Whole-genome resequencing of Dulong Chicken reveal signatures of selection

ABSTRACT

1. Dulong Chickens (DLCs) live at high altitude (~3000 m) and humidity (~90%), are endemic to the Yunnan province, and have gradually developed unique physiological characteristics, but their genetic basis is still unclear. Using the fixation index (F_ST) approach, based on whole-genome resequencing, DLCs were analysed to uncover the genomic architecture of the population and candidate genes involved in selection during domestication.

2. A total of 469 candidate genes were obtained to be putatively under selection in DLCs. Further investigations revealed the genic footprint for local adaptation (high-altitude and high-humidity) as the genic signatures that are involved in economic traits (related to egg production).

3. Candidate genes were identified that may be associated with disease resistance, aggressiveness, small body size and positive selection of vision in DLCs.

4. These data revealed loci of selective signals that operate during selection for production at high altitude and humidity.

KEYWORDS:

• Dulong chicken
• genetic diversity
• whole-genome resequencing
• selection
• adaptation

Disclosure statement

The authors declare that they have no competing interests.

Supplementary material

Supplemental data for this article can be accessed here.

Data availability

Whole-genome resequencing data are available at NCBI with the accession number: PRJNA559932.

Additional information

Funding

This work was supported by Yunnan agricultural joint key project [2017FG001(−006)]; National Natural Science Foundation of China [31860624,31860650]; Key Discipline Construction Project of Biology in Yunnan province [50097505]; Project of technical leader of Yunnan Province [2016HB009]; scientific research fund project of the Yunnan Provincial Education Department [2018Y128,2020Y0400]; and Talent support program of Southwest Forestry University and by the Doctoral Scientific Research Foundation of Southwest Forestry University [111441];