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Article

Copy Number Variation Analysis Revealed the Evolutionary Difference between Chinese Indigenous Pigs and Asian Wild Boars

by
Shuhao Fan
1,†,
Chengcheng Kong
1,2,†,
Yige Chen
1,
Xianrui Zheng
1,
Ren Zhou
1,
Xiaodong Zhang
1,
Xudong Wu
3,
Wei Zhang
3,
Yueyun Ding
1 and
Zongjun Yin
1,*
1
College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
2
School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230036, China
3
Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Genes 2023, 14(2), 472; https://doi.org/10.3390/genes14020472
Submission received: 18 November 2022 / Revised: 8 February 2023 / Accepted: 9 February 2023 / Published: 12 February 2023
(This article belongs to the Special Issue Recent Advances in Pig Molecular Genetics and Breeding)
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Abstract

Copy number variation (CNV) has been widely used to study the evolution of different species. We first discovered different CNVs in 24 Anqingliubai pigs and 6 Asian wild boars using next-generation sequencing at the whole-genome level with 10× depth to understand the relationship between genetic evolution and production traits in wild boars and domestic pigs. A total of 97,489 CNVs were identified and divided into 10,429 copy number variation regions (CNVRs), occupying 32.06% of the porcine genome. Chromosome 1 had the most CNVRs, and chromosome 18 had the least. Ninety-six CNVRs were selected using VST 1% based on the signatures of all CNVRs, and sixty-five genes were identified in the selected regions. These genes were strongly correlated with traits distinguishing groups by enrichment in Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways, such as growth (CD36), reproduction (CIT, RLN), detoxification (CYP3A29), and fatty acid metabolism (ELOVL6). The QTL overlapping regions were associated with meat traits, growth, and immunity, which was consistent with CNV analysis. Our findings increase the understanding of evolved genome structural variations between wild boars and domestic pigs, and provide new molecular biomarkers to guide breeding and the efficient use of available genetic resources.
Keywords: CNV; CNVR; Anqingliubai pig; wild boar; QTL CNV; CNVR; Anqingliubai pig; wild boar; QTL

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MDPI and ACS Style

Fan, S.; Kong, C.; Chen, Y.; Zheng, X.; Zhou, R.; Zhang, X.; Wu, X.; Zhang, W.; Ding, Y.; Yin, Z. Copy Number Variation Analysis Revealed the Evolutionary Difference between Chinese Indigenous Pigs and Asian Wild Boars. Genes 2023, 14, 472. https://doi.org/10.3390/genes14020472

AMA Style

Fan S, Kong C, Chen Y, Zheng X, Zhou R, Zhang X, Wu X, Zhang W, Ding Y, Yin Z. Copy Number Variation Analysis Revealed the Evolutionary Difference between Chinese Indigenous Pigs and Asian Wild Boars. Genes. 2023; 14(2):472. https://doi.org/10.3390/genes14020472

Chicago/Turabian Style

Fan, Shuhao, Chengcheng Kong, Yige Chen, Xianrui Zheng, Ren Zhou, Xiaodong Zhang, Xudong Wu, Wei Zhang, Yueyun Ding, and Zongjun Yin. 2023. "Copy Number Variation Analysis Revealed the Evolutionary Difference between Chinese Indigenous Pigs and Asian Wild Boars" Genes 14, no. 2: 472. https://doi.org/10.3390/genes14020472

APA Style

Fan, S., Kong, C., Chen, Y., Zheng, X., Zhou, R., Zhang, X., Wu, X., Zhang, W., Ding, Y., & Yin, Z. (2023). Copy Number Variation Analysis Revealed the Evolutionary Difference between Chinese Indigenous Pigs and Asian Wild Boars. Genes, 14(2), 472. https://doi.org/10.3390/genes14020472

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