Genomic Analysis Suggests KITLG is Responsible for a Roan Pattern in two Pakistani Goat Breeds

Abstract

The roan coat color pattern is described as the presence of white hairs intermixed with pigmented hairs. This kind of pigmentation pattern has been observed in many domestic species, including the goat. The molecular mechanisms and inheritance that underlie this pattern are known for some species and the KITLG gene has been shown associated with this phenotype. To date, no research effort has been carried out to find the gene(s) that control(s) roan coat color pattern in goats. In the present study, after genotyping with the GoatSNP50 BeadChip, 35 goats that showed a roan pattern and that belonged to two Pakistan breeds (Group A) were analyzed and then compared to 740 goats of 39 Italian and Pakistan goat breeds that did not have the same coat color pattern (Group B). Runs of homozygosity-based and XP-EHH analyses were used to identify unique genomic regions potentially associated with the roan pattern. A total of 3 regions on chromosomes 5, 6, and 12 were considered unique among the group A versus group B comparisons. The A region > 1.7 Mb on chromosome 5 was the most divergent between the two groups. This region contains six genes, including the KITLG gene. Our findings support the hypothesis that the KITLG gene may be associated with the roan phenotype in goats.

Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation

“…Domestication is often associated with changes in the coat colour of domesticated populations 71 . Consistent with previous findings in livestock and other domestic species, strong signals of putative selection in Russian breeds of European and Asian origin were detected by the hapFLK analyses in the genomic regions that include the genes KIT and KITLG , both of which contribute to coat colour in a variety of species 72 , 73 . Interestingly, in the region including KITLG a long interval under putative selection (BTA5: 13.27–27.03 Mbp (13.76 Mbp)) was reported by hapFLK in the EUR2 breed set, while in the EUR1 set the overlapping region was shorter (BTA5:17.15–20.49 (3.34 Mbp)).…”

Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication

“…Variation at the KITLG gene, which controls melanocyte differentiation and migration, has also been associated with coat/ skin colour in cattle 29 and other species 11,30 and both elevated XP-EHH and XP-CLR scores were observed upstream of KITLG in various comparisons of water buffalo breeds ( Supplementary Fig. 4A).…”

High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia

“…KITLG is associated with pigmentation in sheep [49], roan coat phenotype in goats [50], and cattle [51]. The DCMS method reported this gene to be the top-ranked candidate in the selected regions of the Buubei and roan Edilbai breeds.…”