Abstract
BACKGROUND: Coat color is one of the most easily recognizable appearance traits used to discriminate livestock breeds and individuals. This study investigated the genetic loci and candidate genes affecting pigmented spots in Tianfu (TF) goats. RESULTS: The pigmented spot scores in 96 TF goats ranged from 0.20 to 3.95. Whole-genome sequencing identified 15,132,291 bi-allelic autosomal SNPs in these animals. Linear mixed-model analyses identified a major locus near the EDNRA gene on chromosome 17 and a second strong association signal on chromosome 4. Annotation of short variants within the major locus revealed no apparent causal mutations. Further analysis of short-read data revealed a complex genomic rearrangement spanning ~ 1.1 Mb in TF goats, primarily comprising one inverted duplication, one direct duplication, and two deletion events. These structural variations (SVs) were validated using PacBio HiFi sequencing data from Boer goats, one of the parental breeds of TF goats. Among the SVs, an 83,630-bp inverted duplication approximately 80 kb upstream of EDNRA showed the strongest association with the phenotype, as demonstrated by a univariate model in which this duplication explained 30.99% of the phenotypic variation. In silico analysis revealed that this duplication contains putative binding sites for pigmentation-related transcription factors, including MITF and PAX3. Furthermore, this inverted duplication, combined with the lead SNP on chromosome 4, accounted for 55.79% of the phenotypic variation. CONCLUSION: We identified a genomic region with complex SVs near EDNRA on chromosome 17 as a major locus influencing pigmented spot sizes in TF goats. We further pinpointed the causal mutations to an approximately 80-kb inverted duplication. Additionally, we detected a strong secondary association signal on chromosome 4. Our findings deepen the understanding of genetic variations underlying pigmentation in goats and provide valuable insights for selective breeding and conservation efforts.