Abstract
// Danyang Zou 1, * , Bo Zuo 1, 2, * , Mingfei Zhu 1 , Lei Rong 1 , Huimin Mao 3 , Hongdan Niu 1 , Ling Wang 1 and Rong Zheng 1 1 Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, P.R. China 2 The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, P.R. China 3 The Tianpeng Group, Jiangshan, Zhejiang, 324111, P.R. China * These authors share co-first authorship Correspondence to: Rong Zheng, email: zhengrong@mail.hzau.edu.cn Keywords: GWAS; SLAF-seq; inguinal/scrotal hernia; pig; farmCPU Received: October 06, 2017 Accepted: October 27, 2017 Epub: December 22, 2017 ABSTRACT Inguinal and scrotal hernias are the most frequent congenital disorders in pigs, and they may cause severe economic loss in the pig breeding industry. Genetic factors play a significant role in the susceptibility to hernias, but the genetic mechanisms of inguinal/scrotal hernia are poorly understood. In this study, we performed a genome-wide association study (GWAS) with specific-locus amplified fragment sequencing (SLAF-seq) on 120 (59 cases and 61 controls) full and half sib pigs to identify genetic loci underlying variations in inguinal/scrotal hernias. A total of 218,460 high-quality SNPs were generated for further statistical analysis with case-controls and the farmCPU model. Based on these two methods, a total of 59 SNPs were significantly ( P < 0.01) associated with inguinal/scrotal hernia. Finally, 14 novel candidate genes implicated in the defect were identified, and 5 genes ( CPNE5 , DEGS1 , PLCG2 , PRKCE and NUAK1 ) were related to cell apoptosis, which is one of the pivotal pathogenesis factors of inguinal/scrotal hernia. In addition, 4 of them were shown strong associations with the hernia were confirmed in 270 samples ( P < 0.05). This finding provides new evidence that genes related to cell apoptosis may be associated with inguinal/scrotal hernias.
Highlights
Inguinal and scrotal hernias, which occur in the weak areas of the inguinal canal [1, 2] or the processus vaginalis [3, 4], are some of the most frequent congenital disorders observed in pigs and humans [5, 6]
There have been few reports about the application of SLAFseq technology in resistance breeding of livestock, and to our best knowledge, this study is the first report of pig inguinal/scrotal hernias at genome-wide significance using SLAF-seq technology
Compared with the SLAF-seq technology, SNP chip cannot be used when a reference genome is unavailable, suggesting that only known SNP markers could be detected by SNP-arrays [37]
Summary
Inguinal and scrotal hernias, which occur in the weak areas of the inguinal canal [1, 2] or the processus vaginalis [3, 4], are some of the most frequent congenital disorders observed in pigs and humans [5, 6]. They cause severe economic loss in the pig breeding industry [7]. Candidate genes related to the development of inguinal/scrotal hernias have been inspected. Only a few candidate genes have been reported and the molecular mechanism of the etiology remains unclear
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