Genome-Wide Detection of Copy Number Variations and Evaluation of Candidate Copy Number Polymorphism Genes Associated With Complex Traits of Pigs

Abstract

Copy number variation (CNV) has been considered to be an important source of genetic variation for important phenotypic traits of livestock. In this study, we performed whole-genome CNV detection on Suhuai (SH) (n = 23), Chinese Min Zhu (MZ) (n = 11), and Large White (LW) (n = 12) pigs based on next-generation sequencing data. The copy number variation regions (CNVRs) were annotated and analyzed, and 10,885, 10,836, and 10,917 CNVRs were detected in LW, MZ, and SH pigs, respectively. Some CNVRs have been randomly selected for verification of the variation type by real-time PCR. We found that SH and LW pigs are closely related, while MZ pigs are distantly related to the SH and LW pigs by CNVR-based genetic structure, PCA, VST, and QTL analyses. A total of 14 known genes annotated in CNVRs were unique for LW pigs. Among them, the cyclin T2 (CCNT2) is involved in cell proliferation and the cell cycle. The FA Complementation Group M (FANCM) is involved in defective DNA repair and reproductive cell development. Ten known genes annotated in 47 CNVRs were unique for MZ pigs. The genes included glycerol-3-phosphate acyltransferase 3 (GPAT3) is involved in fat synthesis and is essential to forming the glycerol triphosphate. Glutathione S-transferase mu 4 (GSTM4) gene plays an important role in detoxification. Eleven known genes annotated in 23 CNVRs were unique for SH pigs. Neuroligin 4 X-linked (NLGN4X) and Neuroligin 4 Y-linked (NLGN4Y) are involved with nerve disorders and nerve signal transmission. IgLON family member 5 (IGLON5) is related to autoimmunity and neural activities. The unique characteristics of LW, MZ, and SH pigs are related to these genes with CNV polymorphisms. These findings provide important information for the identification of candidate genes in the molecular breeding of pigs.

Unveiling the Influence of Copy Number Variations on Genetic Diversity and Adaptive Evolution in China’s Native Pig Breeds via Whole-Genome Resequencing

“…Zhang et al discovered that, compared to Chinese domestic pigs and Large White pigs, the identified Neural Glycoprotein 4 X-linked (NLGN4X) and Neural Glycoprotein 4 Y-linked (NLGN4Y) in Su-Huai pigs are associated with neurological diseases and neural signal transduction. This suggests that Su-Huai pigs are more docile and easier to domesticate than Large White pigs [ 21 ]. In enriched environments, swine have a higher level of proteins related to protein synthesis and neural activity, enabling them to better cope with stressful conditions like those found in slaughterhouses [ 35 ].…”

A composite strategy of genome-wide association study and copy number variation analysis for carcass traits in a Duroc pig population

“…Among these 758 CNVRs, we identified 19 CNVRs that overlapped with the reported CNVRs in this study with a total CNVR length of 699,128 bp. Zhang et al [ 22 ] performed genome-wide CNV detection on 46 pigs including Suhai, Minzhu, and Large White based on NGS data and 11,173 CNVRs were detected. Among these CNVRs, we identified 323 CNVRs that overlapped with the reported CNVRs in this study.…”

“…To determine whether the CNVRs identified in our study overlapped with those reported in previous studies, we compared our results in Duroc pigs to those CNVRs identified in several different swine studies[8,10,[19][20][21][22]. All CNVRs identified in other studies were converted to Sscrofa 11.1 genome assembly using the liftOver tool.…”