| Soybean is an important food and oil crop around the world,and is widely planted throughout China.The Southwest provinces,located in the mountainous aera of China,have complex and diverse geographical climates,which promotes the formation of the unique and aboundant genetic diversity of soybean germplasms.At present,only a few studies have been carried out to evaluate the phenotypic performance of quality traits of soybean germplasm in Yunnan.However,there is no report on the study of genetic diversity and association analysis for important quality traits using molecular markers in soybean germplasms originated from southern China.In this study,248 elite landraces and cultivars from Yunnan and 36 cultivars from southern provinces of China were used to evaluate the contents of oil,fatty acids and protein.High-throughput sequencing(HTS)technology was used to re-sequence the whole genome and to analyze the Single Nucleotide Polymorphisms(SNP)genotype of the population.The genetic structure and kinship of the population were analyzed.Based on the phenotypic and genotypic date,genome-wide association analysis for the quality traits was carried out.The main results were as follows:1.Field experiment showed that the average contens of oil,oleic acid,linoleic acid,linolenic acid,stearic acid,palmitic acid and protein were 18.64%,25.66%,55.53%,6.44%,3.63%,10.57%and 45.09%,respectively.Oleic acid and linolenic acid showed higher coefficient of variation,which were 21%and 18.48%,respectively.Correlation analysis of the quality traits showed that protein content was negatively correlated with oil and oleic acid contents,and positively correlated with linoleic acid,stearic acid and palmitic acid.Oil content was positively correlated with oleic acid and negatively correlated with other quality traits.Oleic acid content was negatively correlated with the other four fatty acids and protein.2.Through quality control,39193 high-quality SNP markers covering the whole genome of soybean were obtained.Among which,79.9%markers were distributed on 20 chromosomes of soybean and 20.1%markers were distributed on SCAFFOLD fragments.Except for SCAFFOLD fragments,the number of markers distributed on chromosome 19 was the most,and the markers on chromosomes 11 and 12 were the least.The number of SNP markers distributed on chromosomes ranged from 494 to 4,665.The markers on chromosomes 1,3,4,6,9,10,13,15,16 and 18 covered the entire chromosomes evenly,with hign density in some regions.3.Using SNP markers,the genetic diversity of the population was analyzed.The polymorphism index of the SNP markers ranged from 0.0198 to 0.5013,with an average of 0.3648 and 51.8%of the marker polymorphism index was greater than 0.49.The nucleotide diversity index at the chromosome level was between 0.2318 and 0.4390,among which the diversity index of chromosome 8 was the highest and that of chromosome 19 was the lowest.Neighbor-Joining(NJ)cluster analysis showed that the population was divided into 7 groups,which included 11,95,26,91,30,12 and 19 lines,respectively.According to the results of NJ cluster classification,the differentiation index between the seven groups was calculated.The Fsr value between each groups was between 0.004 and 0.012,which indicated a low degree of differentiation between the groups.SNP-labeled population structure analysis was performed using ADMIXTURE version 1.3.0,and the population was divided into 7 subgroups according to the minimum cross-validation error rate.Using TASSEL version 5.0,the genetic relationship between two lines was estimated,with 21.40%of the relative coefficient greater than 0.5.4.Linkage Disequilibrium(LD)analysis of the population showed that when half of the maximum value of r2(0.41)was used as the threshold,the LD attenuation distance of the population was about 116 kb.5.Using the MLM(Q+K)model in TASSEL version 5.0,a total of 75,23,40,20,53,56,and 91 SNP markers were detected to associate with oil,oleic acid,linoleic acid,linolenic acid,stearic acid,palmitic acid and protein contents,respectively.The effects of the 358 loci associated with the quality traits were calculated.Alleles with increasing effects for oil,oleic,linoleic,linolenic,stearic,palmitic and protein were 28,12,26,13,41,32 and 40,respectively,while alleles with decreasing effects for the above quality traits were 47,11,14,7,12,24 and 51 respectivley.6.Of the SNP markers significantly associated with the quality traits,228 SNP markers were located on the chromosomes regions of soybean.Location information was analyzed by using ANNOVAR.A total of 32 SNP markers were found to locate close to related genes,among which 11 markers were located in the coding regions,11 markers were located in the 1 kb regions downstream of the related genes,and 8 markers were located in the 1 kb regions upstream of the related genes.The sequence information of the markers located closely to the related genes were used to retrieve gene information by using the reference genome of Wm82(Glyma2.0)at the Soybase website(https://soybase.org).A total of 42 genes homologous to soybean or Arabidopsis were found. |
