Identification of Copy Number Variations and Selection Signatures in Wannan Spotted Pigs by Whole Genome Sequencing Data: A Preliminary Study DOI Creative Commons
Wei Zhang, Yao Jiang,

Zelan Ni

et al.

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

Cataloging copy number variation regions and allied diversity in goat breeds spanning pan India DOI
Nidhi Sukhija,

K K Kanaka,

Indrajit Ganguly

et al.

Mammalian Genome, Journal Year: 2025, Volume and Issue: unknown

Published: April 2, 2025

Language: Английский

Citations

3
Multiomics analysis reveals signatures of selection and loci associated with complex traits in pigs DOI Creative Commons
Lei Liu, Guoqiang Yi, Yilong Yao

et al.

iMeta, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 15, 2024

Abstract The genetic basis of complex traits and phenotypic differentiation remains unclear in pigs. Using nine genomes—seven which were newly generated, high‐quality de novo assembled genomes—and 1081 resequencing genomes, we built a pan‐genome identified 134.24 Mb nonredundant nonreference sequences, 1099 novel protein‐coding genes, 187,927 structural variations (SVs) 30,143,962 single‐nucleotide polymorphisms (SNPs). Analysis selective domestication revealed BRCA1 associated with enhanced adipocyte growth fat deposition, ABCA3 linked to an alleviated immune response reduced lung injury. Integrating 162 transcriptomes methylomes skeletal muscle across 27 developmental stages the regulatory mechanism between Eastern Western breeds. Artificial selection reshaped local DNA methylation status imparted effects on progression patterns heterochronic genes such as GHSR BDH1 , particularly during embryonic development. Altogether, our work provides valuable resources for understanding molecular mechanisms behind enhancing improvement programs

Language: Английский

Citations

3
Identification of Copy Number Variations and Selection Signatures in Wannan Spotted Pigs by Whole Genome Sequencing Data: A Preliminary Study DOI Creative Commons
Wei Zhang, Yao Jiang,

Zelan Ni

et al.

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

Citations

0