Study of the Genetic Structure and Diversity of Holstein cattle in the small holder system in Mexico

Abstract

The objective was to know the population structure of Holstein animals in the family dairy system, to identify possible origins of the genetic material, to know the degree of inbreeding and to identify possible traces of selection in the genome, which allow glimpses of the traits that have been improved over the years. The study included 270 animals genotyped with the GGP-50K® chip. After genotype quality control, 43,548 autosomal SNPs were included. To know the population structure, analyses of mixtures and principal components (PCs) were performed. To know genomic inbreeding and detect traces of selection, information on runs of homozygosity (ROH) was used. Mixture analysis was performed with the Admixture software, and PC, ROH and inbreeding analyses were performed with SVS-v7.6.8. Mixture analysis showed evidence of six components, all linked to Holstein bulls families with different country of origin. The PCs did not show stratification of the population by herd. The mean inbreeding coefficient was 0.59 ± 0.53 %. In the regions of the genome with ROHs most frequent in the population (≥20 animals), numerous associations, QTLs and genes related to milk production and composition, fertility parameters, susceptibility to diseases, body conformation, feed efficiency and some characteristics of carcass composition have been reported. The results reflect the existence of a wide genetic diversity in this population and the possibility of carrying out genetic improvement work through selection without affecting inbreeding levels.