Pairwise principal component analysis of African goat breeds identifies loci involved in meat and/or milk production

The selection process in Africa, both environmentally and human-driven, is expected to have led to distinctive variations on the genome between milk and meat goat breeds. We used genotypic data from the caprine 50k Illumina BeadChip to assess the genetic differentiation between nine milk-type and 12 meat-type breeds from Africa by applying a novel pairwise principal component analysis (PCA) method. Using the PCA approach, 95 comparisons contribute to the optimal dissipation on PC1 for milk-type versus meat-type breeds. We identified nine genomic regions that highly differed between milk-type and meat-type breeds in over 25% of comparisons. These SNPs are located on chromosomes 2, 3, 4, 5, 7, 12, 18, and 25. In particular, near these SNPs, candidate genes that might potentially control milk and meat production traits were located. The novel PCA approach helps the identification of genomic regions that contributed to the genomic variation of milk-type versus meat-type breeds.