Evaluation of runs of homozygosity and genomic inbreeding in Holstein cattle from Colombia

Abstract

Traditional selection programs for dairy cattle, based on quantitative principles, have worked well and allowed strong selection processes in the world over many decades. The objectives of this work were to estimate linkage disequilibrium (LD) levels at varying SNPs densities, to evaluate the effective population size of Holstein cattle, to characterize runs of homozygosity (ROH) distribution through Holstein cattle from Nariño and, to estimate and compare inbreeding coefficient (F) based on genomic markers information, runs of homozygosity (FROH), genomic relationship matrix (FGRM), and excess of homozygous (FSNP). After quality control, the dataset used was composed of 606 Holstein animals and 22200 SNP markers. PLINK program was used to identify LD, Ne, ROH segment and FROH and FSNP, FGRM was calculated with BLUPF90 family of programs. The average of r2 in all chromosomes was 0.011, the highest r2 was found in BTA3 (0.0323), and the lowest in BTA12 (0.0039). 533 ROH segments were identified in 319 animals; findings obtained in this study suggest that on average 0,28% of Holstein genome is autozygous. Total length of ROH was composed mostly of small segments (ROH1-4Mb and ROH4-8Mb). These segments accounted for approximately 96%, while larger ROH (ROH>8Mb) were 3.37% of all ROH detected. Inbreeding averages FROH, FSNP and FGRM methodologies were 0.28%, 3.11% and 3.36% respectively. The Pearson’s correlation among these different F values was: 0.49 (FROH-FSNP), 0.25 (FROH-FGRM), 0.22 (FSNP-FGRM). The distribution of ROH shared regions identified on 19 autosome chromosomes, cover a relevant number of genes inside these ROH. Our result evidenced lowest LD extension levels compared with other Holstein populations; inbreeding results suggest that FGRM and FSNP may be useful estimators of individual autozygosity in Holstein from Colombia. Genes related with production and reproduction were found, but the most important are the two that may be related to adaptation to Colombian high tropics. This work is a pioneer and be the starting point for programs of genetic improvement and genomic population studies in the country and mainly in high tropic areas where the dairy breeds have an important production.

Identification of Runs of Homozygosity Islands and Genomic Estimated Inbreeding Values in Caqueteño Creole Cattle (Colombia)

“…We identified a higher proportion of short ROH segments in the CAQ genome. Similar results have been reported by Zambrano et al [ 25 ] for a population of Holstein cattle from the Nariño Department, in which short segments accounted for approximately 96% of all identified ROH, indicating the likely low recent selection in the studied population. In this way, short ROH have been associated with ancient inbreeding [ 25 ].…”

Genetic diversity analysis in dairy cows of Nariño, southwestern Colombia

“…Among livestock species, this technology has been successfully applied in cattle thanks to many factors such as evolutionary history, genetic structure, and economic conditions, which render cattle particularly suitable for the application of genome-assisted selection (Nicolazzi et al, 2014). Genome-wide comparison of populations from different geographical regions can also detect potential candidate genes associated with ecological adaptations (Edea et al, 2015;Zambrano et al, 2020;Verardo et al, 2021). In livestock populations, approximately half of the genetic diversity is shared across breeds, while the other half is observed within single breeds (Sponenberg & Bixby, 2007).…”

“…Dairy cattle in Nariño have been subjected to selection through breeding programs (Solarte-Portilla & Zambrano-Burbano, 2012;Zambrano et al, 2020). In addition, these cattle have undergone changes due mainly to indirect selection by the use of reproductive biotechnology States, Canada, and some European countries).…”