Home LiteratureArticle Details
PMID: 21076406 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

Nature genetics ·Vol. 42 ·No. 12 ·2010-12-00 ·Pages 1053-9

Lam HM, Xu X, Liu X, Chen W, Yang G, Wong FL, Li MW, He W, Qin N, Wang B, Li J, Jian M, Wang J, Shao G, Wang J, Sun SS, Zhang G

Abstract

We report a large-scale analysis of the patterns of genome-wide genetic variation in soybeans. We re-sequenced a total of 17 wild and 14 cultivated soybean genomes to an average of approximately ×5 depth and >90% coverage using the Illumina Genome Analyzer II platform. We compared the patterns of genetic variation between wild and cultivated soybeans and identified higher allelic diversity in wild soybeans. We identified a high level of linkage disequilibrium in the soybean genome, suggesting that marker-assisted breeding of soybean will be less challenging than map-based cloning. We report linkage disequilibrium block location and distribution, and we identified a set of 205,614 tag SNPs that may be useful for QTL mapping and association studies. The data here provide a valuable resource for the analysis of wild soybeans and to facilitate future breeding and quantitative trait analysis.

MeSH Terms
Agriculture Chromosomes, Plant/genetics Genes, Plant/genetics Genetic Variation Genome, Plant/genetics Inbreeding Linkage Disequilibrium/genetics Mutation/genetics Phylogeny Polymorphism, Single Nucleotide/genetics Selection, Genetic Sequence Analysis, DNA Soybeans/genetics
Authors & Affiliations
17 authors, click to expand affiliations / ORCID
Lam Hon-Ming
State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong. honming@cuhk.edu.hk
Xu Xun
Liu Xin
Chen Wenbin
Yang Guohua
Wong Fuk-Ling
Li Man-Wah
He Weiming
Qin Nan
Wang Bo
Li Jun
Jian Min
Wang Jian
Shao Guihua
Wang Jun
Sun Samuel Sai-Ming
Zhang Gengyun
References (43)
43 references, click to expand
  1. On the number of segregating sites in genetical models without recombination.
    Theor Popul Biol. 1975 Apr;7(2):256-76 PMID: 1145509
  2. Impacts of genetic bottlenecks on soybean genome diversity.
    Proc Natl Acad Sci U S A. 2006 Nov 7;103(45):16666-71 PMID: 17068128
  3. Genome sequence, comparative analysis and haplotype structure of the domestic dog.
    Nature. 2005 Dec 8;438(7069):803-19 PMID: 16341006
  4. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data.
    PLoS Genet. 2009 Oct;5(10):e1000695 PMID: 19851460
  5. Evolutionary relationship of DNA sequences in finite populations.
    Genetics. 1983 Oct;105(2):437-60 PMID: 6628982
  6. Circos: an information aesthetic for comparative genomics.
    Genome Res. 2009 Sep;19(9):1639-45 PMID: 19541911
  7. The diploid genome sequence of an Asian individual.
    Nature. 2008 Nov 6;456(7218):60-5 PMID: 18987735
  8. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.
    BMC Bioinformatics. 2006 Feb 09;7:62 PMID: 16469098
  9. BLAT--the BLAST-like alignment tool.
    Genome Res. 2002 Apr;12(4):656-64 PMID: 11932250
  10. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana.
    Science. 2007 Jul 20;317(5836):338-42 PMID: 17641193
  11. Identification of QTL underlying vitamin E contents in soybean seed among multiple environments.
    Theor Appl Genet. 2010 May;120(7):1405-13 PMID: 20069414
  12. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds.
    Science. 2009 Apr 24;324(5926):528-32 PMID: 19390050
  13. Genome-wide patterns of nucleotide polymorphism in domesticated rice.
    PLoS Genet. 2007 Sep;3(9):1745-56 PMID: 17907810
  14. Interrogating a high-density SNP map for signatures of natural selection.
    Genome Res. 2002 Dec;12(12):1805-14 PMID: 12466284
  15. Modeling gene and genome duplications in eukaryotes.
    Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5454-9 PMID: 15800040
