Genetic Background and Inbreeding Depression in Romosinuano Cattle Breed in Mexico.

Jorge Hidalgo,Rafael Núñez,Andre Garcia,José Guadalupe García,Enrico Mancin,Rodolfo Ramírez,Neon Larios,Pattarapol Sumreddee,Alberto Cesarani

doi:10.3390/ani11020321

Abstract

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

Highlights

Creole cattle breeds in the American continent originated from the Iberian Peninsula cattle five centuries ago
The first objective of the present study was to evaluate the genetic background of the Romosinuano beef cattle breed in Mexico, using different approaches: (i) pedigree analysis; (ii); inbreeding coefficients estimated by pedigree and genomic information; (iii) analysis of linkage disequilibrium and effective population size
StoROH found in other studies with cosmopolitan breeds, the found in the present study found in other studies with cosmopolitan breeds, runs of homozygosity (ROH)

Summary

Introduction

Creole cattle breeds in the American continent originated from the Iberian Peninsula cattle five centuries ago. One of them is the Romosinuano breed, developed from isolation and adaptation to harsh environments in Colombia and has spread mainly to Costa Rica, the United States of America, Venezuela, and Mexico [1]. The Creole cattle breeds have adapted to adverse tropical conditions; genes associated with extreme environments and parasite resistance have been selected by natural selection. In Mexico, the national herd of Romosinuano beef cattle was established with the use of germplasm from Costa Rica (Turrialba) and later from the United States (Florida State University) [1]. The Romosinuano breed captured the attention of Mexican beef producers because animals of this breed have good growth performance and meat quality, high fertility, and the ability to adapt to hot and humid conditions and large parasite infestation (e.g., ticks; De Alba [1]). With the creation of AMCROLET, performance information started being recorded to establish a genetic evaluation to improve birth weight and weaning weights [2]

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