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Single nucleotide polymorphism was widely used to perform genetic and evolution research in pigs. However, little is known about the effect of copy number variation (CNV) on characteristics in pigs. This study performed a genome-wide comparison of CNVs between Wannan black pigs (WBP) and Asian wild boars (AWB), using whole genome resequencing data. By using Manta, we detected in total 28,720 CNVs that covered approximately 1.98% of the pig genome length. We identified 288 selected CNVs (top 1%) by performing Fst statistics. Functional enrichment analyses for genes located in selected CNVs were found to be muscle related ( NDN , TMOD4 , SFRP1 , and SMYD3 ), reproduction related ( GJA1 , CYP26B1 , WNT5A , SRD5A2 , PTPN11 , SPEF2 , and CCNB1 ), residual feed intake (RFI) related ( MAP3K5 ), and ear size related ( WIF1 ). This study provides essential information on selected CNVs in Wannan black pigs for further research on the genetic basis of the complex phenotypic and provides essential information for direction in the protection and utilization of Wannan black pig.

Titel:	Population Structure and Selection Signatures Underlying Domestication Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Pigs.
Autor/in / Beteiligte Person:	Zhang, W ; Zhou, M ; Liu, L ; Su, S ; Dong, L ; Meng, X ; Li, X ; Wang, C
Link:	Full Text Finder (Volltext)
Zeitschrift:	Genes, Jg. 13 (2022-11-03), Heft 11
Veröffentlichung:	Basel : MDPI, 2022
Medientyp:	academicJournal
ISSN:	2073-4425 (electronic)
DOI:	10.3390/genes13112026
Schlagwort:	Swine genetics Animals Genome Sequence Analysis, DNA China DNA Copy Number Variations genetics Domestication
Sonstiges:	Nachgewiesen in: MEDLINE Sprachen: English Publication Type: Journal Article; Research Support, Non-U.S. Gov't Language: English [Genes (Basel)] 2022 Nov 03; Vol. 13 (11). <i>Date of Electronic Publication: </i>2022 Nov 03. MeSH Terms: DNA Copy Number Variations* / genetics ; Domestication* ; Swine / genetics ; Animals ; Genome ; Sequence Analysis, DNA ; China References: Placenta. 2010 Oct;31(10):839-47. (PMID: 20716463) ; PLoS One. 2012;7(2):e30619. (PMID: 22312429) ; Natl Sci Rev. 2020 Feb;7(2):391-402. (PMID: 34692055) ; PLoS One. 2014 Jul 09;9(7):e102085. (PMID: 25006967) ; Mol Cell Endocrinol. 2006 Jun 27;252(1-2):102-6. (PMID: 16647194) ; BMC Mol Biol. 2015 Mar 08;16:4. (PMID: 25888412) ; PLoS Genet. 2011 Oct;7(10):e1002316. (PMID: 22022279) ; Genome Res. 2002 Dec;12(12):1805-14. (PMID: 12466284) ; BMC Genomics. 2022 Sep 13;23(1):649. (PMID: 36096727) ; Genome Biol. 2019 Dec 19;20(1):291. (PMID: 31856913) ; FASEB J. 2016 Apr;30(4):1534-47. 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(PMID: 24728479) Contributed Indexing: Keywords: Asian wild boar; Wannan black pig; copy number variation (CNV); fixation index (FST); selection signatures; whole genome resequencing Entry Date(s): Date Created: 20221111 Date Completed: 20221114 Latest Revision: 20221126 Update Code: 20240513 PubMed Central ID: PMC9690591

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Population Structure and Selection Signatures Underlying Domestication Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Pigs.