  16. Adaptive protein evolution at the Adh locus in Drosophila.
    Nature. 1991 Jun 20;351(6328):652-4 PMID: 1904993
  17. The evolutionary fate and consequences of duplicate genes.
    Science. 2000 Nov 10;290(5494):1151-5 PMID: 11073452
  18. The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication.
    Trends Genet. 2006 Mar;22(3):126-31 PMID: 16443304
  19. Structure of linkage disequilibrium in plants.
    Annu Rev Plant Biol. 2003;54:357-74 PMID: 14502995
  20. A first-generation haplotype map of maize.
    Science. 2009 Nov 20;326(5956):1115-7 PMID: 19965431
  21. Genome sequence of the palaeopolyploid soybean.
    Nature. 2010 Jan 14;463(7278):178-83 PMID: 20075913
  22. The structure of haplotype blocks in the human genome.
    Science. 2002 Jun 21;296(5576):2225-9 PMID: 12029063
  23. SOAP2: an improved ultrafast tool for short read alignment.
    Bioinformatics. 2009 Aug 1;25(15):1966-7 PMID: 19497933
  24. GeneWise and Genomewise.
    Genome Res. 2004 May;14(5):988-95 PMID: 15123596
  25. Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice.
    Mol Biol Evol. 2007 Mar;24(3):875-88 PMID: 17218640
  26. Building the sequence map of the human pan-genome.
    Nat Biotechnol. 2010 Jan;28(1):57-63 PMID: 19997067
  27. Human-mouse alignments with BLASTZ.
    Genome Res. 2003 Jan;13(1):103-7 PMID: 12529312
  28. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice.
    Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12273-8 PMID: 19597147
  29. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution.
    Plant Cell. 2004 Jul;16(7):1679-91 PMID: 15208398
  30. Haploview: analysis and visualization of LD and haplotype maps.
    Bioinformatics. 2005 Jan 15;21(2):263-5 PMID: 15297300
  31. QTL mapping of domestication-related traits in soybean (Glycine max).
    Ann Bot. 2007 Nov;100(5):1027-38 PMID: 17684023
  32. SNP detection for massively parallel whole-genome resequencing.
    Genome Res. 2009 Jun;19(6):1124-32 PMID: 19420381
  33. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.
    Mol Biol Evol. 2007 Aug;24(8):1596-9 PMID: 17488738
  34. Generating samples under a Wright-Fisher neutral model of genetic variation.
    Bioinformatics. 2002 Feb;18(2):337-8 PMID: 11847089
  35. Inference of population structure using multilocus genotype data.
    Genetics. 2000 Jun;155(2):945-59 PMID: 10835412
  36. Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques.
    Science. 2007 Apr 13;316(5822):240-3 PMID: 17431170
  37. Highly variable patterns of linkage disequilibrium in multiple soybean populations.
    Genetics. 2007 Apr;175(4):1937-44 PMID: 17287533
  38. Recombination and linkage disequilibrium in Arabidopsis thaliana.
    Nat Genet. 2007 Sep;39(9):1151-5 PMID: 17676040
  39. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
    Genetics. 1989 Nov;123(3):585-95 PMID: 2513255
  40. Essential genes are more evolutionarily conserved than are nonessential genes in bacteria.
    Genome Res. 2002 Jun;12(6):962-8 PMID: 12045149
  41. Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx).
    Science. 2009 Oct 16;326(5951):433-6 PMID: 19713493
  42. Basic local alignment search tool.
    J Mol Biol. 1990 Oct 5;215(3):403-10 PMID: 2231712
  43. Plant pathogens and integrated defence responses to infection.
    Nature. 2001 Jun 14;411(6839):826-33 PMID: 11459065
Article Info
Journal
Nature genetics
Abbr.
Nat Genet
ISSN
1546-1718
DOI
10.1038/ng.715
Email
honming@cuhk.edu.hk
Published
2010-12-00
Epub
2010-00-14
Pages
1053-9
Language
English
Region
United States
NLM ID
9216904
Subset
IM
Corrections
ErratumIn
-
External Links
PubMed source DOI: 10.1038/ng.715 View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2