Functional polymorphisms at insulin growth factor-1 and prolactin candidate genes for meat and egg production in indigenous chickens of Kenya

Abstract

Indigenous chickens are important livestock in Kenya since they provide a large proportion of quality protein in human diet as of meat and eggs. Indigenous chicken are primarily reared under the free range system where they are left to scavenge for food, with minimal feed supplementation or veterinary inputs. This study aimed to 1) characterize the phenotypes associated with meat and egg production in indigenous chickens in Kenya, 2) assess the functional polymorphisms at IGF-1 gene, a candidate for meat production in indigenous chickens in Kenya 3) assess the functional polymorphisms at PRL gene, a candidate for egg production in indigenous chickens in Kenya from Lake Turkana basin, Lamu archipelago and Mt. Elgon catchment. Data on 296 indigenous chickens was collected from farmers by the use of questionnaires. Blood samples were stored on FTA® cards. Analysis of variance (ANOVA) for the phenotypic traits was carried out across the agro-climatic zones. There were significant interactions between shank length, body length and live weight for meat production and the number of yolks per egg for egg production. All the other traits (numbers of eggs laid per hen per clutch, the number of eggs incubated per hen per clutch and the number of eggs hatched per hen per clutch) had no significant difference in the various agro-climatic zones. Despite being the lightest and small bodied, chickens from Lake Turkana basin produced more eggs than the heaviest and big bodied. Lamu Archipelago produced the highest number of double-yolked eggs. For molecular work, Insulin like growth factor 1(IGF-1) gene and Prolactin gene (PRL) were amplified using PCR, purified and sequenced. Editing of the sequences was done and the sequences aligned. A total of 3 IGF-1 haplotypes were mapped. Phylogenetic analysis displayed haplotype 9C as the ancestral haplotype since it was in the same clade with the ancestral red jungle fowl and it dominated in Lake Turkana basin. Haplotype 11C dominated Mt.Elgon catchment and Lamu archipelago zones while haplotype 9A was least in all the zones. Analyses of molecular variance (AMOVA) values were highest within individuals at 87.85% an indication of high phenotypic variation for potential genotypic phenotype association. No recombination events were observed. Two PRL haplotypes; 154 and 130 were mapped. Phylogenetic analysis displayed haplotype 130 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 154 was dominant in all the agro-climatic zones. The AMOVA values were highest within individuals, an indication of high phenotypic variation for potential genotypic phenotype association. No recombination events were observed. In conclusion this study successfully characterized the phenotypes associated with meat and egg production. Functional Polymorphisms in IGF-1 and PRL for meat and egg production were established. These initial results should pave way towards the development of molecular breeding tools for meat and eggs in indigenous chicken and their conservation by sustainable use.