Dataset Information

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

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.

SUBMITTER: Fan S

PROVIDER: S-EPMC9957247 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature

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

Fan Shuhao S Kong Chengcheng C Chen Yige Y Zheng Xianrui X Zhou Ren R Zhang Xiaodong X Wu Xudong X Zhang Wei W Ding Yueyun Y Yin Zongjun Z

Genes 20230212 2

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 geno ...[more]

PMID: 36833399

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Project description:Purpose: The goal of this study was to perform a transcriptome-wide analysis of variation in brain gene expression between domesticated pig and wild boars using illumina sequencing strategy. Methods: Brain mRNA profiles of wild boars and Rongchang pigs were generated by deep sequencing, in triplicate, using Illumina Hiseq2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: We identified 808 widely-expressed conserved and 697 species-specific novel miRNAs in two species. In addition, although two organs showed similar high expression miRNAs, larger differentiation was present in lung than heart between two species. In addition, miRNAs with significantly differentiated patterns of expression in two organs exhibited obvious co-operation effect in high altitude adaptation in form of miRNA family and cluster. Functional analysis revealed that a large amount of differentially expressed miRNAs were enriched in hypoxia-related pathways, such as VEGF signaling pathway, HIF-1α signaling pathway, insulin signaling pathway, DNA damage response, apoptosis, fatty acid metabolism and glucose metabolism. These results suggested the diverse degrees of epigenetic variation in different tissues between yak and cattle, and revealed extensive roles of miRNAs in high altitude adaptation. Conclusions: First, we totally identified 20,805 genes in two groups, of which 18,904 in wild boar and 17,980 in Rongchang pigs, respectively. Second, we detected substantial variation in expression profiles between wild boar and Rongchang pig, including substantial wild boar/Rongchang specifically expressed genes and differentially expressed genes. The functional enrichment analysis revealed immune response was enriched for genes upregulated in wild boars. Finally, we compared our results against previous study and identified seven genes that were associated with domestication.The work performed here will provide a typical demonstration for future deciphering the mechanism of pig domestication.

Dataset Information

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

Publications

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

Similar Datasets

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