Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits
Impact factor: 12.121 (Year: 2020)
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Xin Li, Ji Yang, Xing-Long Xie, Ya-Xi Xu, Feng-Hua Lv, Min Shen, Hua Yang, Yong-Lin Yang, Chang-Bin Liu, Ping Zhou, Peng-Cheng Wan, Yun-Sheng Zhang, Lei Gao, Jing-Quan Yang, Wen-Hui Pi, Yan-Ling Ren, Zhi-Qiang Shen, Feng Wang, Juan Deng, Song-Song Xu, Hosein Salehian-Dehkordi, Eer Hehua, Ali Esmailizadeh, Mostafa Dehghani-Qanatqestani, Ondřej Štěpánek, Christina Weimann, Georg Erhardt, Agraw Amane, Joram Mwacharo, Han Jianlin, Olivier Hanotte, Johannes A Lenstra, Juha Kantanen, David W. Coltman, James W. Kijas, Michael W Bruford, Kathiravan Periasamy, Xin-Hua Wang, Meng-Hua Li. (4/6/2020). Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits. Nature Communications, 11, pp. 1-16.
Understanding the genetic changes underlying phenotypic variation in sheep (Ovis aries) may facilitate our efforts towards further improvement. Here, we report the deep resequencing of 248 sheep including the wild ancestor (O. orientalis), landraces, and improved breeds. We explored the sheep variome and selection signatures. We detected genomic regions harboring genes associated with distinct morphological and agronomic traits, which may be past and potential future targets of domestication, breeding, and selection. Furthermore, we found non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds. We identified PDGFD as a likely causal gene for fat deposition in the tails of sheep through transcriptome, RT-PCR, qPCR, and Western blot analyses. Our results provide insights into the demographic history of sheep and a valuable genomic resource for future genetic studies and improved genome-assisted breeding of sheep and other domestic animals.
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Author(s)Deng, Juan; Xie, Xing-Long; wang, Dong-Feng; Zhao, Chao; Lv, Feng-Hua; Li, Xin; Yang, Ji; Yu, Jia-Lin; Shen, Min; Gao, Lei; Yang, Jing-Quan; Liu, Ming-Jun; Li, Wen-Rong; Wang, Yu-Tao; Wang, Feng; Li, Jin-Quan; Hehua, Eer; Liu, Yong-Gang; Shen, Zhi-Qiang; Ren, Yan-Ling; Liu, Guang-Jian; Chen, Ze-Hui; Gorkhali, Neena A; E Rushdi, Hossam; Salehian-Dehkordi, Hosein; Esmailizadeh, Ali; Nosrati, Maryam; R. Paiva, Samuel; R Caetano, Alexandre; Štěpánek, Ondřej; Olsaker, Ingrid; Weimann, Christina; Erhardt, Georg; Curik, Ino; Kantanen, Juha; Mwacharo, Joram; Hanotte, Olivier; W Bruford, Michael; Ciani, Elena; Periasamy, Kathiravan; Amills, Marcel; A Lenstra, Johannes; Jianlin, Han; Zhang, Hong-Ping; Li, Li; Li, Meng-HuaDate: 2020-10-19Status: Open accessThe domestication and subsequent global dispersal of livestock are crucial events in human history, but the migratory episodes during the history of livestock remain poorly documented [1, 2, 3]. Here, we first developed a ...
Title: Historical Introgression from Wild Relatives Enhanced Climatic Adaptation and Resistance to Pneumonia in Sheep Author(s)Cao, Yin-Hong; Xu, Song-Song; Shen, Min; Chen, Ze-Hui; Gao, Lei; Lv, Feng-Hua; Xie, Xing-Long; Wang, Xin-Hua; Yang, Hua; Liu, Chang-Bin; Zhou, Ping; Wan, Peng-Cheng; Zhang, Yun-Sheng; Yang, Jing-Quan; Pi, Wen-Hui; Hehua, Eer; P. Berry, Donagh; Barbato, Mario; Esmailizadeh, Ali; Nosrati, Maryam; Salehian-Dehkordi, Hosein; Dehghani-Qanatqestani, Mostafa; Dotsev, Arsen V.; Deniskova, Tatiana E.; Zinovieva, Natalia A.; Brem, Gottfried; Stepanek, Ondrej; Ciani, Elena; Weimann, Christina; Erhardt, Georg; Mwacharo, Joram; Ahbara, Abulgasim; Jianlin, Han; Hanotte, Olivier; Miller, Joshua M.; Sim, Zijian; Coltman, David W.; Kantanen, Juha; W Bruford, Michael; A Lenstra, Johannes; Kijas, James W.; Li, Meng-HuaDate: 2020-09-17Status: Open accessHow animals, particularly livestock, adapt to various climates and environments over short evolutionary time is of fundamental biological interest. Further, understanding the genetic mechanisms of adaptation in indigenous ...
Title: The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication Author(s)Zhuang, Weijian; Chen, Hua; Yang, Meng; Wang, Jianping; Pandey, Manish K; Zhang, Chong; Chang, Wen-Chi; Zhang, Liangsheng; Zhang, Xingtan; Tang, Ronghua; Vanika, Garg; Wang, Xingjun; Tang, Haibao; Chow, Chi-Nga; Wang, Jinpeng; Deng, Ye; Wang, Depeng; Khan, Aamir; Yang, Qiang; Cai, Tiecheng; Bajaj, Prasad; Wu, Kangcheng; Guo, Baozhu; Zhang, Xinyou; Li, Jingjing; Liang, Fan; Hu, Jiang; Liao, Boshou; Liu, Shengyi; Chitikineni, Annapurna; Yan, Hansong; Zheng, Yixiong; Shan, Shihua; Liu, Qinzheng; Xie, Dongyang; Wang, Zhenyi; Khan, Shahid; Ali, Niaz; Zhao, Chuanzhi; Li, Xinguo; Luo, Ziliang; Zhang, Shubiao; Zhuang, Ruirong; Peng, Ze; Wang, Shuaiyan; Mamadou, Gandeka; Zhuang, Yuhui; Zhao, Zifan; Yu, Weichang; Xiong, Faqian; Quan, Weipeng; Yuan, Mei; Li, Yu; Zou, Huasong; Xia, Han; Zha, Li; Fan, Junpeng; Yu, Jigao; Xie, Wenping; Yuan, Jiaqing; Chen, Kun; Zhao, Shanshan; Chu, Wenting; Chen, Yuting; Sun, Pengchuan; Meng, Fanbo; Zhuo, Tao; Zhao, Yuhao; Li, Chunjuan; He, Guohao; Zhao, Yongli; Wang, Congcong; Kavi Kishor, Polavarapu B.; Pan, Rong-Long; Paterson, Andrew H.; wang, xiyin; Ming, Ray; Varshney, RajeevDate: 2019-05-01Status: Open accessHigh oil and protein content make tetraploid peanut a leading oil and food legume. Here we report a high-quality peanut genome sequence, comprising 2.54 Gb with 20 pseudomolecules and 83,709 protein-coding gene models. We ...