Identification of loci associated with environmental adaptation in indigenous cattle of Uganda

Abstract

Cattle are invaluable to the people of Uganda. They are a source of pride of tribes and are also used in social functions. In Uganda, local breeds of cattle are kept due to their tolerance to locally prevailing animal pests and disease despite their poorer productivity when compared to exotic breeds such as Holstein and Jersey. Local adaptation of these indigenous breeds is still poorly understood and under-studied in genomics studies. The study utilized whole-genome sequencing data to identify genetic loci under strong positive selection that may be associated with the local adaptability to prevailing environmental conditions. Whole-genome sequence data from 51 cattle composed of six cattle breeds indigenous to Uganda, four exotic breeds and four cattle breeds indigenous to other parts of Africa were utilised in this study. From comparative genome-wide single nucleotide polymorphism analysis between cattle groups, it was observed that cattle breeds indigenous to Uganda have a higher admixture and average nucleotide diversity when compared to other groups. Functional enrichment analysis of genes with strong signals of positive selection revealed that these genes were associated with processing of information from the environment and calcium signalling (USH2A, GABRB1, QRFPR, PTAFR, HTS5A, EDNRA, VFGFC), neuronal function, immunity (CD34, CD69, CD86, IFNAH, IL16, IL7, IL1R2, IL21R, ILDR1, and STING1 in Zebu and CD86, IL20RB, IL7, IL26, IL13RA2, ILDR1, NLRC4, and BOLA-DQB (MHC class II antigen) in Ankole cattle.), growth (CDK19, FGF18), metabolism (PLA2G2D3 in Ankole; PLA2G2E and FHIT in Zebu, FOXP1) and apoptosis. Results from this study indicate that indigenous cattle breeds from Uganda have undergone extensive adaptation to locally prevailing environmental conditions that allow them to live in environments with endemic cattle diseases such as tick-borne diseases and trypanosomiasis. Loci identified in this study to be under positive natural selection can serve as useful genetic tools for breed amelioration efforts in Uganda that look at introgression of traits from indigenous breeds to exotic breeds.