Genetic Background and Inbreeding Depression in Romosinuano Cattle Breed in Mexico

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 (FPED) and genomic information based on the genomic relationship matrix (FGRM) and runs of homozygosity (FROH) of different length classes. Linkage disequilibrium (LD) was evaluated using the correlation between pairs of loci, and the effective population size (Ne) 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 Ne estimated using genomic information decreased from 610 to 72 animals (from 109 to 1 generation ago), the Ne 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 FPED, FGRM, and FROH, respectively. The correlation between FPED and FGRM was −0.25, and the correlations among FPED and FROH of different length classes were low (from 0.16 to 0.31). The correlations between FGRM and FROH 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.

Manifestation of living and post-slaughter traits of productivity in inbred and outbred bull calves of Ukrainian meat cattle breed

“…[15] and Hidalgo, et al [12] also established the manifestation of inbred depression by neonatal weight. There is a tendency to increase the average daily weight gain by 10.2% from birth to 8 months in inbred bull calves.…”

“…In dams, the degree of inbreeding prolongs the age of first calving [8] and reduces the number of unfertilized oocytes [9], increasing dystocia in firstborns and stillbirths [10], [11]. The 1% increase in the inbreeding coefficient leads to a decrease in live weight: newborns by 0.103 kg [12], at 205 days by 0.24 kg [13], at 365 days by 0.514 and 0.57 kg [14]. As for the impact of inbreeding on meat productivity, the published data are contradictory.…”

Inbreeding Calculated with Runs of Homozygosity Suggests Chromosome-Specific Inbreeding Depression Regions in Line 1 Hereford

“…Studies with ROH in dairy cattle have shown that chromosomal ROH vary widely [ 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 ]. Similarly, in beef cattle the contributions of different chromosomes also fluctuate [ 7 , 34 , 35 ]. The variation in effect and distribution of deleterious ROH suggests that a mating design can be devised to reduce inbreeding depression, similarly to what is suggested by VanRaden et al [ 2 ] with lethal haplotypes.…”

Genome-Wide Association Studies, Runs of Homozygosity Analysis, and Copy Number Variation Detection to Identify Reproduction-Related Genes in Bama Xiang Pigs

“…The ROH length was classified into four classes: 0–6, 6–12, 12–24, and 24–48 Mb. The F ROH for Bama Xiang pigs was estimated using the following formula ( 30 ):…”