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Whole-genome resequencing analysis of Pengxian Yellow Chicken to identify genome-wide SNPs and signatures of selection

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Abstract

Chinese indigenous chickens have experienced strong selective pressure in genes or genomic regions controlling critical agricultural traits. To exploit the genetic features that may be useful in agriculture and are caused by artificial selection, we performed whole-genome sequencing of six Pengxian Yellow Chickens and downloaded the sequence data of five Red Jungle fowls from the NCBI. Through selective sweep analysis, we detected several regions with strong selection signals, containing 497 protein-coding genes. These genes were involved in developmental processes, metabolic processes, the response to external stimuli and other biological processes including digestion (ABCG5, ABCG8 and ADRB1), muscle development and growth (SMPD3, NELL1, and BICC1) and reduced immune function (CD86 and MTA3). Interestingly, we identified several genes with extremely strong selection signals associated with the loss of visual capability of domestic chickens relative to their wild ancestors. Amongst them, we propose that CTNND2 is involved in the evolutionary changes of domestic chickens toward reduced visual ability through the diopter system. VAT1 was also likely to contribute to these processes through its regulation of mitochondrial fusion. In summary, these data illustrate the patterns of genetic changes in Pengxian yellow chickens during domestication and provide valuable genetic resources that facilitate the utilization of chickens in agricultural production.

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Acknowledgements

This work was supported by Sichuan Science and Technology Program (2016NYZ0050), and Technology Planning Project of Chengdu (2015-NY01-00036-NC).

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Authors and Affiliations

  1. Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China

    Huadong Yin, Diyan Li, Yan Wang & Qing Zhu

Authors
  1. Huadong Yin
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  2. Diyan Li
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  3. Yan Wang
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  4. Qing Zhu
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Contributions

Conceptualization, HY and QZ; methodology, HY and YW; software, HY and DL; formal analysis, HY and DL; resources, QZ; writing—original draft preparation, HY; writing—review and editing, HY and QZ; supervision, QZ; project administration, YW; funding acquisition, QZ and HY.

Corresponding author

Correspondence to Qing Zhu.

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Conflict of interest

All the authors report no conflicts of interest in this work.

Ethics approval

All experimental operations were approved by the Animal Ethics Committee of Sichuan Agricultural University (approval number: 20171410401). Relevant guidelines and regulations were followed for all methods.

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Yin, H., Li, D., Wang, Y. et al. Whole-genome resequencing analysis of Pengxian Yellow Chicken to identify genome-wide SNPs and signatures of selection. 3 Biotech 9, 383 (2019). https://doi.org/10.1007/s13205-019-1902-6

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  • DOI: https://doi.org/10.1007/s13205-019-1902-6

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