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

Liu, Zhangxiong; Li, Huihui; Zhang, Wen; Fan, Xuhong; Li, Yinghui; Guan, Rongxia; Guo, Yong; Wang, Shuming; Wang, Dechun; Qiu, Lijuan

doi:10.3389/fpls.2017.02014

Cited by 59 publications

(54 citation statements)

References 64 publications

(73 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These genotypes were similar in days to 50% flowering and 100 seed weight (S2). The fact that genotypes with similar flowering response were grouped together by SSR marker‐based cluster analysis gives some credence to the suggestion that the origin of genotypes is the principal factor driving differentiation in cultivated soybean (Liu et al, ; Roberts et al, ). High variation in days to flowering among the accessions studied can be exploited to develop varieties for the different agroecologies in Ghana, especially, the Guinea and Sudan savannah ecologies with monomodal rainfall pattern.…”

Section: Discussionmentioning

confidence: 83%

“…On the other hand, Zhangxiong et al, () obtained gene diversity of 0.34 despite using 5,195 SNP markers to genotype 577 accessions of soybean. Despite a large number of markers and accessions used in this study, diversity parameters reported were lower than what has been reported by most SSR marker‐based studies including the present study.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Genetic diversity, population structure and key phenotypic traits driving variation within soyabean (Glycine max) collection in Ghana

Denwar¹,

Awuku²,

Diers

et al. 2019

Plant Breeding

View full text Add to dashboard Cite

Soybean [Glycine max (L.) Merrill] is an important oilseed crop worldwide and it has recently become the crop of interest in Ghana. In this study, 142 soybean accessions were genotyped with 34 SSR markers and concurrently evaluated for five quantitative and two qualitative phenotypic traits. Twenty‐nine of the SSR markers were polymorphic with mean allele number of 5.3, polymorphic information content (PIC) of 0.51 and gene diversity of 0.55. Molecular analysis based on unweighted paired group arithmetic mean (UPGMA) clustering and principal coordinate analysis (PCoA) was similar in explaining the extent of diversity within the accessions. Structure analysis placed most of the accessions into two subpopulations with 18 (12.7%) as admixtures. Principal component analysis (PCA) based on phenotypic traits revealed two clusters. Both UPGMA clustering‐based SSR data and PCA from phenotypic data showed similar results. The assembled germplasm is genetically diverse with high variation in flowering and maturity period, and key yield components which could be exploited in developing superior varieties well adapted to Ghana and West Africa.

show abstract

Section: Discussionmentioning

confidence: 83%

Section: Discussionmentioning

confidence: 99%

Genetic diversity, population structure and key phenotypic traits driving variation within soyabean (Glycine max) collection in Ghana

Denwar¹,

Awuku²,

Diers

et al. 2019

Plant Breeding

View full text Add to dashboard Cite

show abstract

“…Two iSelect Illumina Infinium BeadChip arrays are publicly available for assaying soybean SNPs: the SoySNP50K (Song et al., 2013; SoyBase, 2018) with 50,000 SNPs and the BARCSoySNP6k with SNPs selected from the SoySNP50K chip by the Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, MD (Illumina, Inc., 2015; Song et al., 2014). The SoySNP50K and BARCSoySNP6k SNP sets have been used in various mapping and genetic characterization studies (Akond et al., 2013; Gibson, 2015; Huang et al., 2018; Liu et al., 2017b; Urrea, Rupe, Chen, & Rothrock, 2017). The SoySNP50K chip was also used to genotype the full 20,087 USDA soybean germplasm collection (soybean GRIN collection) (Song et al., 2015) and those SNP data were generously made available to the soybean research community (https://soybase.org/dlpages/).…”

