Runs of homozygosity: current knowledge and applications in livestock

Abstract

This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a population's genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping to minimize the inbreeding rate and also helping to expose deleterious variants in the genome. The frequency, size and distribution of ROH in the genome are influenced by factors such as natural and artificial selection, recombination, linkage disequilibrium, population structure, mutation rate and inbreeding level. Calculating the inbreeding coefficient from molecular information from ROH (F ) is more accurate for estimating autozygosity and for detecting both past and more recent inbreeding effects than are estimates from pedigree data (F ). The better results of F suggest that F can be used to infer information about the history and inbreeding levels of a population in the absence of genealogical information. The selection of superior animals has produced large phenotypic changes and has reshaped the ROH patterns in various regions of the genome. Additionally, selection increases homozygosity around the target locus, and deleterious variants are seen to occur more frequently in ROH regions. Studies involving ROH are increasingly common and provide valuable information about how the genome's architecture can disclose a population's genetic background. By revealing the molecular changes in populations over time, genome-wide information is crucial to understanding antecedent genome architecture and, therefore, to maintaining diversity and fitness in endangered livestock breeds.

Unraveling the genetic diversity of Belgian Milk Sheep using medium‐density SNP genotypes

“…Only three of 19 studies using medium‐density SNP data, reviewed by Peripolli et al (), imposed similar or stronger restrictions, whereas other cited studies allowed one heterozygous SNP and between two and five missing SNPs in the same run, combined with a minimum constraint of 20 or 30 SNPs (or even none). Only two of 19 studies reviewed by Peripolli et al () used the requirement of at least 30 consecutive SNPs to identify an ROH. Although Purfield et al () and Ferenčaković et al () indicate that the minimum length of correctly identified ROH on a 50K SNP array should extend for at least 5 or 4 Mb respectively, they do not impose stringent conditions on the minimal number of SNPs in the ROH.…”

Genome‐wide identification of runs of homozygosity islands in the Gyr breed (Bos indicus)

“…These scenarios could facilitate the interpretation of the selection signatures. However, the inconsistencies in the criteria used to define the ROH islands impair the comparison between studies because of the lack of consensus regarding the best parameter and different signals are therefore obtained (Peripolli et al, ). The results obtained for the ROH, F ROH and ROH islands are consistent with the history of the two populations, which underwent different breeding programmes that focused on specific phenotypes through artificial selection, altering allele frequencies and producing ROH islands or selection signatures in the populations.…”

Research Article Study of genetic variability in pigs after the traditional breeding program.

“…Every day the need for the use of molecular markers is becoming more evident, whether it is to help in assisted breeding programs or genetic analyses and the determination of population inbreeding (Herrero-Medrano et al, 2014;Schiavo et al, 2016;Peripolli et al, 2017).…”