Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing

BMC Genomics

Research Article

Jian-xin Ma¹  Michael Purugganan²  Peng-yin Chen³  Meng-chen Zhang⁴  Xiao-tian Qi⁵  Rong-xia Guan⁵  Xiao-bo Wang⁵  Yu-lin Liu⁵  Ying-hui Li⁵  Le Zhang⁵  Ke-jing Wang⁵  Yong Guo⁵  Long-guo Jin⁵  Zhang-xiong Liu⁵  Ru-zhen Chang⁵  Li-juan Qiu⁵  Li-juan Zhang⁵  Long Yan⁶  Wen-bin Li⁷  Jun Li⁸  Wei-ming He⁸  Shan-cen Zhao⁸  Chen Ye⁸  Jian Wang⁸  Rui-qiang Li⁸  Qin-si Liang⁸  Xiao-sen Guo⁸  Jie Chen⁸  Xiu-qing Zhang⁸  Dong Li⁸  Jun Wang⁹  Yong Tao⁹  Rasmus Nielsen^1,10  Jun-yi Wang^1,11  Jochen C Reif^1,12 

[1] Department of Agronomy, Purdue University, 47907, West Lafayette, IN, USA;Department of Biology and Centre for Genomics and Systems Biology, 12 Waverly Place, New York University, 10003, New York, USA;Department of Crop, Soil, and Environmental Sciences, University of Arkansas, 72701, Fayetteville, Arkansas, USA;Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences / Shijiazhuang Branch Center of National Center for Soybean Improvement / the Key Laboratory of Crop Genetics and Breeding, 050031, Shijiazhuang, China;Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) / Key Lab of Germplasm Utilization (MOA), Chinese Academy of Agricultural Sciences, 100081, Beijing, China;Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) / Key Lab of Germplasm Utilization (MOA), Chinese Academy of Agricultural Sciences, 100081, Beijing, China;Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences / Shijiazhuang Branch Center of National Center for Soybean Improvement / the Key Laboratory of Crop Genetics and Breeding, 050031, Shijiazhuang, China;Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, 150030, Harbin, China;Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, 518083, Shenzhen, China;Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, 518083, Shenzhen, China;Department of Biology, University of Copenhagen, Copenhagen, Denmark;Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, 518083, Shenzhen, China;Department of Biology, University of Copenhagen, Copenhagen, Denmark;Department of Integrative Biology and Department of Statistics, University of California Berkeley, 94820, Berkeley, CA, USA;Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, 518083, Shenzhen, China;The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, National Centre for Plant Gene Research, Beijing, China;State Plant Breeding Institute, University of Hohenheim, Hohenheim, Germany;

关键词: Artificial selection;    Evolution;    Genetic diversity;    Population genomics;    Soybean;   

DOI  :  10.1186/1471-2164-14-579

 received in 2012-07-27, accepted in 2013-07-04,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundArtificial selection played an important role in the origin of modern Glycine max cultivars from the wild soybean Glycine soja. To elucidate the consequences of artificial selection accompanying the domestication and modern improvement of soybean, 25 new and 30 published whole-genome re-sequencing accessions, which represent wild, domesticated landrace, and Chinese elite soybean populations were analyzed.ResultsA total of 5,102,244 single nucleotide polymorphisms (SNPs) and 707,969 insertion/deletions were identified. Among the SNPs detected, 25.5% were not described previously. We found that artificial selection during domestication led to more pronounced reduction in the genetic diversity of soybean than the switch from landraces to elite cultivars. Only a small proportion (2.99%) of the whole genomic regions appear to be affected by artificial selection for preferred agricultural traits. The selection regions were not distributed randomly or uniformly throughout the genome. Instead, clusters of selection hotspots in certain genomic regions were observed. Moreover, a set of candidate genes (4.38% of the total annotated genes) significantly affected by selection underlying soybean domestication and genetic improvement were identified.ConclusionsGiven the uniqueness of the soybean germplasm sequenced, this study drew a clear picture of human-mediated evolution of the soybean genomes. The genomic resources and information provided by this study would also facilitate the discovery of genes/loci underlying agronomically important traits.

【 授权许可】

Unknown   
© Li et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.