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

Frontiers in Veterinary Science, Journal Year: 2024, Volume and Issue: 11

Published: March 5, 2024

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

Language: Английский

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Whole-genome selective sweep analysis of Danish Large White and Chinese indigenous pig populations

Animal Biotechnology, Journal Year: 2025, Volume and Issue: 36(1)

Published: March 1, 2025

Language: Английский

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

Genes, Journal Year: 2022, Volume and Issue: 13(11), P. 2026 - 2026

Published: Nov. 3, 2022

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 This study performed a genome-wide comparison CNVs between Wannan black pigs (WBP) Asian wild boars (AWB), using whole genome resequencing data. By Manta, we detected total 28,720 that covered approximately 1.98% pig length. We identified 288 selected (top 1%) by performing Fst statistics. Functional enrichment analyses for genes located were found be muscle related (NDN, TMOD4, SFRP1, SMYD3), reproduction (GJA1, CYP26B1, WNT5A, SRD5A2, PTPN11, SPEF2, CCNB1), residual feed intake (RFI) (MAP3K5), ear size (WIF1). provides essential information further basis complex phenotypic direction protection utilization pig.

Language: Английский

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

Genes, Journal Year: 2023, Volume and Issue: 14(2), P. 472 - 472

Published: Feb. 12, 2023

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

Language: Английский

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Identification of Breed-Specific SNPs of Danish Large White Pig in Comparison with Four Chinese Local Pig Breed Genomes

Genes, Journal Year: 2024, Volume and Issue: 15(5), P. 623 - 623

Published: May 14, 2024

Genetic variation facilitates the evolution, environmental adaptability, and biodiversity of organisms. Danish Large White (LW) pigs have more desirable phenotypes compared with local Chinese pigs, which difficulty adapting to modern swine industry. However, genome-wide mutational differences between these pig breeds are yet be evaluated. Therefore, this study aimed evaluate genomic identify breed-specific SNPs in LW pigs. Here, 43 LW, 15 Diqing Tibetan (DQZ), Diannan small-ear (DN) whose genomes were re-sequenced 5× depth selected. This was followed by a conjoined analysis our previous resequencing data 24 Anqing six-end white (AQ) six Asian wild (SS) In total, 39,158,378 13,143,989 insertion–deletions obtained all breeds. The number lowest, 287,194 1289 non-synonymous Functional indicated that mutations mainly associated reproductive performance, feed intake, conversion ratio These findings provide theoretical basis for genetic improvements

Language: Английский

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Genome-Wide Detection for Runs of Homozygosity in Baoshan Pigs Using Whole Genome Resequencing

Genes, Journal Year: 2024, Volume and Issue: 15(2), P. 233 - 233

Published: Feb. 12, 2024

Baoshan pigs (BS) are a local breed in Yunnan Province that may face inbreeding owing to its limited population size. To accurately evaluate the level of BS pig population, we used whole-genome resequencing identify runs homozygosity (ROH) regions pigs, calculated coefficient based on pedigree and ROH, screened candidate genes with important economic traits from ROH islands. A total 22,633,391 SNPS were obtained whole genome 201 ROHs detected 532,450 after quality control. The number medium-length (1–5 Mb) was highest (98.43%), long (>5 lowest (1.57%), mainly occurred distant generations. FROH, 0.018 ± 0.016, FPED, pedigree, 0.027 0.028, which positively correlated. Forty islands identified, containing 507 891 QTLs. Several associated growth development (IGFALS, PTN, DLX5, DKK1, WNT2), meat (MC3R, ACSM3, ECI1, CD36, ROCK1, CACNA2D1), reproductive (NPW, TSHR, BMP7). This study provides reference for protection utilization pigs.

