Novel genetic variants data for adaptation to hypoxia in native chickens

Abstract

Objective: The genomic response and the role of genetic variants in hypoxia condition are always interesting issues about adaption pathways at genomic level. Herein, we carried out a comparative genomic study between highland and lowland native chickens, in order to identify the adaptive variants in hypoxia condition. We generated more than 20 million genetic variants in highland and lowland chickens. Finally, 3877 SNVs including the mtDNA ones, were discovered as novel adaptive genetic variants. The generated data set can provide new insight about mechanism of adaptation to hypoxia at genomic level.

Data description: To investigate the role of genetic variants in adaptation to hypoxia, 10 whole-genome sequencing data sets associated to highland and lowland native chickens were provided. DNA was extracted by salting-out protocol. Paired-end 125 bp short reads were sequenced by Illumina Hiseq 2000. Variants calling of highland and lowland native chickens were performed by fix ploidy algorithm in CLC Genomic Workbench. Total genetic variants of highland chickens were compared to lowland chickens in order to identify the differential genetic variants (DGVs) between highland and lowland chickens. In this way, 3877 novel SNVs (VCF format) including the mtDNA ones, were deposited at EBI database ( https://identifiers.org/ena.embl:ERZ491574 ) for the first time.

Keywords: Genetic variants; Hypoxia; Native chicken.