high-yield conventional rice,selecting varieties with excellent haplotype aggregation of cloned genes at heading stage maybe a better choice.While in the F₁ generation of hybrids,the haplotype combination of cloned genes with the highest yield average value（44.99 g）was Hd1（Hap.D）＿Hd17（Hap.I）＿Hd3a（Hap.G）＿HGW（Hap.H）＿Ghd2（Hap.E）,and its average value of heading stage is 92.30d.Its yield average value was lower than that of Ghd2（Hap.H）（48.05 g）.So it was not found that the aggregation of superior haplotypes at heading date could increase the yield in F₁population.One reason is that the sample size of the hybrid population is limited,and there is no excellent haplotype aggregation of 5 cloned genes was observed in the population.Another reason is that,the heading date genetic basis of the hybrid F₁ generation population are more complex.Negative interaction between genes and negative regulation mechanism may affect heading date of F₁ lines,which needs further exploration with advance research methods.To sum up,in order to obtain high-yield conventional rice,priority can be given to selecting varieties with excellent haplotype aggregation of cloned genes at heading stage in rice breeding.At the same time,for the improvement of heading traits of indica hybrid populations,Ghd2（Hap.H）hybrid rice is selected,and high-yield hybrid rice is expected to be cultivated.In addition,the combination of genome-wide association analysis and haplotype analysis can make use of the linkage disequilibrium information provided by multiple SNPs,which improves the efficiency of genetic testing and is of great significance for breeding high-yield rice varieties and hybrid rice.