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Asian-Australas J Anim Sci > Accepted Articles
DOI: https://doi.org/10.5713/ajas.18.0658    [Accepted] Published online February 7, 2019.
Selection signature reveals genes associated with susceptibility loci affecting respiratory disease due to pleiotropic and hitchhiking effect in Chinese indigenous pigs
Zhong Xu1, Hao Sun1, Zhe Zhang1, Cheng-Yue Zhang1, Qing-bo Zhao1, Qian Xiao1, Babatunde Shittu Olasege1, Pei-Pei Ma1, Xiang-Zhe Zhang1, Qi-Shan Wang1,*, Yu-Chun Pan1,2,*
Shanghai Jiao Tong University, Shanghai, China
Correspondence:  Qi-Shan Wang,Email: panyuchun1963@aliyun.com
Yu-Chun Pan,Email: panyuchun1963@aliyun.com
Received: 3 September 2018   • Revised: 20 November 2018   • Accepted: 3 September 2018
Abstract
Background: Porcine respiratory disease is one of the most important health problems which causes significant economic losses. Objective: To understand the genetic basis for susceptibility to swine enzootic pneumonia (EP) in pigs, we detected 102,809 SNPs in a total of 249 individuals based on genome-wide sequencing data.

Methods

Genome comparison of three susceptibility to swine EP pig breeds (Jinhua, Erhualian and Meishan) with two western lines that are considered more resistant (Duroc and Landrace) using XP-EHH and FST statistical approaches identified 691 positively selected genes. Based on QTLs, GO terms and literature search, we selected 14 candidate genes that have convincible biological functions associated with swine EP or human asthma.

Results

Most of these genes were tested by several methods including transcription analysis and candidated genes association study. Among these genes: CYP1A1 and CTNNB1 are involved in fertility; TGFBR3 plays a role in meat quality traits; WNT2, CTNNB1 and TCF7 take part in adipogenesis and fat deposition simultaneously; PLAUR (completely linked to AXL, r2=1) plays an essential role in the successful ovulation of matured oocytes in pigs; CLPSL2 (strongly linked to SPDEF, r2=0.848) is involved in male fertility.
Conclusion
These adverse genes susceptible to swine EP may be selected while selecting for economic traits (especially reproduction traits) due to pleiotropic and hitchhiking effect of linked genes. Our study provided a completely new point of view to understand the genetic basis for susceptibility or resistance to swine EP in pigs thereby, provide insight for designing sustainable breed selection programs. Finally, the candidate genes are crucial due to their potential roles in respiratory diseases in a large number of species, including human.
Keywords: Pigs; Selection Signature; Respiratory Disease; XP-EHH; FST
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