Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China

Abstract

The Chinese genebank contains 23,587 soybean landraces collected from 29 provinces. In this study, a representative collection of 1,863 landraces were assessed for genetic diversity and genetic diVerentiation in order to provide useful information for eVective management and utilization. A total of 1,160 SSR alleles at 59 SSR loci were detected including 97 unique and 485 low-frequency alleles, which indicated great richness and uniqueness of genetic variation in this core collection. Seven clusters were inferred by STRUCTURE analysis, which is in good agreement with a neighbor-joining tree. The cluster subdivision was also supported by highly signiWcant pairwise F st values and was generally in accordance with diVerences in planting area and sowing season. The cluster HSuM, which contains accessions collected from the region between 32.0 and 40.5°N, 105.4 and 122.2°E along the central and downstream parts of the Yellow River, was the most genetically diverse of the seven clusters. This provides the Wrst molecular evidence for the hypotheses that the origin of cultivated soybean is the Yellow River region. A high proportion (95.1%) of pairs of alleles from diVerent loci was in LD in the complete dataset. This was mostly due to overall population structure, since the number of locus pairs in LD was reduced sharply within each of the clusters compared to the complete dataset. This shows that population structure needs to be accounted for in association studies conducted within this collection. The low value of LD within the clusters can be seen as evidence that much of the recombination events in the past have been maintained in soybean, Wxed in homozygous self-fertilizing landraces.

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

“…In addition, analyses of more samples are needed to probe how soybean subpopulations have adapted to different geographic areas 14 and to identify the large number of rare alleles that have been lost during soybean domestication and improvement 4 . These rare alleles could benefit future soybean improvement as they constitute excellent genetic variances, especially for resistant genes 4 .…”

Bayesian analysis of the genetic structure of a Brazilian popcorn germplasm using data from simple sequence repeats (SSR)

“…In fact, Vaz Patto et al (2009) found 12 private alleles in 54 populations of maize, which were evaluated using 13 microsatellite markers, whereas Bracco et al (2009) found 33 private alleles in six maize landraces using 10 microsatellite markers. According to Li et al (2008), rare SSR loci, especially in plants with rare alleles at multiple loci, may indicate that these landraces have had limited genetic exchange with other landraces, and therefore may have rare alleles for various functional traits as well. Because these unique or rare alleles are likely caused by natural mutation and selection (Mousadik and Petit, 1996), they can be used not only in the specific categorization of germplasm collections but also in breeding and plant development as unique markers (Li et al, 2008).…”

Genetic Diversity and Population Structure of Korean Soybean Collection Using 75 Microsatellite Markers

“…Microsatellite or simple sequence repeats (SSRs) markers has been used for genetic diversity analysis because microsatellites are plentiful variations over the genome and highly reproducible and easy for genotyping as a codominant markers. The high level of polymorphism was detected in several soybean collections; 18.3 alleles (6 microsatellite loci) in Korean soybean accessions (Yoon et al, 2009), 25.5 alleles (46 microsatellite loci) in wild soybean collection (Lee et al, 2008), 12.2 alleles (60 microsatellite loci) in Chinese soybean accessions (Wang et al, 2006), 19.7 alleles (59 microsatellite loci) in soybean landraces of China (Li et al, 2008). Using microsatellite markers, Choi et al (1999) analyzed the collection acquired from five major rivers in Korea and they supported that SSR markers are useful tool to classify cultivated soybeans and wild soybeans, and Dong et al (2004) analyzed genetic diversity of cultivated soybean accessions collected from several provinces of China and proposed one possible diversity center.…”

“…Especially, landraces collected in center of origins are useful for genetic improvement of cultivars in that wild relatives generally reveal many unwanted traits and show low introgression rate (Song et al, 2013). Genetic analysis using molecular markers have been consistently studied to understand the genetic variability of soybeans, and have revealed the genetic structure and diversity of various soybean collections (Choi et al, 1999;Dong et al, 2004;Guan et al, 2010;Lee et al, 2008;Li et al, 2008;Wang et al, 2006;Yoon et al, 2009). Microsatellite or simple sequence repeats (SSRs) markers has been used for genetic diversity analysis because microsatellites are plentiful variations over the genome and highly reproducible and easy for genotyping as a codominant markers.…”