Integrative 3D genomics with multi-omics analysis and functional validation of genetic regulatory mechanisms of abdominal fat deposition in chickens

Linyong Shen, Xue Bai, Liru Zhao, Jiamei Zhou, Cheng Chang, Xinquan Li, Zhiping Cao, Yumao Li, Peng Luan, Hui Li () and Hui Zhang ()
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Linyong Shen: Northeast Agricultural University
Xue Bai: Northeast Agricultural University
Liru Zhao: Northeast Agricultural University
Jiamei Zhou: Northeast Agricultural University
Cheng Chang: Northeast Agricultural University
Xinquan Li: Northeast Agricultural University
Zhiping Cao: Northeast Agricultural University
Yumao Li: Northeast Agricultural University
Peng Luan: Northeast Agricultural University
Hui Li: Northeast Agricultural University
Hui Zhang: Northeast Agricultural University

Nature Communications, 2024, vol. 15, issue 1, 1-20

Abstract: Abstract Chickens are the most abundant agricultural animals globally, with controlling abdominal fat deposition being a key objective in poultry breeding. While GWAS can identify genetic variants associated with abdominal fat deposition, the precise roles and mechanisms of these variants remain largely unclear. Here, we use male chickens from two lines divergently selected for abdominal fat deposition as experimental models. Through the integration of genomic, epigenomic, 3D genomic, and transcriptomic data, we build a comprehensive chromatin 3D regulatory network map to identify the genetic regulatory mechanisms that influence abdominal fat deposition in chickens. Notably, we find that the rs734209466 variant functions as an allele-specific enhancer, remotely enhancing the transcription of IGFBP2 and IGFBP5 by the binding transcription factor IRF4. This interaction influences the differentiation and proliferation of preadipocytes, which ultimately affects phenotype. This work presents a detailed genetic regulatory map for chicken abdominal fat deposition, offering molecular targets for selective breeding.

Date: 2024
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DOI: 10.1038/s41467-024-53692-6

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