Genome-Wide Screening of Candidate Genes for Coat Color Variation in Ethiopian Cattle Populations

In farm animals, coat color is an important qualitative trait for economic, biological and aesthetic reasons. Despite the striking variation of coat color and patterns maintained within and between many cattle populations, genes underlying this variation have not been well known. To shed light on the genetic basis of coat color variation among indigenous Ethiopian cattle populations, we sampled 226 animals representing 7 populations characterized by diverse phenotypes and adapted to different agro-ecologies. A total of 150 SNP markers located within 29 candidate genes known to determine the coat color variation or pigmentation were identified from 80K indicus derived chip. We compared allelic and genotypic frequencies between spotted and non-spotted groups of cattle populations. Our results show that the variability of SNPs upstream of MITF (rs137845005) gene on BTA 22 (31Mb), TYR  (rs41594685) gene on BTA 29 (6Mb) and LEF1 on BTA 6 (18Mb) were different between non-spotted (white) and spotted (black spotted) phenotypes. These genes have previously been known to be involved in the regulation of melanogenesis. Taking into account the role of upstream SNPs in regulating the level of gene expression, along with that of other genes the identified variants are likely potential candidates for the observed variability in coat color patterns in the study populations. Our results further provide important insight into adaptive evolution of coat color in cattle breeds sampled from heterogeneous landscapes.

 

Keywords: Coat color variation, Ethiopian cattle, genome-wide