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

Authors
  • Zheng, Xianrui1
  • Zhao, Pengju1
  • Yang, Kaijie1
  • Ning, Chao1
  • Wang, Haifei1, 2
  • Zhou, Lei1
  • Liu, Jianfeng1
  • 1 China Agricultural University, Beijing, 100193, China , Beijing (China)
  • 2 Yangzhou University, Yangzhou, 225009, China , Yangzhou (China)
Type
Published Article
Journal
Journal of Animal Science and Biotechnology
Publisher
BioMed Central
Publication Date
Apr 21, 2020
Volume
11
Issue
1
Identifiers
DOI: 10.1186/s40104-020-00442-5
Source
Springer Nature
Keywords
License
Green

Abstract

BackgroundReproductive 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.ResultsIn this study, we investigated copy number variations (CNVs) of 32 Meishan pigs and 29 Duroc pigs by next-generation 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.ConclusionsThe 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.

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