Genetic polymorphisms on heat-shock protein 70 gene and mitochondrial DNA d-loop variations: implications on selection for heat stress in indigenous chickens in Kenya
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Abstract
Background: Climate change resulting in heat stress, is one of the most challenging environmental conditions affecting poultry. Studying thermotolerance is crucial in the prevention of heat stress in chickens because it may lead to the identification of genetic lines that can withstand adverse effects of heat stress. This study aimed at investigating polymorphisms in heat shock protein 70 (HSP70) gene in indigenous chicken ecotypes. We also analyzed the mitochondrial DNA (mtDNA) D-loop of indigenous chickens to assess their origins and genetic diversity.
Methods: We collected samples From Turkana basin, Mt. Elgon catchment, Lake Victoria basin and Lamu chicken ecotypes in Kenya. Genomic DNA was extracted from 280 chicken samples. The first 360 bp region of HSP70 and the first 760 bp region of the mtDNA were then amplified via PCR. These were later sequenced using Sanger ABI 3730 method.
Results: We reveal through a detailed analysis of the HSP70 gene fragment in 20 indigenous chickens the presence of three HSP70 haplotypes (GC, AC, and AG) and 28 mtDNA haplotypes. Phylogenetic analysis of HSP70 revealed the presence of the ancestral haplotype GC which dominated in Turkana basin ecotype. The 28 mtDNA haplotypes clustered in haplogroups A, B, C, D, E and I. Haplogroup E which has never been reported in commercial chickens dominated in Turkana basin ecotype indicating no admixture with commercial chickens. mtDNA haplogroups were shown to have originated from various parts of South and Southeast Asia. Lack of population structure in indigenous chicken ecotypes could be an indication of genetic admixture. The mtDNA nucleotide and haplotype diversity indices were low for Turkana basin ecotype and high for Lamu ecotype. High HSP70 nucleotide diversity indices were recorded in Turkana basin ecotype, while low values were recorded in Lamu ecotype. Most of the mtDNA genetic variations occurred within individuals for the three hierarchical categories considered while most variations in HSP70 gene occurred within populations.
Conclusions: This is the first study to analyze the HSP70 polymorphisms in indigenous chickens in Africa and results obtained should pave the way for further in-depth studies on heat stress.
Cite this as
2019. Genetic polymorphisms on heat-shock protein 70 gene and mitochondrial DNA d-loop variations: implications on selection for heat stress in indigenous chickens in Kenya. PeerJ Preprints 7:e27589v1 https://doi.org/10.7287/peerj.preprints.27589v1Author comment
This is a submission to PeerJ for review.
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Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Grace M Kennedy performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Philip M Panyako analyzed the data, approved the final draft.
Philip A Oyier analyzed the data, contributed reagents/materials/analysis tools, approved the final draft.
Emmanuel K Ndiema approved the final draft.
Jacqueline K Lichoti approved the final draft.
Sheila C Ommeh conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, approved the final draft.
Animal Ethics
The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):
This study received a “no objection to the research” from the Directorate of Veterinary Services, Ministry of Agriculture, Livestock and Fisheries in Kenya under permit number RES/POL/VOL.XXVII/162 to sample indigenous chickens in Kenya.
Field Study Permissions
The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):
Directorate of Veterinary Services, Ministry of Agriculture, Livestock and Fisheries in Kenya under permit number RES/POL/VOL.XXVII/162 to sample indigenous chickens in Kenya.
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
The mtDNA haplotype sequences described here are accessible via GenBank accession numbers MH681612 to MH681639
The HSP70 haplotype sequences described here are accessible via GenBank accession numbers KT948639, KT948640 and KT948641
Data Deposition
The following information was supplied regarding data availability:
GenBank
GenBank accession numbers MH681612 to MH681639, KT948639, KT948640 and KT948641
Funding
Jomo Kenyatta University of Agriculture and Technology (grant no. JKU/2/4/RP/181) The Japan International Cooperation Agency Africa –ai-JAPAN project/task force research fellowship awarded through the innovation center for molecular biology and biochemistry (iCMoB) (reference number: iCMoB/01/2014). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
