Genome‐wide association analysis reveals novel loci for hypoxia adaptability in Tibetan chicken |
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| Authors: | S. Y. Jiang H. Y. Xu Z. N. Shen C. J. Zhao C. Wu |
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| Affiliation: | 1. College of Animal Science and Technology, China Agricultural University, Beijing, China;2. Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, University of Texas at Austin, Austin, TX, USA;3. National Engineering Laboratory for Animal Breeding, Beijing, China;4. Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China;5. Beijing Key Laboratory of Animal Genetic Improvement, Beijing, China |
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| Abstract: | The Tibetan chicken (TBC), an indigenous chicken breed of the Tibetan Plateau, has adapted to its hypoxic, high‐altitude environment over hundreds of years. The objective of this study was to identify the polymorphisms and genes associated with adaptation to hypoxia in this chicken breed. In the present study, samples were collected during days 18–21 of the incubation period from both surviving chicks and dead embryos, all of which were hatched under hypoxic conditions. A genome‐wide association study was conducted using the Illumina iSelect 60K SNP array with a case–control design, in which the case group consisted of the dead chicken embryos (n = 54) and controls were the surviving chicks (n = 82). Four significant SNPs were detected at the genome‐wide level (P < 0.05), and the results indicated that fork head box G1 (FOXG1) was the main candidate gene. The lead SNP NC_006092.4:g.33368893T>C was confirmed with a polymerase chain reaction‐restriction fragment length polymorphism analysis of 122 cases and 212 controls. A chi‐square test showed a significant association between NC_006092.4:g.33368893T>C and hatchability under hypoxic conditions (P < 0.01). Our results revealed novel polymorphisms and a candidate gene associated with hypoxic adaptation, facilitating further study in this field. |
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| Keywords: | embryos genome‐wide association study hatchability single nucleotide polymorphism |
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