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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. [ABSTRACT FROM AUTHOR]

Background: Modern breeding in the poultry industry mainly aims to produce high-performance poultry lines and breeds in two main directions of productivity, meat and eggs. To understand more about the productive potential of lowly selected Chinese native chicken populations, we selected 14 representative SNP markers strongly associated with growth traits or carcass traits and 14 SNP markers strongly associated with egg laying traits through previous reports. By using the MassArray technology, we detected the genotype frequency distributions of these 28 SNP markers in seven populations including four lowly selected as well as one moderately selected Sichuan native chicken populations, one commercial broiler line and one commercial layer line. Results: Based on the genotype frequency distributions of these 28 SNP markers in 5 native chicken populations and 2 commercial lines, the results suggested that these Chinese indigenous chicken populations have a relatively close relationship with the commercial broiler line but a marked distinction from the commercial layer line. Two native chicken breeds, Shimian Caoke Chicken and Daheng Broilers, share similar genetic structure with the broiler line. Conclusions: Our observations may help us to better select and breed superior domestic chickens and provide new clues for further study of breeding programs in local chicken populations. [ABSTRACT FROM AUTHOR]