Genetic Background and Inbreeding Depression in Romosinuano Cattle Breed in Mexico

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 (F-PED) and genomic information based on the genomic relationship matrix (F-GRM) and runs of homozygosity (F-ROH) of different length classes. Linkage disequilibrium (LD) was evaluated using the correlation between pairs of loci, and the effective population size (N-e) was calculated based on LD and pedigree information. The pedigree file consisted of 4875 animals born between 1950 and 2019, of which 71 had genotypes. LD decreased with the increase in distance between markers, and N-e estimated using genomic information decreased from 610 to 72 animals (from 109 to 1 generation ago), the N-e 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 F-PED, F-GRM, and F-ROH, respectively. The correlation between F-PED and F-GRM was -0.25, and the correlations among F-PED and F-ROH of different length classes were low (from 0.16 to 0.31). The correlations between F-GRM and F-ROH 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.

Automated summary

The goal of genetic selection is to improve genetic progress, but it can lead to inbreeding and accumulation of harmful alleles, reducing genetic diversity. The study on Mexican Romosinuano cattle revealed a decreased effective population size, genetic bottlenecks, and declining genetic diversity as potential challenges.