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Genome‐wide association analysis reveals novel loci for hypoxia adaptability in Tibetan chicken
Author(s) -
Jiang S. Y.,
Xu H. Y.,
Shen Z. N.,
Zhao C. J.,
Wu C.
Publication year - 2018
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12678
Subject(s) - biology , single nucleotide polymorphism , candidate gene , snp , genetics , breed , restriction fragment length polymorphism , genotype , gene
Summary 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 iS elect 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 SNP s were detected at the genome‐wide level ( P < 0.05), and the results indicated that fork head box G1 ( FOXG 1 ) 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.