Genome-wide assessment of genetic diversity in Mexican Sardo Negro breed

Sardo Negro is a Mexican zebu cattle breed utilized in tropical regions in America due to its ability to cope with hot and humid weather and its resistance to parasites such as ticks. This study aimed to characterize the genetic identity through within-and across-breed genetic diversity studies. The study included 555 Sardo Negro geno-types from the 65k SNP array. In addition, genomic data of 134 other worldwide cattle breeds were retrieved from an open-access repository. Within-breed genetic diversity was evaluated by observed and expected het-erozygosity, effective population size, and inbreeding coefficients. The latter was computed by PLINK (FIS), by subtracting one from the diagonal elements of the genomic relationship matrix (FGRM), and by runs of homo-zygosity (FROH) of different length classes. Genetic diversity across breeds was assessed by pairwise Wright FST, principal components, and cluster analysis. Observed and expected heterozygosity, FIS, FGRM, FROH and effective population size were 0.268, 0.275,-0.02, 0.11, 0.08 and 220, respectively. Correlations between FIS and all FROH were significant. Sardo Negro cattle show little differentiation with indigenous Indian and Pakistan zebu breeds. With a cluster plot, Sardo Negro cattle showed weak differentiation in the reference populations due to their near historical development and the low differentiation among zebu breeds. This research study suggests no imme-diate risks associated with loss of genetic variation in this breed, and Sardo Negro retains enough genetic variability from their founder's populations.