Genetic Background and Inbreeding Depression in Romosinuano Cattle Breed in Mexico

SIMPLE SUMMARY: The objective of this study was to evaluate the genetic background and inbreeding depression in the Mexican Romosinuano cattle using pedigree and genomic information. Inbreeding was estimated using pedigree ([Formula: see text]) and genomic information based on the genomic relationship matrix ([Formula: see text]) and runs of homozygosity ([Formula: see text]). Linkage disequilibrium ([Formula: see text]) was evaluated using the correlation between pairs of loci, and the effective population size ([Formula: see text]) was calculated based on [Formula: see text] and pedigree information. The pedigree file consisted of 4875 animals; 71 had genotypes. [Formula: see text] decreased with the increase in distance between markers, and [Formula: see text] estimated using genomic information decreased from 610 to 72 animals (from 109 to 1 generation ago), the [Formula: see text] estimated using pedigree information was 86.44. The number of runs of homozygosity per animal ranged between 18 and 102 segments with an average of 55. The average inbreeding was 2.98 ± 2.81, 2.98 ± 4.01, and 7.28 ± 3.68% for [Formula: see text] , [Formula: see text] , and [Formula: see text] , respectively. A 1% increase in inbreeding decreased birth weight by 0.103 kg and weaning weight by 0.685 kg. A strategy such as optimum genetic contributions to maximize selection response and manage the long-term genetic variability and inbreeding could lead to sustainable breeding programs for the Mexican Romosinuano cattle breed. ABSTRACT: The ultimate goal of genetic selection is to improve genetic progress by increasing favorable alleles in the population. However, with selection, homozygosity, and potentially harmful recessive alleles can accumulate, deteriorating genetic variability and hampering continued genetic progress. Such potential adverse side effects of selection are of particular interest in populations with a small effective population size like the Romosinuano beef cattle in Mexico. The objective of this study was to evaluate the genetic background and inbreeding depression in Mexican Romosinuano cattle using pedigree and genomic information. Inbreeding was estimated using pedigree ([Formula: see text]) and genomic information based on the genomic relationship matrix ([Formula: see text]) and runs of homozygosity ([Formula: see text]) of different length classes. Linkage disequilibrium ([Formula: see text]) was evaluated using the correlation between pairs of loci, and the effective population size ([Formula: see text]) was calculated based on [Formula: see text] and pedigree information. The pedigree file consisted of 4875 animals born between 1950 and 2019, of which 71 had genotypes. [Formula: see text] decreased with the increase in distance between markers, and [Formula: see text] estimated using genomic information decreased from 610 to 72 animals (from 109 to 1 generation ago), the [Formula: see text] estimated using pedigree information was 86.44. The reduction in effective population size implies the existence of genetic bottlenecks and the decline of genetic diversity due to the intensive use of few individuals as parents of the next generations. The number of runs of homozygosity per animal ranged between 18 and 102 segments with an average of 55. The shortest and longest segments were 1.0 and 36.0 Mb long, respectively, reflecting ancient and recent inbreeding. The average inbreeding was 2.98 ± 2.81, 2.98 ± 4.01, and 7.28 ± 3.68% for [Formula: see text] , [Formula: see text] , and [Formula: see text] , respectively. The correlation between [Formula: see text] and [Formula: see text] was −0.25, and the correlations among [Formula: see text] and [Formula: see text] of different length classes were low (from 0.16 to 0.31). The correlations between [Formula: see text] and [Formula: see text] of different length classes were moderate (from 0.44 to 0.58), indicating better agreement. A 1% increase in population inbreeding decreased birth weight by 0.103 kg and weaning weight by 0.685 kg. A strategy such as optimum genetic contributions to maximize selection response and manage the long-term genetic variability and inbreeding could lead to more sustainable breeding programs for the Mexican Romosinuano beef cattle breed.