Assessment of a Reduced SNP Panel Targeting Prolificacy and Coat Color Genes in Brazilian Sheep Breeds

Prolificacy and coat color are key economic traits influencing sheep production. This study evaluated a reduced panel of 48 SNPs previously associated with these traits and assessed its applicability to locally adapted Brazilian sheep breeds. A total of 1152 samples from 15 breeds, conserved in situ at conservation nuclei and ex situ in the Brazilian Animal Germplasm Bank, were genotyped. Allelic, genotypic, and haplotypic frequencies were estimated to compare genetic variability between in situ and ex situ populations. Additionally, linkage disequilibrium (LD) among SNPs within GDF9, a key gene associated with prolificacy, was evaluated across local breeds, revealing strong LD among specific markers. The results highlight the importance of the FecGE (GDF9) variant for prolificacy in hair sheep, confirming the presence of mutant allele E in prolific breeds, such as Santa Inês and Morada Nova, and identifying, for the first time, a high frequency of such allele in the Brazilian Blackbelly, which provides new insights into the genetic basis of this prolific hair breed. Other prolificacy-related genes, BMP15 and BMPR1B, appear to have no functional role in locally adapted breeds, as initially hypothesized, considering genetic differences among European and tropical sheep. Allelic and genotypic variation in ASIP, MC1R, TYRP1, and MITF genes reflected differences between wool and hair sheep and between local and commercial breeds. Overall, the results indicate that the germplasm bank effectively preserves in situ diversity. In conclusion, the reduced SNP panel efficiently genotyped Brazilian sheep for prolificacy and coat color SNPs, confirming which markers are present and segregating in these breeds. However, its utility could be improved by removing markers of limited relevance in the targeted breeds.