Section: Methodsmentioning

confidence: 99%

Single nucleotide polymorphisms facilitate distinctness‐uniformity‐stability testing of soybean cultivars for plant variety protection

et al. 2020

View full text Add to dashboard Cite

Plant variety protection (PVP), or plant breeders’ rights, provides intellectual property protection (IPP) for cultivars. Technical requirements are distinctness, uniformity, and stable (DUS) reproduction. However, field trials are increasingly resource demanding and potentially inconclusive for soybean (Glycine max [L.] Merr.). Our objective was to establish methodologies using molecular markers to facilitate DUS testing while maintaining current IPP levels. We determined that DNA from 10–15 bulked plants represented cultivar genotype. Single nucleotide polymorphism (SNP) data were highly robust in the face of missing and mistyped data; concordances among five laboratories were >.9888. We used SNP, morphological, physiological, and pedigree information to examine 322 publicly available cultivars including 187 with PVPs. Associations among cultivars following multivariate analyses of genetic distances from SNP data and from pedigree kinship data were very similar. A SNP similarity of 98.6% was the maximum at which cultivars also differed for morphological characteristics. Many (38%) cultivar pairs with members >90% SNP similarity expressed different morphologies with SNP similarities ranging 96–98.6%. Of cultivars <96% SNP similar, only a single pair differed by a single morphological difference; all others differed by more than two morphological characteristics. A SNP similarity of 96% between soybean cultivars represents an initial and conservative point of demarcation between cultivars that have morphological differences and those that do not. Chronological monitoring of pedigree–kinship and SNP similarities showed little evidence that a lack of genetic diversity in F2 breeding populations contributed to challenges in DUS among U.S. soybean cultivars.

show abstract

“…However, these endemic varieties were severely destroyed in the late of the last century due to the competitive substitutes of tung oil-derived products. Wild species always have a relatively high genetic diversity, giving them more potential in genetic adaptability to a new environment [26,27], and thus they may have a high risk of invasion compared to their cultivars. For the cultivar, many genes of agronomical importance were artificially selected while a body of other genes were also lost during the process of improvement [28].…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity and Geographic Differentiation of Tung Tree, Vernicia Fordii (Euphorbiaceae), A Potential Biodiesel Plant Species with Low Invasion Risk

2019

View full text Add to dashboard Cite

The tung tree, Vernicia fordii (Herbert Kenneth Airy Shaw), is a woody species native to South-East Asia (from Central and Southwest China to North Vietnam), which is also cultivated in China for the production of industrial oil. It is listed as a Category II invasive plant species in Florida, USA. During the introduction period of the tung tree from China to other countries in the last century, its low invasion feature led to its successful establishment in only a few countries. However, the genetic consideration for the population in its widespread native environment remains lacking. In this study, a set of 95 accessions covering most of the tung tree distribution areas in China were collected. Fifty simple sequence repeat (SSR) primer pairs were selected for the genotyping of the germplasm. Population genetics analysis indicated a medium level of genetic variation within the collected samples. The genetic diversity of the tung tree from the main production region was obviously higher than those from the marginal regions. A significant genetic differentiation occurred between the two regions, as well as among the 12 regional groups of administration. The dendrogram based on Nei’s gene diversity showed that the clustering pattern for the germplasm collections basically coincided with their geographic distribution. In their native environment, human activities have had a significant impact on the gene flow via seed movement among the production areas of the tung tree in history. This study will be helpful for molecular breeding and germplasm preservation of the tung tree, and for understanding the tung tree as a biodiesel plant species with a low invasion risk when introduced into foreign countries.

show abstract

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

Cited by 59 publications

References 64 publications

Genetic diversity, population structure and key phenotypic traits driving variation within soyabean (Glycine max) collection in Ghana

Genetic diversity, population structure and key phenotypic traits driving variation within soyabean (Glycine max) collection in Ghana

Single nucleotide polymorphisms facilitate distinctness‐uniformity‐stability testing of soybean cultivars for plant variety protection

Genetic Diversity and Geographic Differentiation of Tung Tree, Vernicia Fordii (Euphorbiaceae), A Potential Biodiesel Plant Species with Low Invasion Risk

Contact Info

Product

Resources

About