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

Zhang, Wei; Liu, Linqing; Su, Shiguang; Lin, Dong; Meng, Xinxin; Li, Xueting; Wang, Chonglong

doi:10.3390/genes13112026

Cited by 4 publications

(6 citation statements)

References 84 publications

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“…Genome-wide comparison of copy number variation between Wannan black pigs (WBP) and Wannan black pigs (AWB) was carried out using genome-wide resequencing data. The results showed that genes such as Ndn , Tmod3 , Sfrp1 and Smyd3 were related to muscle development ( Zhang et al, 2022 ). It can up-regulate the expression of adipogenic factors, moderately delay muscle development, promote adipogenesis, and play an important role in microfilament length regulation and myofibril assembly ( Zhao et al, 2013 ).…”

Section: Discussionmentioning

confidence: 99%

Identification of key genes in bovine muscle development by co-expression analysis

Zhang

Sheng

Pan

et al. 2023

PeerJ

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Background Skeletal muscle is not only an important tissue involved in exercise and metabolism, but also an important part of livestock and poultry meat products. Its growth and development determines the output and quality of meat to a certain extent, and has an important impact on the economic benefits of animal husbandry. Skeletal muscle development is a complex regulatory network process, and its molecular mechanism needs to be further studied. Method We used a weighted co-expression network (WGCNA) and single gene set enrichment analysis (GSEA) to study the RNA-seq data set of bovine tissue differential expression analysis, and the core genes and functional enrichment pathways closely related to muscle tissue development were screened. Finally, the accuracy of the analysis results was verified by tissue expression profile detection and bovine skeletal muscle satellite cell differentiation model in vitro (BSMSCs). Results In this study, Atp2a1, Tmod4, Lmod3, Ryr1 and Mybpc2 were identified as marker genes in muscle tissue, which are mainly involved in glycolysis/gluconeogenesis, AMPK pathway and insulin pathway. The assay results showed that these five genes were highly expressed in muscle tissue and positively correlated with the differentiation of bovine BSMSCs. Conclusions In this study, several muscle tissue characteristic genes were excavated, which may play an important role in muscle development and provide new insights for bovine molecular genetic breeding.

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Section: Discussionmentioning

confidence: 99%

Identification of key genes in bovine muscle development by co-expression analysis

Zhang

Sheng

Pan

et al. 2023

PeerJ

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“…Specifically, Manta was used for CNV identification and Paragraph for genotyping the variants in each sample. The methods for obtaining high-quality CNVs were based on our previous study ( 29 ). PLINK software v.1.90 ( 30 ) was used to determine frequency, with visualization conducted using R (v4.2.0).…”

Section: Methodsmentioning

confidence: 99%

Copy number variants selected during pig domestication inferred from whole genome resequencing

Zhang,

Xu,

Zhou

et al. 2024

Front. Vet. Sci.

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Over extended periods of natural and artificial selection, China has developed numerous exceptional pig breeds. Deciphering the germplasm characteristics of these breeds is crucial for their preservation and utilization. While many studies have employed single nucleotide polymorphism (SNP) analysis to investigate the local pig germplasm characteristics, copy number variation (CNV), another significant type of genetic variation, has been less explored in understanding pig resources. In this study, we examined the CNVs of 18 Wanbei pigs (WBP) using whole genome resequencing data with an average depth of 12.61. We identified a total of 8,783 CNVs (~30.07 Mb, 1.20% of the pig genome) in WBP, including 8,427 deletions and 356 duplications. Utilizing fixation index (Fst), we determined that 164 CNVs were within the top 1% of the Fst value and defined as under selection. Functional enrichment analyses of the genes associated with these selected CNVs revealed genes linked to reproduction (SPATA6, CFAP43, CFTR, BPTF), growth and development (NR6A1, SMYD3, VIPR2), and immunity (PARD3, FYB2). This study enhances our understanding of the genomic characteristics of the Wanbei pig and offers a theoretical foundation for the future breeding of this breed.

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“…The WIF1 was found as selected in pigs in our previous study [29]. Based on an association analysis, WIF1 was found to regulate the ear size of pigs and dogs [29,67]. Feed efficiency is one of the main factors determining production costs in the pig industry.…”

Section: Patterns Of Selection Signaturesmentioning

confidence: 98%

“…WNT inhibitory factor 1 (WIF1) could inhibit activity of the Wnt/β-catenin pathway that can regulate proliferation and differentiation in many tissues, such as controlling the growth of connective tissue by regulating the connective tissue growth factor [66]. The WIF1 was found as selected in pigs in our previous study [29]. Based on an association analysis, WIF1 was found to regulate the ear size of pigs and dogs [29,67].…”

Section: Patterns Of Selection Signaturesmentioning

confidence: 99%

“…These genotypes were used to calculate the allele frequency of each CNV locus. The genetic differentiation of the two populations based on CNVs was calculated using the "-weir-fst-pop" in VCFtools [27] with the fixation index (Fst) method [28], which is a widely used statistic in CNV studies [29,30]. The value of Fst ranged from 0 to 1.…”

Section: Identification Of Selection Signaturesmentioning

confidence: 99%

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Identification of Copy Number Variations and Selection Signatures in Wannan Spotted Pigs by Whole Genome Sequencing Data: A Preliminary Study

Zhang,

Jiang,

et al. 2024

Animals

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Copy number variation (CNV) is an important structural variation used to elucidate complex economic traits. In this study, we sequenced 25 Wannan spotted pigs (WSPs) to detect their CNVs and identify their selection signatures compared with those of 10 Asian wild boars. A total of 14,161 CNVs were detected in the WSPs, accounting for 0.72% of the porcine genome. The fixation index (Fst) was used to identify the selection signatures, and 195 CNVs with the top 1% of the Fst value were selected. Eighty genes were identified in the selected CNV regions. Functional GO and KEGG analyses revealed that the genes within these selected CNVs are associated with key traits such as reproduction (GAL3ST1 and SETD2), fatty acid composition (PRKG1, ACACA, ACSL3, UGT8), immune system (LYZ), ear size (WIF1), and feed efficiency (VIPR2). The findings of this study contribute novel insights into the genetic CNVs underlying WSP characteristics and provide essential information for the protection and utilization of WSP populations.

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

Cited by 4 publications

References 84 publications

Identification of key genes in bovine muscle development by co-expression analysis

Identification of key genes in bovine muscle development by co-expression analysis

Copy number variants selected during pig domestication inferred from whole genome resequencing

Identification of Copy Number Variations and Selection Signatures in Wannan Spotted Pigs by Whole Genome Sequencing Data: A Preliminary Study

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