Haplotype‐resolved genome and pan‐genome graphs reveal the impacts of structural variation on functional genome and feather colors in chickens DOI Creative Commons
Lihong Gu, Peng Chen,

An-Hong Chen

et al.

iMetaOmics., Journal Year: 2025, Volume and Issue: unknown

Published: May 24, 2025

Abstract Structural variation (SV) refers to a wide range of genetic variations that significantly affect genome biology and complex phenotypes. However, the population‐level SV landscape its functional impacts on chickens are largely unknown. Here, we generated haplotype‐resolved assemblies for Chinese Wenchang chicken then integrated them with another 29 354 resequencing data construct pan‐genome graph genotyping. We detected 185,205 high‐confidence SVs found one‐third were derived from homology‐based transposable element (TE) insertion‐based mutational mechanisms. By examining ChickenGTEx resource, discovered 1728 associated molecular phenotypes (e.g., gene expression alternative splicing), including 2.7‐kb insertion in exon EEF1A2 related egg‐laying rates, which showed significant difference frequency between broilers layers. Additionally, identified lncRNA Variable Number Tandem Repeats (VNTR)‐mediated influencing white feathers due flow Overall, our study provides valuable resource genetics genomics sheds light as well potential contributions structure, regulation, traits.

Language: Английский

Haplotype‐resolved genome and pan‐genome graphs reveal the impacts of structural variation on functional genome and feather colors in chickens DOI Creative Commons
Lihong Gu, Peng Chen,

An-Hong Chen

et al.

iMetaOmics., Journal Year: 2025, Volume and Issue: unknown

Published: May 24, 2025

Abstract Structural variation (SV) refers to a wide range of genetic variations that significantly affect genome biology and complex phenotypes. However, the population‐level SV landscape its functional impacts on chickens are largely unknown. Here, we generated haplotype‐resolved assemblies for Chinese Wenchang chicken then integrated them with another 29 354 resequencing data construct pan‐genome graph genotyping. We detected 185,205 high‐confidence SVs found one‐third were derived from homology‐based transposable element (TE) insertion‐based mutational mechanisms. By examining ChickenGTEx resource, discovered 1728 associated molecular phenotypes (e.g., gene expression alternative splicing), including 2.7‐kb insertion in exon EEF1A2 related egg‐laying rates, which showed significant difference frequency between broilers layers. Additionally, identified lncRNA Variable Number Tandem Repeats (VNTR)‐mediated influencing white feathers due flow Overall, our study provides valuable resource genetics genomics sheds light as well potential contributions structure, regulation, traits.

Language: Английский

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