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

Ying-hui Li1, Shan-cen Zhao2, Jian-xin Ma3, Dong Li2, Long Yan14, Jun Li2, Xiao-tian Qi1, Xiao-sen Guo2, Le Zhang1, Wei-ming He2, Ru-zhen Chang1, Qin-si Liang2, Yong Guo1, Chen Ye2, Xiao-bo Wang1, Yong Tao25, Rong-xia Guan1, Jun-yi Wang26, Yu-lin Liu1, Long-guo Jin1, Xiu-qing Zhang2, Zhang-xiong Liu1, Li-juan Zhang1, Jie Chen2, Ke-jing Wang1, Rasmus Nielsen257, Rui-qiang Li2, Peng-yin Chen8, Wen-bin Li9, Jochen C Reif10, Michael Purugganan11, Jian Wang2, Meng-chen Zhang4, Jun Wang25* and Li-juan Qiu1*

Author Affiliations

1 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

2 Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, 518083 Shenzhen, China

3 Department of Agronomy, Purdue University, 47907, West Lafayette, IN, USA

4 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

5 Department of Biology, University of Copenhagen, Copenhagen, Denmark

6 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

7 Department of Integrative Biology and Department of Statistics, University of California Berkeley, 94820 Berkeley, CA, USA

8 Department of Crop, Soil, and Environmental Sciences, University of Arkansas, 72701 Fayetteville, Arkansas, USA

9 Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, 150030 Harbin, China

10 State Plant Breeding Institute, University of Hohenheim, Hohenheim, Germany

11 Department of Biology and Centre for Genomics and Systems Biology, 12 Waverly Place, New York University, 10003 New York, USA

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BMC Genomics 2013, 14:579  doi:10.1186/1471-2164-14-579

Published: 28 August 2013



Artificial 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.


A 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.


Given 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.

Artificial selection; Evolution; Genetic diversity; Population genomics; Soybean