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Asian-Australas J Anim Sci > Accepted Articles
DOI: https://doi.org/10.5713/ajas.19.0289    [Accepted] Published online August 23, 2019.
Genomic analysis reveals selection signatures of the Wannan Black pig during domestication and breeding
Wei Zhang1  , Min Yang1  , Yuanlang Wang1  , Xudong Wu1  , Xiaodong Zhang1  , Yueyun Ding1,*  , Zongjun Yin1,* 
College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
Correspondence:  Yueyun Ding,Email: dingyueyunahau.edu.cn
Zongjun Yin,Email: yinzongjun@ahau.edu.cn
Received: 7 April 2019   • Revised: 9 June 2019   • Accepted: 1 August 2019
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 in the south of Anhui province by artificial selection 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.
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.
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.
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.
Keywords: Wannan Black Pig; Selection Signature; Genome Variation; Porcine Industry

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