Dataset Information

Comparison of Genetic Diversity between Chinese and American Soybean (Glycine max (L.)) Accessions Revealed by High-Density SNPs.

ABSTRACT: Soybean is one of the most important economic crops for both China and the United States (US). The exchange of germplasm between these two countries has long been active. In order to investigate genetic relationships between Chinese and US soybean germplasm, 277 Chinese soybean accessions and 300 US soybean accessions from geographically diverse regions were analyzed using 5,361 SNP markers. The genetic diversity and the polymorphism information content (PIC) of the Chinese accessions was higher than that of the US accessions. Population structure analysis, principal component analysis, and cluster analysis all showed that the genetic basis of Chinese soybeans is distinct from that of the USA. The groupings observed in clustering analysis reflected the geographical origins of the accessions; this conclusion was validated with both genetic distance analysis and relative kinship analysis. F_ST-based and EigenGWAS statistical analysis revealed high genetic variation between the two subpopulations. Analysis of the 10 loci with the strongest selection signals showed that many loci were located in chromosome regions that have previously been identified as quantitative trait loci (QTL) associated with environmental-adaptation-related and yield-related traits. The pattern of diversity among the American and Chinese accessions should help breeders to select appropriate parental accessions to enhance the performance of future soybean cultivars.

SUBMITTER: Liu Z

PROVIDER: S-EPMC5715234 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Comparison of Genetic Diversity between Chinese and American Soybean (<i>Glycine max</i> (L.)) Accessions Revealed by High-Density SNPs.

Liu Zhangxiong Z Li Huihui H Wen Zixiang Z Fan Xuhong X Li Yinghui Y Guan Rongxia R Guo Yong Y Wang Shuming S Wang Dechun D Qiu Lijuan L

Frontiers in plant science 20171130

Soybean is one of the most important economic crops for both China and the United States (US). The exchange of germplasm between these two countries has long been active. In order to investigate genetic relationships between Chinese and US soybean germplasm, 277 Chinese soybean accessions and 300 US soybean accessions from geographically diverse regions were analyzed using 5,361 SNP markers. The genetic diversity and the polymorphism information content (PIC) of the Chinese accessions was higher ...[more]

PMID: 29250088

Similar Datasets

Project description:BackgroundThe genetic base of soybean cultivars in India has been reported to be extremely narrow, due to repeated use of few selected and elite genotypes as parents in the breeding programmes. This ultimately led to the reduction of genetic variability among existing soybean cultivars and stagnation in crop yield. Thus in order to enhance production and productivity of soybean, broadening of genetic base and exploring untapped valuable genetic diversity has become quite indispensable. This could be successfully accomplished through molecular characterization of soybean genotypes using various DNA based markers. Hence, an attempt was made to study the molecular divergence and relatedness among 29 genotypes of soybean using SSR markers.Methods and resultsA total of 35 SSR primers were deployed to study the genetic divergence among 29 genotypes of soybean. Among them, 14 primer pairs were found to be polymorphic producing a total of 34 polymorphic alleles; and the allele number for each locus ranged from two to four with an average of 2.43 alleles per primer pair. Polymorphic information content (PIC) values of SSRs ranged from 0.064 to 0.689 with an average of 0.331. The dendrogram constructed based on dissimilarity indices clustered the 29 genotypes into two major groups and four sub-groups. Similarly, principal coordinate analysis grouped the genotypes into four major groups that exactly corresponded to the clustering of genotypes among four sub-groups of dendrogram. Besides, the study has reported eight unique and two rare alleles that could be potentially utilized for genetic purity analysis and cultivar identification in soybean.ConclusionIn the present investigation, two major clusters were reported and grouping of large number of genotypes in each cluster indicated high degree of genetic resemblance and narrow genetic base among the genotypes used in the study. With respect to the primers used in the study, the values of PIC and other related parameters revealed that the selected SSR markers are moderately informative and could be potentially utilized for diversity analysis of soybean. The clustering pattern of dendrogram constructed based on SSR loci profile displayed good agreement with the cultivar's pedigree information. High level of genetic similarity observed among the genotypes from the present study necessitates the inclusion of wild relatives, land races and traditional cultivars in future soybean breeding programmes to widen the crop gene pool. Thus, hybridization among diverse gene pool could result in more heterotic combinations ultimately enhancing genetic gain, crop yield and resistance to various stress factors.

Project description:Soybean (Glycine max) is an important leguminous crop that is grown throughout the United States and around the world. In 2016, soybean was valued at $41 billion USD in the United States alone. Increasingly, soybean farmers are adopting alternative management strategies to improve the sustainability and profitability of their crop. Various benefits have been demonstrated for alternative management systems, but their effects on soybean-associated microbial communities are not well-understood. In order to better understand the impact of crop management systems on the soybean-associated microbiome, we employed DNA amplicon sequencing of the Internal Transcribed Spacer (ITS) region and 16S rRNA genes to analyze fungal and prokaryotic communities associated with soil, roots, stems, and leaves. Soybean plants were sampled from replicated fields under long-term conventional, no-till, and organic management systems at three time points throughout the growing season. Results indicated that sample origin was the main driver of beta diversity in soybean-associated microbial communities, but management regime and plant growth stage were also significant factors. Similarly, differences in alpha diversity are driven by compartment and sample origin. Overall, the organic management system had lower fungal and bacterial Shannon diversity. In prokaryotic communities, aboveground tissues were dominated by Sphingomonas and Methylobacterium while belowground samples were dominated by Bradyrhizobium and Sphingomonas. Aboveground fungal communities were dominated by Davidiella across all management systems, while belowground samples were dominated by Fusarium and Mortierella. Specific taxa including potential plant beneficials such as Mortierella were indicator species of the conventional and organic management systems. No-till management increased the abundance of groups known to contain plant beneficial organisms such as Bradyrhizobium and Glomeromycotina. Network analyses show different highly connected hub taxa were present in each management system. Overall, this research demonstrates how specific long-term cropping management systems alter microbial communities and how those communities change throughout the growth of soybean.

Dataset Information

Comparison of Genetic Diversity between Chinese and American Soybean (Glycine max (L.)) Accessions Revealed by High-Density SNPs.

Publications

Comparison of Genetic Diversity between Chinese and American Soybean (<i>Glycine max</i> (L.)) Accessions Revealed by High-Density SNPs.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets