Inbreeding depression and runs of homozygosity islands in Asturiana de los Valles cattle breed after 30 years of selection

Abstract

Inbreeding depression results in a decrease in the average phenotypic values of affected traits. It has been traditionally estimated from pedigree-based inbreeding coefficients. However, with the development of single-nucleotide polymorphism arrays, novel methods were developed for calculating the inbreeding coefficient, and consequently, inbreeding depression. The aim of the study was to analyse inbreeding depression in 6 growth and 2 reproductive traits in the Asturiana de los Valles cattle breed using both genealogical and molecular information. The pedigree group comprised 225,848 records and an average equivalent number of complete generations of 2.3. The molecular data comprised genotypes of 2693 animals using the Affymetrix medium-density chip. Using the pedigree information, three different inbreeding coefficients were estimated for the genotyped animals: the full pedigree coefficient (F_PED), and the recent and ancient inbreeding coefficients based on the information of the last three generations (F_PED<3G) and until the last three generations (F_PED>3G), respectively. Using the molecular data, seven inbreeding coefficients were calculated. Four of them were estimated based on runs of homozygosity (ROH), considering (1) the total length (F_ROH), (2) segments shorter than 4 megabases (F_ROH<4), (3) between 4 and 17 megabases (F_ROH4-17), and (4) longer than 17 Mb (F_ROH>17). Additionally, the three inbreeding coefficients implemented in the Plink software (F_HAT1-3) were estimated. Inbreeding depression was estimated using linear mixed-effects model with inbreeding coefficients used as covariates. All analysed traits (birth weight, preweaning average daily gain, weaning weight adjusted at 180 days, carcass weight, calving ease, age at first calving, calving interval) showed a statistically significant non-zero effect of inbreeding depression estimated from the pedigree group, except for the Postweaning Average Daily Gain trait. When inbreeding coefficients were based on the genomic group, statistically significant inbreeding depression was observed for two traits, Preweaning Average Daily Gain and Weaning Weight based on F_ROH, F_ROH>17, and F_HAT3 inbreeding coefficients. Nevertheless, similar to inbreeding depression estimated based on pedigree information, estimates of inbreeding depression based on genomic information had no relevant economic impact. Despite this, from a long-term perspective, genotyped data could be included to maximize genetic progress in genetic programs following an optimal genetic contribution strategy and to consider individual inbreeding load instead global inbreeding. ROH islands were identified on chromosomes 2, 3, 8, 10, and 16. Such regions contain several candidate genes for growth development, intramuscular fat, body weight and lipid metabolism that are related to production traits selected in Asturiana de los Valles breed.