Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

2010 ◽  
Vol 42 (12) ◽  
pp. 1053-1059 ◽  
Author(s):  
Hon-Ming Lam ◽  
Xun Xu ◽  
Xin Liu ◽  
Wenbin Chen ◽  
Guohua Yang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cultivated Soybean

Genetic Diversity of Chinese Cultivated Soybean Revealed by SSR Markers

Crop Science ◽  
2006 ◽  
Vol 46 (3) ◽  
pp. 1032-1038 ◽  
Author(s):  
Lixia Wang ◽  
Rongxia Guan ◽  
Liu Zhangxiong ◽  
Ruzhen Chang ◽  
Lijuan Qiu
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Cultivated Soybean

scholarly journals Genetic diversity center of cultivated soybean (Glycine max) in China – New insight and evidence for the diversity center of Chinese cultivated soybean

2016 ◽  
Vol 15 (11) ◽  
pp. 2481-2487 ◽  
Author(s):  
Li-xia WANG ◽  
Fan-yun LIN ◽  
Lin-hai LI ◽  
Wei LI ◽  
Zhe YAN ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Glycine Max ◽  
Cultivated Soybean

Genetic diversity analysis using simple sequence repeat markers in soybean

2014 ◽  
Vol 12 (S1) ◽  
pp. S87-S90 ◽  
Author(s):  
Zhenbin Hu ◽  
Guizhen Kan ◽  
Guozheng Zhang ◽  
Dan Zhang ◽  
Derong Hao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Wild Soybean ◽  
Sequence Repeat ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Cultivated Soybean ◽  
Simple Sequence ◽  
Nei's Genetic Distance

To evaluate the genetic diversity (GD) of wild and cultivated soybeans and determine the genetic relationships between them, in this study, 127 wild soybean accessions and 219 cultivated soybean accessions were genotyped using 74 simple sequence repeat (SSR) markers. The results of the study revealed that the GD of the wild soybeans exceeded that of the cultivated soybeans. In all, 924 alleles were detected in the 346 soybean accessions using 74 SSRs, with an average of 12.49 alleles per locus. In the 219 cultivated soybean accessions, 687 alleles were detected, with an average of 9.28 alleles per locus; in the 127 wild soybean accessions, 835 alleles were detected, with an average of 11.28 alleles per locus. We identified 237 wild-soybean-specific alleles and 89 cultivated-soybean-specific alleles in the 346 soybean accessions, and these alleles accounted for 35.28% of all the alleles in the sample. Principal coordinates analysis and phylogenetic analysis based on Nei's genetic distance indicated that all the accessions could be classified into two major clusters, corresponding to wild and cultivated soybeans. These results will increase our understanding of the genetic differences and relationships between wild and cultivated soybeans and provide information to develop future breeding strategies to improve soybean yield.

scholarly journals A versatile resource of 1500 diverse wild and cultivated soybean genomes for post-genomics research

2020 ◽  
Author(s):  
Hengyou Zhang ◽  
He Jiang ◽  
Zhenbin Hu ◽  
Qijian Song ◽  
Yong-qiang Charles An
Keyword(s):  
Genetic Diversity ◽  
Genome Sequencing ◽  
Wild Soybean ◽  
Genomic Research ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
The Public ◽  
Population Structure Analysis ◽  
Public Data ◽  
Cultivated Soybean

SummaryWith the advance of next-generation sequencing technologies, over 15 terabytes of raw soybean genome sequencing data were generated and made available in the public. To develop a consolidated, diverse, and user-friendly genomic resource to facilitate post-genomic research, we sequenced 91 highly diverse wild soybean genomes representing the entire US collection of wild soybean accessions to increase the genetic diversity of the sequenced genomes. Having integrated and analyzed the sequencing data with the public data, we identified and annotated 32 million single nucleotide polymorphisms (32mSNPs) with a resolution of 30 SNPs/kb and 12 non-synonymous SNPs/gene in 1,556 accessions (1.5K). Population structure analysis showed that the 1.5K accessions represent the genetic diversity of the 20,087 (20K) soybean accessions in the U.S. collection. Inclusion of wild soybean genomes significantly increased the genetic diversity and shorten linkage disequilibrium distance in the panel of soybean accessions. We identified a collection of paired accessions sharing the highest genomic identity between the 1.5K and 20K accessions as genomically “equivalent” accessions to maximize the use of the genome sequences. We demonstrated that the 32mSNPs in the 1.5K accessions can be effectively used for in-silico genotyping, discovering trait QTL, gene alleles/mutations, identifying germplasms containing beneficial allele and domestication selection of trait alleles. We made the 32mSNPs and 1.5K accessions with detailed annotation available at SoyBase and Ag Data Commons. The dataset could serve as a versatile resource to release the potential of the huge amount of genome sequencing data for a variety of postgenomic research.

