CNV analysis of Meishan pig by next-generation sequencing and effects of AHR gene CNV on pig reproductive traits

Abstract

Background: Reproductive performance of livestock is an economically important aspect of global food production. The Chinese Meishan pig is a prolific breed, with an average of three to five more piglets per litter than European breeds; however, the genetic basis for this difference is not well understood. Results: In this study, we investigated copy number variations (CNVs) of 32 Meishan pigs and 29 Duroc pigs by nextgeneration sequencing. A genome-wide analysis of 61 pigs revealed 12,668 copy number variable regions (CNVRs) that were further divided into three categories based on copy number (CN) of the whole population, i.e., gain (n = 7,638), and loss (n = 5,030) CNVRs. We then compared Meishan and Duroc pigs and identified 17.17 Mb of 6,387 CNVRs that only existing in Meishan pigs CNVRs that overlapped the reproduction-related gene encoding the aryl hydrocarbon receptor (AHR) gene. We found that normal AHR CN was more frequent than CN loss in four different pig breeds. An association analysis showed that AHR CN had a positive effect on litter size (P < 0.05) and that a higher CN was associated with higher total number born (P < 0.05), number born alive (P < 0.05), number of weaned piglets, and birth weight. Conclusions: The present study provides comprehensive CNVRs for Meishan and Duroc pigs through large-scale population resequencing. Our results provide a supplement for the high-resolution map of copy number variation in the porcine genome and valuable information for the investigation of genomic structural variation underlying traits of interest in pig. In addition, the association results provide evidence for AHR as a candidate gene associated with reproductive traits that can be used as a genetic marker in pig breeding programs.

Genome-wide detection of CNV regions and their potential association with growth and fatness traits in Duroc pigs

“…Gene set enrichment analysis revealed that many terms might be relevant to growth and fatness traits (see Additional le 7: Table S7). In brief, the KEGG analysis uncovers that these genes mainly signi cantly participated in Rap1 signaling pathway, which was consistent with Zheng et al [17] and Wang et al [43] Furthermore, the top terms of GO analysis were primarily enriched in negative regulation of lipid biosynthetic and metabolic process. Given that, we further identi ed the functions of these genes involved in the critical pathways and biological processes from the GeneCards database and relevant literature.…”

“…[50] using Porcine SNP60 BeadChip, there were approximately 70.6% gains and 29.4% losses, Zheng et al [17] also reported that the frequency of duplications was higher than that of deletions in Duroc and Meishan pigs through Nextgeneration sequencing. This phenomenon suggests that although CNVs can cause duplications or deletions at the same locus in different populations [51], the genome has a greater tolerant for duplication than deletion [52], and is more likely to occur in large-scale CNVs (> 10 kb) [5,53].…”

“…Meanwhile, to further decrease false-positive CNVs, CNVs with consecutive SNPs ≥ 3 and CNV length ≥ 10 kb were remained. We also used the bedtools software v2.26.0 [30,31] to merge CNVs with at least 1bp overlap in all samples to de ne CNV region (CNVR) [17], and CNVRuler software [32] was used to de ne three types of CNVR: loss, gain and mixed (gain and loss occur in the same region). Besides, we matched the CNVs of respective populations with the corresponding CNVR to obtain the CNVRs of each Duroc pig population.…”

“…Due to the uncertain boundary of the identi ed CNVRs, we used Oligo 7 software [33] to design primers for the speci c region of ADGRA1, PUSL1, MAPRE2, SGMS2, PCID2, DSCAM, GATD3A, ELFN1 and LIFR genes (see Additional le 4: Table S4). We also selected the GCG gene as the reference locus since this gene was highly conserved among pigs and existed as a single copy in animals [17,34,35]. Normal samples identi ed with no copy number change in the test region were used as a reference.…”

“…In reproductive performance, the CNV of the MTHFSD gene was correlated with litter size traits of Xiang pigs [16]. Zheng et al [17] also showed that a higher CN of the AHR gene had a positive effect on litter size. In productive performance, Revilla et al [18] discovered a CNVR containing the GPAT2 gene, which might be associated with several growth-related traits.…”