Genetic Diversity and Population Structure of Two Mexican Creole Cattle Populations

The descendants of the first cattle that arrived in America in 1493 are known as Creole cattle. The objective of this study was to characterize the diversity and genetic structure of two Creole cattle populations in Mexico. A total of 75 cattle were included: 36 Coreño (CC) and 39 Raramuri (CR). Genotyping was performed using an SNP microarray. Quality control, estimation of genetic diversity, and analysis of homozygosity by runs of homozygosity (ROH) and linkage disequilibrium (LD) analyses were performed in PLINK v1.9. The effective population size (Ne) was calculated using GONE2 and CurrentNe2. The structure was analyzed by principal component analysis (PCA), discriminant analysis of principal components (DAPC) and ADMIXTURE. The expected heterozygosity was high in both populations (CC 0.379 and CR 0.398). The short segments of classes > 0.5–4 represented 84.41% in the CC cattle and 92.83% in the CR cattle. The contemporary Ne was 32 in the CC cattle and 473 in the CR cattle. The Creole cattle were closely grouped with European cattle populations. The ADMIXTURE revealed 70.60% of a Creole ancestral component in the CR cattle, whereas the CC cattle shared 38.67% of this component with the CR cattle and exhibited 46.44% of a differentiated Creole component. In conclusion, the two Mexican Creole cattle populations had high genetic diversity and low homozygosity; a greater extension of LD was observed for the CC cattle, and consequently, the Ne was lower. The CC cattle exhibited shared ancestry with the CR cattle.