Language: Английский

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Identification of consensus homozygous regions and their associations with growth and feed efficiency traits in American mink

BMC Genomic Data, Journal Year: 2024, Volume and Issue: 25(1)

Published: July 10, 2024

Abstract The recent chromosome-based genome assembly and the newly developed 70K single nucleotide polymorphism (SNP) array for American mink ( Neogale vison ) facilitate identification of genetic variants underlying complex traits in this species. objective study was to evaluate association between consensus runs homozygosity (ROH) with growth feed efficiency mink. A subsample two populations n = 2,986) were genotyped using Affymetrix Mink SNP array. identified ROH segments included simultaneously, concatenated into regions, ROH-based studies carried out linear mixed models considering a genomic relationship matrix 11 implemented ASReml-R version 4. In total, 298,313 across all individuals, an average length coverage 4.16 Mb 414.8 Mb, respectively. After merging segments, 196 regions detected used genome-wide analysis. Thirteen significantly P < 0.01) associated traits. Several candidate genes within significant are known their involvement body size development, including MEF2A , ADAMTS17 POU3F2 TYRO3 . addition, we found ten defined as islands, frequencies over 80% population. These islands harbored 12 annotated genes, some which related immune system processes such DTX3L PARP9 PARP14 CD86 HCLS1 This is first explore associations homozygous Our findings shed light on effects traits, that can be utilized developing sustainable breeding program

Language: Английский

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Assessing Population Structure and Signatures of Selection in Wanbei Pigs Using Whole Genome Resequencing Data

Animals, Journal Year: 2022, Volume and Issue: 13(1), P. 13 - 13

Published: Dec. 20, 2022

Wanbei pig (WBP) is one of the indigenous resources in China and has many germplasm characteristics. However, research on its genome lacking. To assess genomic variation, population structure, selection signatures, we resequenced 18 WBP for first time performed a comprehensive analysis with data 10 Asian wild boars. In total, 590.03 Gb approximately 41 million variants were obtained. Polymorphism level (θπ) ratio genetic differentiation (fixation index)-based cross approaches applied, 539 regions, which harbored 176 genes, selected. Functional selected genes revealed that they associated lipid metabolism (SCP2, APOA1, APOA4, APOC3, CD36, BCL6, ADCY8), backfat thickness (PLAG1, CACNA2D1), muscle (MYOG), reproduction (CABS1). Overall, our results provide valuable resource characterizing uniqueness basis future breeding.

Language: Английский

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

Animals, Journal Year: 2024, Volume and Issue: 14(10), P. 1419 - 1419

Published: May 9, 2024

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

Language: Английский

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Detection of Selection Signatures in Anqing Six-End-White Pigs Based on Resequencing Data

Genes, Journal Year: 2022, Volume and Issue: 13(12), P. 2310 - 2310

Published: Dec. 8, 2022

As a distinguished Chinese indigenous pig breed that exhibits disease resistance and high meat quality, the Anqing six-end-white (AQ) represents valuable germplasm resource for improving quality of breeding industry. In this study, 24 AQ pigs were distantly blood-related 6 Asian Wild Boar (AWB) selected 10× deep-genome resequencing. The signatures selection analyzed to explore genetic basis their characteristics identify excellent germplasm-related functional genes based on NGS data. A total 49,289,052 SNPs 6,186,123 indels detected across genome in 30 pigs. Most variations synonym mutations existed intergenic region. We identified 275 regions (top 1%) harboring 85 by applying crossover approach differentiation (FST) polymorphism levels (π ratio). Some found be positively pigs' breeding. SMPD4 DDX18 involved immune response pseudorabies virus (PRV) porcine reproductive respiratory syndrome (PRRSV). BCL6 P2RX6 biological regulation T cells phagocytes. SLC7A4 SPACA4 related performance. MSTN HIF1A fat deposition muscle development. Moreover, 138 overlapping ROH islands Additionally, we QTLs with most back thickness, color, pH value, fatty acid content, cells, parasitic immunity, bacterial immunity. Based enrichment analysis mapping, conducted further research molecular traits (disease quality). These results are reliable conserving resources exploiting markers

Language: Английский

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