Diversity, Genetic Background and Hsp70 Gene Functional Polymorphisms for Heat Tolerance in Indigenous Chickens in Kenya

Abstract

The arid and semi-arid regions occupy the highest percentage of land mass in Kenya and are worst hit by the ongoing climate change across the horn of Africa. Indigenous chickens in the arid and semi-arid lands (ASALs) have a challenge of having to deal with heat stress. The crossbreeding programs in the 1970's to date have also led to the dilution of indigenous chickens which are known to be hardy and adapt well to the local climate as compared to commercial chickens. This study aimed to 1) characterize the phenotypes for heat tolerance in indigenous chickens of Kenya, 2) investigate the genetic background of indigenous chickens of Kenya 3) characterize the functional polymorphisms on the HSP70 gene in indigenous chickens of Kenya from Lake Turkana basin, Lake Victoria basin, Lamu archipelago and Mt. Elgon catchment. Data was collected from 296 indigenous chickens by the use of questionnaires. Blood samples were stored on FTA® cards. Analysis of variance (ANOVA) for the phenotypic traits was calculated in response to ambient temperature. There was significant relationship between the comb types and the ambient temperature. Similarly, the plumage density and the body temperature had significant relationship. All the other traits (skin color, shank color, comb color, earlobe color and the crested phenotype and feathered shanks phenotype) had no significant relationship to the ambient temperature. Indigenous chickens in Lake Turkana basin had the highest temperatures while those from Mt. Elgon catchment had the least temperatures. Lake Turkana basin had the highest outside temperature while Mt. Elgon catchment had the least temperature. For molecular work, heat shock protein 70 (HSP70) gene and the D-loop region of the Mitochondrial DNA (mtDNA) were amplified using PCR, purified and sequenced. Editing of the sequences was done and the sequences aligned. A total of 28 mtDNA haplotypes were mapped. Most of the samples were Haplotype 1 and most of them were from Lake Turkana basin. The other major haplotypes were 4, 7 and 26. Phylogenetic analysis for mtDNA clustered the 28 haplotypes in 4 out of the 9 reference haplogroups from GenBank. Most of the samples were haplogroup E with a high percentage comprising samples from Lake Turkana basin. None of the samples clustered in haplogroups C, G, F, H, and I. This information was clearly displayed in xix the splits decomposition and the Network analysis. Analysis of molecular variance (AMOVA) clearly indicated greater diversity within populations at 78.06%. Three HSP70 haplotypes; AG, AC and GC were mapped. Phylogenetic analysis displayed haplotype GC as the ancestral haplotype since it was in the same clade with the ancestral red jungle fowl and it dominated in Lake Turkana basin. Haplogroup AG was dominant in Lamu archipelago while AC haplogroup had least frequencies in all the agro-climatic zones. The AMOVA values were highest within individuals at 89.62%. No recombination events were observed. In conclusion this study successfully characterized the phenotypes implicated for heat tolerance. The origin of indigenous chickens in Kenya was also established and polymorphisms in the heat HSP70 implicated in heat tolerance was also established. These initial results should pave way towards first step to genetic breeding for heat tolerant indigenous chickens and conservation efforts of indigenous chickens.