The chicken pan-genome reveals gene content variation and a promoter region deletion in IGF2BP1 affecting body size.

Wang, Kejun, Hu, Haifei, Tian, Yadong, Li, Jingyi, Scheben, Armin, Zhang, Chenxi, Li, Yiyi, Wu, Junfeng, Yang, Lan, Fan, Xuewei, Sun, Guirong, Li, Donghua, Zhang, Yanhua, Han, Ruili, Jiang, Ruirui, Huang, Hetian, Yan, Fengbin, Wang, Yanbin, Li, Zhuanjian, Li, Guoxi, Liu, Xiaojun, Li, Wenting, Edwards, David, Kang, Xiangtao (July 2021) The chicken pan-genome reveals gene content variation and a promoter region deletion in IGF2BP1 affecting body size. Molecular Biology and Evolution. ISSN 0737-4038

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Abstract

Domestication and breeding have reshaped the genomic architecture of chicken, but the retention and loss of genomic elements during these evolutionary processes remain unclear. We present the first chicken pan-genome constructed using 664 individuals, which identified an additional ∼66.5 Mb sequences that are absent from the reference genome (GRCg6a). The constructed pan-genome encoded 20,491 predicated protein-coding genes, of which higher expression level are observed in conserved genes relative to dispensable genes. Presence/absence variation (PAV) analyses demonstrated that gene PAV in chicken was shaped by selection, genetic drift, and hybridization. PAV-based GWAS identified numerous candidate mutations related to growth, carcass composition, meat quality, or physiological traits. Among them, a deletion in the promoter region of IGF2BP1 affecting chicken body size is reported, which is supported by functional studies and extra samples. This is the first time to report the causal variant of chicken body size QTL located at chromosome 27 which was repeatedly reported. Therefore, the chicken pan-genome is a useful resource for biological discovery and breeding. It improves our understanding of chicken genome diversity and provides materials to unveil the evolution history of chicken domestication.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics Investigative techniques and equipment organism description > animal Investigative techniques and equipment > assays organism description > animal > bird organism description > animal > bird > chicken Investigative techniques and equipment > assays > genome wide association studies bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > single nucleotide polymorphism
CSHL Authors:	Scheben, Armin
Communities:	CSHL labs > Siepel lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	30 July 2021
Date Deposited:	04 Aug 2021 13:16
Last Modified:	25 Jan 2024 20:47
PMCID:	PMC8557422
URI:	https://repository.cshl.edu/id/eprint/40306

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