Dataset Information

Genotype frequency contributions of Mx1 gene in eight chicken breeds under different selection pressures.

ABSTRACT: Chicken Mx1 gene, as a positive antiviral gene, has been reported to provide resistance to several viruses especially avian influenza virus. In present research, the genotype frequency contributions of chicken Mx1 polymorphisms were characterized in five lowly selected as well as one moderately selected Sichuan native chicken populations and two highly selected commercial chicken breeds. Together with two newly-identified mutation sites (r.8A > G and r.1257T > C), a total of 13 single nucleotide polymorphisms (SNPs), including seven nonsynonymous mutation and six synonymous mutation, were found in the coding region of chicken Mx1 gene. Local Chinese chicken populations exhibited higher nucleotide diversity than commercial populations. Moreover, amino acid substitution sites as well as positive selection sites were located only in the domain not determined and GTPase domain, implying that amino acids mutations were likely needed in the modulatory and structural regions to better adapt the environment. Collectively, our results suggest that different selection pressures greatly influenced the genotype frequency contributions of chicken Mx1 gene. Understanding the interaction between genetic diversity and artificial selection may help us to better select and breed superior domestic chickens.

SUBMITTER: Li J

PROVIDER: S-EPMC6235823 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Genotype frequency contributions of Mx1 gene in eight chicken breeds under different selection pressures.

Li Jingjing J Yang Chaowu C Ran Jinshan J Jiang Xiaosong X Du Huarui H Li Zhiqiang Z Liu Yiping Y Zhang Long L

3 Biotech 20181114 11

Chicken Mx1 gene, as a positive antiviral gene, has been reported to provide resistance to several viruses especially avian influenza virus. In present research, the genotype frequency contributions of chicken Mx1 polymorphisms were characterized in five lowly selected as well as one moderately selected Sichuan native chicken populations and two highly selected commercial chicken breeds. Together with two newly-identified mutation sites (r.8A > G and r.1257T > C), a total of 13 single nucleotide ...[more]

PMID: 30456017

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Project description:Natural selection is likely a major factor in shaping genomic variation of the African indigenous rural chicken, driving the development of genetic footprints. Selection footprints are expected to be associated with adaptation to locally prevailing environmental stressors, which may include diverse factors as high altitude, disease resistance, poor nutrition, oxidative and heat stresses. To determine the existence of a selection footprint, 268 birds were randomly sampled from three indigenous ecotypes from East Africa (Rwanda and Uganda) and North Africa (Baladi), and two registered Egyptian breeds (Dandarawi and Fayoumi). Samples were genotyped using the chicken Affymetrix 600K Axiom® Array. A total of 494,332 SNPs were utilized in the downstream analysis after implementing quality control measures. The intra-population runs of homozygosity (ROH) that occurred in >50% of individuals of an ecotype or in >75% of a breed were studied. To identify inter-population differentiation due to genetic structure, FST was calculated for North- vs. East-African populations and Baladi and Fayoumi vs. Dandarawi for overlapping windows (500 kb with a step-size of 250 kb). The ROH and FST mapping detected several selective sweeps on different autosomes. Results reflected selection footprints of the environmental stresses, breed behavior, and management. Intra-population ROH of the Egyptian chickens showed selection footprints bearing genes for adaptation to heat, solar radiation, ion transport and immunity. The high-altitude-adapted East-African populations' ROH showed a selection signature with genes for angiogenesis, oxygen-heme binding and transport. The neuroglobin gene (GO:0019825 and GO:0015671) was detected on a Chromosome 5 ROH of Rwanda-Uganda ecotypes. The sodium-dependent noradrenaline transporter, SLC6A2 on a Chromosome 11 ROH in Fayoumi breed may reflect its active behavior. Inter-population FST among Egyptian populations reflected genetic mechanisms for the Fayoumi resistance to Newcastle Disease Virus (NDV), while FST between Egyptian and Rwanda-Uganda populations indicated the Secreted frizzled related protein 2, SFRP2, (GO:0009314) on Chromosome 4, that contributes to melanogenic activity and most likely enhances the Dandarawi chicken adaptation to high-intensity of solar radiation in Southern Egypt. These results enhance our understanding of the natural selection forces role in shaping genomic structure for adaptation to the stressful African conditions.

Dataset Information

Genotype frequency contributions of Mx1 gene in eight chicken breeds under different selection pressures.

Publications

Genotype frequency contributions of Mx1 gene in eight chicken breeds under different selection pressures.

Similar Datasets

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