Genomic analysis reveals selection signatures of the Wannan Black pig during domestication and breeding
Genomic analysis reveals selection signatures of the Wannan Black pig during domestication and breeding
复制标题
基因组分析揭示皖南黑猪驯化和繁殖过程中的选择特征
DOI：
10.5713/ajas.19.0289
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发表时间：
2019-08
期刊：
影响因子：
--
通讯作者：
Zongjun Yin
中科院分区：
文献类型：
--
作者：
weizhang;minyang;Yuanlang Wang;Xudong Wu;Xiaodong Zhang;Yueyun Ding;Zongjun Yin
Objective The Wannan Black pig is a typical Chinese indigenous, disease-resistant pig breed with high fertility, and a crude-feed tolerance that has been bred by artificial selection in the south of Anhui province for a long time. However, genome variation, genetic relationships with other pig breeds, and domestication, remain poorly understood. Here, we focus on elucidating the genetic characteristics of the Wannan Black pig and identifying selection signatures during domestication and breeding. Methods We identified the whole-genome variation in the Wannan Black pig and performed population admixture analyses to determine genetic relationships with other domesticated pig breeds and wild boars. Then, we identified the selection signatures between the Wannan Black pig and Asian wild boars in 100-kb windows sliding in 10 kb steps by using two approaches: the fixation index (FST) and π ratios. Results Resequencing the Wannan Black pig genome yielded 501.52 G of raw data. After calling single-nucleotide variants (SNVs) and insertions/deletions (InDels), we identified 21,316,754 SNVs and 5,067,206 InDels (2,898,582 inserts and 2,168,624 deletions). Additionally, we found genes associated with growth, immunity, and digestive functions. Conclusion Our findings help in explaining the unique genetic and phenotypic characteristics of Wannan Black pigs, which in turn can be informative for future breeding programs of Wannan Black pigs.
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影响因子：
16
作者：
Fischl H;Howe FS;Furger A;Mellor J
通讯作者：
Mellor J
影响因子：
16.6
作者：
Alberto FJ;Boyer F;Orozco-terWengel P;Streeter I;Servin B;de Villemereuil P;Benjelloun B;Librado P;Biscarini F;Colli L;Barbato M;Zamani W;Alberti A;Engelen S;Stella A;Joost S;Ajmone-Marsan P;Negrini R;Orlando L;Rezaei HR;Naderi S;Clarke L;Flicek P;Wincker P;Coissac E;Kijas J;Tosser-Klopp G;Chikhi A;Bruford MW;Taberlet P;Pompanon F
通讯作者：
Pompanon F
DOI：
--
发表时间：
2007
期刊：
--
影响因子：
--
作者：
B. Rischkowsky
通讯作者：
B. Rischkowsky
DOI：
--
发表时间：
2012
期刊：
--
影响因子：
--
作者：
Sudhir Kumar;A. Drummond;M. Suchard;Dong Xie;A. Rambaut
通讯作者：
Sudhir Kumar;A. Drummond;M. Suchard;Dong Xie;A. Rambaut
影响因子：
4.6
作者：
Nishi A;Numata S;Tajima A;Zhu X;Ito K;Saito A;Kato Y;Kinoshita M;Shimodera S;Ono S;Ochi S;Imamura A;Kurotaki N;Ueno SI;Iwata N;Fukui K;Imoto I;Kamiya A;Ohmori T
通讯作者：
Ohmori T