Xu Zhong, Sun Hao, Zhang Zhe, Zhang Cheng-Yue, Zhao Qing-Bo, Xiao Qian, Olasege Babatunde Shittu, Ma Pei-Pei, Zhang Xiang-Zhe, Wang Qi-Shan, Pan Yu-Chun
Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
Shanghai Key Laboratory of Veterinary Bio-technology, Shanghai 200240, China.
Asian-Australas J Anim Sci. 2020 Feb 1;33(2):187-196. doi: 10.5713/ajas.18.0658. Epub 2019 Feb 7.
Porcine respiratory disease is one of the most important health problems which causes significant economic losses.
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.
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.
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.
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.
猪呼吸道疾病是导致重大经济损失的最重要的健康问题之一。
为了解猪对猪地方流行性肺炎（EP）易感性的遗传基础，我们基于全基因组测序数据在总共249个个体中检测了102,809个单核苷酸多态性（SNP）。
使用XP-EHH和FST统计方法，对三个易患猪EP的猪品种（金华猪、二花脸猪和梅山猪）与两个被认为更具抗性的西方品系（杜洛克猪和长白猪）进行基因组比较，鉴定出691个正选择基因。基于数量性状基因座（QTL）、基因本体论（GO）术语和文献检索，我们选择了14个具有与猪EP或人类哮喘相关的可信生物学功能的候选基因。
这些基因大多通过多种方法进行了检测，包括转录分析和候选基因关联研究。在这些基因中：细胞色素P450 1A1（CYP1A1）和β-连环蛋白1（CTNNB1）参与生育能力；转化生长因子β受体3（TGFBR3）在肉质性状中起作用；Wnt信号通路成员2（WNT2）、CTNNB1和转录因子7（TCF7）同时参与脂肪生成和脂肪沉积；猪肺抗凝血酶相关蛋白（PLAUR，与AXL完全连锁，r2 = 1）在猪成熟卵母细胞成功排卵中起重要作用；CLPSL2（与SPDEF紧密连锁，r2 = 0.848）参与雄性生育能力。
由于连锁基因的多效性和搭便车效应，在选择经济性状（尤其是繁殖性状）时可能会选择这些易患猪EP的不利基因。我们的研究为理解猪对猪EP易感性或抗性的遗传基础提供了全新的视角，从而为设计可持续的品种选择计划提供了见解。最后，这些候选基因因其在包括人类在内的大量物种的呼吸道疾病中的潜在作用而至关重要。
