Origin, Genetic Diversity and HSP 70 Gene Polymorphisms of Domesticated Rabbits of Kenya

Abstract

Rabbit production in Kenya offers great opportunity for food security among households as a cheap alternative source of animal protein and as a source of income. Rabbits have received limited research, and information on their origins and genetic diversity is scarce. Rabbits in Kenya are neglected and could become extinct, yet they have important traits like heat tolerance and disease resistance. They are also well adapted to the local environmental conditions including high tropical temperatures. Knowledge on local rabbits kept by farmers will shed light on the extent of diversity and adaptation across the country which will facilitate improvement and development of conservation strategies. This study had two objectives. The first objective was to characterize the origins, population structure and genetic diversity of rabbits in Kenya using the mtDNA D-loop hypervariable region. The second objective was to characterize the genetic polymorphisms in Heat Shock Protein 70 gene. A 263-base pair region of mtDNA D-loop region and a 359-base pair region in the gene coding for heat shock protein 70 of 118 rabbits sampled from Kakamega, Vihiga and Bungoma counties in the western region, Laikipia and Nyandarua counties in the central region and Kitui, Machakos and Makueni in the eastern regions were amplified. Sequence analysis revealed 8 mtDNA haplotypes with 5 of these being reported for the first time by this study and 6 HSP70 haplotypes. Network asessment of these haplotypes on a phylogenetic tree and median joining network revealed that the haplotypes and reference sequences obtained from the NCBI database clustered in lineage B and that they diverged from an ancestral sequence; the wild rabbits. The average haplotype (0.40702) and nucleotide (0.01494) diversities observed were low, indicating low genetic diversity within these regions of domesticated rabbits in Kenya. These results suggest that the Kenyan domesticated rabbits originated from Europe. AMOVA revealed a higher variation within populations (85.3%) and low variation among the groups (eastern, central and western) (1.59%), implying a lack of population structure. Nine SNPs sites at positions 277 (C/T), 302 (C/T), 362 (A/G), 365 (T/C), 386 (T/G), 401(T/C), 430(A/G), 431(T/C), 506 (G/C) were identified in the gene coding for heat shock protein 70. 4 out of these SNPs were found in haplotype 4 which occurred in Machakos county spanning agro climatic zones IV and V with higher environmental temperatures. AMOVA revealed a higher within population variation (100%) and low among group variation (1.59%) implying lack of population structure and random occurrence of these SNPs. There was low genetic diversity (Hd 0.09436) in the HSP70 gene. The genetic polymorphisms in the HSP70 gene are not associated with heat tolerance. The results from this study can be built upon by rabbit breeders to enhance rabbit production in Kenya in ways such as informing the breeds that can help combat climate change effects.