Exploring Loci And Candidate Genes Associated With Soybean Seed Germination Vigor Through GWAS

Soybean is one of the important oil crops in my country,which can be widely used as feed raw materials,food raw materials,industrial raw materials,pharmaceutical raw materials,etc.Germination is a key stage of soybean seed development,and germination-related genes play a key role in the regulation of seed germination.Mining genes related to germination vigor in soybean seeds can help reveal the molecular mechanism of soybean seed germination regulation,and can provide a theoretical basis for soybean trait improvement.It also helps to improve the quality and yield of soybeans.Genome-wide association analysis(GWAS)studies are an effective method to find quantitative trait loci that control complex traits and genes associated with complex traits.In this study,the natural soybean population containing 496 accessions were used to conduct germination experiments on the seeds of soybean GWAS population harvested in multiple years and multiple locations.The phenotypes were selected as the area under the germination curve(AUC),the time corresponding to half of the maximum germination number of seeds(T50),and 40 h germination rate(G40),60 h germination rate(G60),germination index(GI)and changes in seed conductivity(ΔC).Combined with the SNPs and Indels variation information of the GWAS population,genome-wide association analysis was performed to screen significant loci related to soybean seed germination,and linkage disequilibrium analysis was performed to determine 4 candidate intervals,and the genes in candidate intervals were subjected to haplotype analysis,etc.Three candidate genes related to soybean seed germination vigor were screened,and a number of germplasms with high germination vigor were screened for soybean trait improvement.The research conclusions are as follows:1.The seed germination vigor phenotypes of the soybean GWAS populations selected in this study were all in line with normal distribution,suitable for genome-wide association analysis.2.95 significant loci related to the germination vigor of soybean seeds were detected by GWAS,and 4 repeat-scanning and highly significant leadsnps loci located on chromosomes 4,8,11 and 18 were carried out.By linkage disequilibrium analysis,four candidate intervals related to the germination vigor of soybean seeds were identified.These candidate intervals were 563.8 kb,690.9 kb,332.5 kb and 187.7 kb respectively,and there were 143 genes in these intervals.3.Screen candidate genes containing SNPs linked to leadsnps in these candidate intervals,perform haplotype analysis,haplotype germination phenotype difference analysis,expression pattern analysis,etc.on the candidate genes,and determine the candidate genes Glyma.11G164500,Glyma.11G164600 and Glyma.18G276600.The Glyma.11G164500 gene of the soybean GWAS population can be divided into two haplotypes.The germination vigor of HT1(haplotype 1)is significantly higher than that of HT2;The Glyma.11G164600 gene in the soybean GWAS population can be divided into three haplotypes.The germination vigor of HT2 is significantly higher than that of HT1 and HT3.The cis-acting element corresponding to the promoter sequence of the HT2-leadsnp-linked SNP site is Unique to HT2;The soybean GWAS population Glyma.18G276600 gene can be divided into 3 haplotypes,the germination vigor phenotype of HT2 is significantly lower than that of HT1 and HT3,and the cis-acting element corresponding to the promoter sequence of the HT2-leadsnp-linked SNP site is unique to HT2,and the differences in germination phenotypes of different haplotypes of candidate genes above may be caused by differences in cis-acting elements.4.Using the germination phenotype of soybean seeds in multiple years and multiple locations,20 excellent germplasms with high germination vigor were screened from these phenotypes above.The high germination vigor haplotypes of Glyma.11G164500,Glyma.11G164600 and Glyma.18G276600 genes accounted for 30%-95% of the elite germplasms with high germination vigor.In this study,germination experiments were carried out on soybean GWAS population materials harvested in multiple years and multiple locations,germination phenotypes were obtained,and genome-wide association analysis was performed to screen three candidate genes related to the germination vigor of soybean seeds.Candidate genes and excellent germplasm can be used for molecular mechanism research of soybean seed germination vigor and improvement of soybean genetic traits.