Genetic Structure Of Inbred Lines From Shaan A Group And Shaan B Group And Association Analysis Of Grain Yield

Increasing grain yield is the primary goal in maize breeding.The key to maize breeding lies in germplasm resources.The germplasm foundation is narrow in our country,which has has limited the cultivation of maize breakthrough varieties.Studying the genetic structure of germplasm and mining excellent genetic variants are important for the improvement of maize yield.In this study,a toal of 126 inbred lines including 122 inbred lines selected from Shaan A group and Shaan B group as well as 4 common inbred lines(PH6WC,4CV,Chang 7-2,Zheng 58)were used as materials.tGBS sequencing and field experiments for 126 inbred lines were carried out.The genotype measured by tGBS sequencing and the grain yield data of 126 inbred lines measured in Yangling and Yulin were used to analyze the genetic structure of the population and dissect genetic mechanism of grain yield.The aim was to guide the breeding and mine superior variants associated with maize grain yield.The main conclusions are as follows:1.A total of 299,598,955 raw reads were obtained through tGBS.After these reads were aligned and filtered,46,046 SNPs were screened according to the missing rate ≤50% and the minimum allele frequency(MAF)≥0.01.The marker density was 46.7 kb and these markers mainly distributed in the intron region(25%)and the downstream region of gene(23%).Among them,31,983 SNPs(MAF ≥ 0.05)has higher quality,and the average marker density is 65.9kb across 10 chromosomes.The SNP distribution in the intron region and downstream region of gene was close to 50%.2.Compared with inbreds from Shaan A group,inbreds from Shaan B group had higher MAF and polymorphism information content(PIC),as well as more unique SNPs.Which indicated that the inbreds from Shaan B group have richer genetic diversity than the inbreds from Shaan A group.Based on admixture,principal component analysis(PCA)and cluster analysis(UPGMA),126 maize inbred lines were divided into six subgroups.Most of inbreds from Shaan A group were mainly clusted into Sub 1 or Subgroup 1.The inbred lines from shaan B group were mainly divided into other Subs or Subgroups.In addition,the Nei’s genetic distance between Sub 1 and Sub 4 was the farthest.3.A total of 33 significant SNP loci or SNP clusters were mapped through genome-wide assocation analysis.One SNP was co-localized in Yulin and Yangling.By searching candidate genes at 150 kb region up-and downstream of the significant SNP locus or SNP cluster,30 candidate genes were predicted.These candidated genes were mainly enriched in different biological functions including defense response signaling pathway,the resistance gene dependence(GO: 0009870),the regulation of the immune system process(GO: 0002682),red light(GO: 0010114)and so on.In summary,these results about the genetic structure of breeding population provide a reference for breeding and population improvement.Dissecting the genetic basis of maize yield contributes to genetic improvement for increase of yield.