scholarly journals Addendum: Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

2011 ◽  
Vol 43 (4) ◽  
pp. 387-387 ◽  
Author(s):  
Hon-Ming Lam ◽  
Xun Xu ◽  
Xin Liu ◽  
Wenbin Chen ◽  
Guohua Yang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cultivated Soybean

Genetic diversity and population structure of wild soybean (Glycine soja Sieb. and Zucc.) accessions in Korea

2014 ◽  
Vol 12 (S1) ◽  
pp. S45-S48 ◽  
Author(s):  
Kil Hyun Kim ◽  
Seukki Lee ◽  
Min-Jung Seo ◽  
Gi-An Lee ◽  
Kyung-Ho Ma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Glycine Soja ◽  
Crop Improvement ◽  
Wild Soybean ◽  
Background Information ◽  
Ssr Loci ◽  
Breeding Programmes ◽  
Western Side ◽  
Cultivated Soybean

Genetic variation in wild soybean (Glycine soja Sieb. and Zucc.) is a valuable resource for crop improvement efforts. Soybean is believed to have originated from China, Korea, and Japan, but little is known about the diversity or evolution of Korean wild soybean. Therefore, in this study, we evaluated the genetic diversity and population structure of 733 G. soja accessions collected in Korea using 21 simple sequence repeat (SSR) markers. The SSR loci produced 539 alleles (25.7 per locus) with a mean genetic diversity of 0.882 in these accessions. Rare alleles, those with a frequency of less than 5%, represented 75% of the total number. This collection was divided into two populations based on the principal coordinate analysis. Accessions from population 1 were distributed throughout the country, whereas most of the accessions from population 2 were distributed on the western side of the Taebaek and Sobaek mountains. The Korean G. soja collection evaluated in this study should provide useful background information for allele mining approach and breeding programmes to introgress alleles into the cultivated soybean (G. max (L). Merr.) from wild soybean.

The genetic diversity of cultivated soybean grown in China

2003 ◽  
Vol 108 (5) ◽  
pp. 931-936 ◽  
Author(s):  
Y. S. Dong ◽  
L. M. Zhao ◽  
B. Liu ◽  
Z. W. Wang ◽  
Z. Q. Jin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cultivated Soybean

Comparison of genetic diversity between Canadian adapted genotypes and exotic germplasm of soybean

Genome ◽  
2010 ◽  
Vol 53 (5) ◽  
pp. 337-345 ◽  
Author(s):  
Elmer Iquira ◽  
Éric Gagnon ◽  
François Belzile
Keyword(s):  
Genetic Diversity ◽  
Glycine Soja ◽  
Distinct Group ◽  
Distance Matrix ◽  
Breeding Program ◽  
Local Conditions ◽  
Plant Introductions ◽  
Trace Back ◽  
Cultivated Soybean ◽  
Almost All

Soybean ( Glycine max (L.) Merr.) was domesticated in China and the greatest genetic diversity for this species is found in Asia. In contrast, in North America, soybean cultivars trace back to a small number of plant introductions from Asia and genetic diversity is typically quite limited. The purpose of this work was to measure and compare the genetic diversity in two sets of soybean lines. The first set (termed “local”) was composed of 100 lines used in a private breeding program in Quebec. The second set (termed “exotic”) was composed of 200 lines from elsewhere in the world (but mostly from Asia) and included a few lines of Glycine soja , the wild progenitor of cultivated soybean. Almost all the genotypes belonged to maturity groups between 000 and II. A total of 39 microsatellites (SSRs) were used to genotype the two collections. The number of alleles per locus was almost twice as great in the exotic set compared with the local set. Also, the number of “unique” alleles, i.e., those uniquely present in one set and absent in the other, was almost fivefold greater (191 vs. 37) in a subset of 108 exotic lines with good adaptation than among the local set. A genetic distance matrix, a UPGMA cluster analysis, and a principal coordinate analysis were conducted based on the SSR data. These analyses all indicated that the exotic set was much more diverse and formed a clearly distinct group from the local set. Interestingly, some of the lines showing the best adaptation to local conditions were quite distinctive in terms of their genotype and could potentially contribute useful novel genetic variation within the breeding program.

Climate change will hit genetic diversity

Nature ◽  
2011 ◽  
Keyword(s):  
Climate Change ◽  
Genetic Diversity

Genetic diversity of malaria vector

Nature India ◽  
2007 ◽  
Author(s):  
Subhra Priyadarshini
Keyword(s):  
Genetic Diversity ◽  
Malaria Vector
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