Fig. 2

Principal component analysis of all individuals. a PC1 (X axis) versus PC2 (Y axis) are shown. Individuals of different breeds are differently colored. PC1 clearly separates between Taggar, Nilotic and a mix between Desert and Nubian goats. The second component allows separating between Desert and Nubian goats. Desert goats are scattered throughout all clusters. The first two principal components, PC1 and PC2, account for 2.5% and 1.9% of the total variance, respectively. b Visual representation of the contribution of individuals to the first 10 principal components. The contribution of each individual to each PC1 through 10 is shown using a heat map image. Green color indicates a high contribution to the PC, while yellow shows average contribution, orange is low contribution, and the red color indicates the lowest contribution. c Genomic location of SNP contributing to the principle component 1 (PC1) – PC1 allows for the separation of the Taggar, Nubian and Nilotic goat breeds