| Soybean(Glycine max(L.) Merri) is the one of the most important sources of plant protein and oil in China. Compared to the global averaged level, the yield potential of soybean in China has a broad space for breeding improvement. The founder parents have played important roles in the about 2000 cultivars released in China. It is important to identify and mine the key genome regions in the founder parents and to elucidate their genetic contribution to derived cultivars, which would be useful for improving the efficiency of breeding.In this study, the Genome-wide Association Analysis(GWAS) was performed to identify the SNPs and haplotypes underlying soybean yield and quality related traits using the founder parent Tokachi nagaha and its 137 derived cultivars as materials, and the genetic contribution from Tokachi nagaha to its derived cultivars on molecular level were analyzed. The main results are as following:ANOVA showed that genotype, environment, interaction between genotype and environment for each trait were significantly different. Plant height possessed the highest broad-sense heritability, followed by number of nodes on main stem, 100-seed weight, and fat content, whereas protein content, number of pods per plant, number of seeds per plant and seed weight per plant possessed the lowest broad-sense heritability. Correlation analysis showed that a reasonable plant height was critical to obtain the ideal seed weight per plant, and the increasing on the number of branches per plant did not significantly improve the seed weight per plant. The number of pods per plant and number of seeds per plant were negatively related to 100-seed weight, and in order to improve the seed weight per plant, it is necessary to consider the relationship among them. Traits stability were analyzed by using the additive main effects and multiplicative interactions(AMMI) model, and the result showed that significant positive correlation between phenotypic means of number of branches per plant, number of pods per plant, number of seeds per plant, seed weight per plant and themselves D i values, which indicated the more branches, pods, seeds and seed weight a cultivar had, the less stable a cultivar was. Thus, it is difficult to develop a good cultivar with both high and stable yield performances at the same time. General stability of Tokachi nagaha was bad because the D i of nine traits were higher in both environments. Comprehensive assessment indicated that Tokachi nagaha had more number of pods per plant, number of seeds per plant and seed weight per plant by using principal component analysis; cluster analysis showed that about 47.4 percent of total cultivars were alike Tokachi nagaha and in same subgroups; all of which mean that Tokachi nagaha had made larger genetic contribution to its derived in number of pods per plant, number of seeds per plant and seed weight per plant.Genome-wide association analysis was performed for agronomic traits and principal component using 4044 SNPs and 499 haplotypes. 138 materials could be divided into two subpopulations, and accessions of each subpopulation were nearly derived from the same province. Certain relatedness was detected between pair-wise accessions within population. LD was obvious in Chromosomes and the average decay distance of linkage disequilibrium intra-chromosome was about 8370 kb. 151 SNPs and haplotypes with significant signal were detected which distributed across 19 chromosomes except LG 1. Some markers were located in or close to the quantitative trait loci reported by linkage analysis in previously. Eleven SNPs were located in the genes, of which one was located in the 3’-UTR region, two SNPs in the 5’-UTR region, and one in the CDS region, and seven in introns. Eighteen SNPs related to agronomic traits, 4 SNPs associated with principal components, and 5 associated haplotypes could be detected in two environments simultaneously; senven SNPs could be detected simultaneously in the association analysis of agronomic traits and principal components; 15 SNPs contained by 5 haplotypes could be detected in agronomic traits association analysis, indicating these loci were more confident. Physical position of some SNPs and haplotypes were clustered in certain chromosome regions, and 10 SNPs and 4 haplotypes were co-associated with two or more different traits, and the QTL/gene underlying those SNPs maybe pleiotropic or tightly linked to each other.In two environments, Tokachi nagaha contained the largest number of faovarable alleles, 37 and 34, in low-dense environment and high-dense environment, respectively. Phenotypic values will be higher if an accession contains more favorable alleles of certain trait. Of the 23 SNPs associated with number of branch per plant, Tokachi nagaha contained 22 positive effective alleles, and the frequency of which were 4.38%~16.79% in derived cultivars. Of the 19 yield related SNPs, Tokachi nagaha contained 15 positive effective alleles, and the frequency of the most of which were more than 57% in derived cultivars. Of 28 SNPs associated with protein content, all alleles of Tokachi nagaha were positive, and the frequency of 22 alleles(78.57%) were more than 30% in the derived cultivars; 10 SNPs were associated with fat content, and all alleles from Tokachi nagaha were negative and their frequencies were low in the derived cultivars. As shown above, a large number of yield-related favorable alleles in Tokachi nagaha with high frequency in derived elite cultivars have made Tokachi nagaha a founder parent.Some modern elite cultivars, such as Tongnong 5, Tongnong 6, Tongnong 14, Heinong 43, Hefeng 25 and Suinong 14, mained a large portion of favorable alleles from Tokachi nagaha, can be used as bone parents in the future breeding in soybean. |
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