Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing
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Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. / Li, Ying-hui; Zhao, Shan-cen; Ma, Jian-xin; Li, Dong; Yan, Long; Li, Jun; Qi, Xiao-tian; Guo, Xiao-sen; Zhang, Le; He, Wei-ming; Chang, Ru-zhen; Liang, Qin-si; Guo, Yong; Ye, Chen; Wang, Xiao-bo; Tao, Yong; Guan, Rong-xia; Wang, Jun-yi; Liu, Yu-lin; Jin, Long-guo; Zhang, Xiu-qing; Liu, Zhang-xiong; Zhang, Li-juan; Chen, Jie; Wang, Ke-jing; Nielsen, Rasmus; Li, Rui-qiang; Chen, Peng-yin; Li, Wen-bin; Reif, Jochen C.; Purugganan, Michael; Wang, Jian; Zhang, Meng-chen; Wang, Jun; Qiu, Li-juan.
In: BMC Genomics, Vol. 14, 579, 2013.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing
AU - Li, Ying-hui
AU - Zhao, Shan-cen
AU - Ma, Jian-xin
AU - Li, Dong
AU - Yan, Long
AU - Li, Jun
AU - Qi, Xiao-tian
AU - Guo, Xiao-sen
AU - Zhang, Le
AU - He, Wei-ming
AU - Chang, Ru-zhen
AU - Liang, Qin-si
AU - Guo, Yong
AU - Ye, Chen
AU - Wang, Xiao-bo
AU - Tao, Yong
AU - Guan, Rong-xia
AU - Wang, Jun-yi
AU - Liu, Yu-lin
AU - Jin, Long-guo
AU - Zhang, Xiu-qing
AU - Liu, Zhang-xiong
AU - Zhang, Li-juan
AU - Chen, Jie
AU - Wang, Ke-jing
AU - Nielsen, Rasmus
AU - Li, Rui-qiang
AU - Chen, Peng-yin
AU - Li, Wen-bin
AU - Reif, Jochen C.
AU - Purugganan, Michael
AU - Wang, Jian
AU - Zhang, Meng-chen
AU - Wang, Jun
AU - Qiu, Li-juan
PY - 2013
Y1 - 2013
N2 - BACKGROUND: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.RESULTS: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.CONCLUSIONS: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.
AB - BACKGROUND: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.RESULTS: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.CONCLUSIONS: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.
U2 - 10.1186/1471-2164-14-579
DO - 10.1186/1471-2164-14-579
M3 - Journal article
VL - 14
JO - BMC Genomics
JF - BMC Genomics
SN - 1471-2164
M1 - 579
ER -
ID: 90616172