Abstract
BackgroundRuns of homozygosity (ROH) have become the state-of-the-art method for analysis of inbreeding in animal populations. Moreover, ROH are suited to detect signatures of selection via ROH islands and are used in other applications, such as genomic prediction and genome-wide association studies (GWAS). Currently, a vast amount of single nucleotide polymorphism (SNP) data is available online, but most of these data have never been used for ROH analysis. Therefore, we performed a ROH analysis on large medium-density SNP datasets in eight animal species (cat, cattle, dog, goat, horse, pig, sheep and water buffalo; 442 different populations) and make these results publicly available.ResultsThe results include an overview of ROH islands per population and a comparison of the incidence of these ROH islands among populations from the same species, which can assist researchers when studying other (livestock) populations or when looking for similar signatures of selection. We were able to confirm many known ROH islands, for example signatures of selection for the myostatin (MSTN) gene in sheep and horses. However, our results also included multiple other ROH islands, which are common to many populations and not identified to date (e.g. on chromosomes D4 and E2 in cats and on chromosome 6 in sheep).ConclusionsWe are confident that our repository of ROH islands is a valuable reference for future studies. The discovered ROH island regions represent a unique starting point for new studies or can be used as a reference for future studies. Furthermore, we encourage authors to add their population-specific ROH findings to our repository.
Highlights
Runs of homozygosity (ROH) have become the state-of-the-art method for analysis of inbreeding in animal populations
We provide an overview of ROH islands in 442 populations (18,633 individuals) from eight animal species using medium-density single nucleotide polymorphism (SNP) data, which were all analyzed using a standardized protocol
The script creates Manhattan plots based on ROH incidence per SNP for every investigated population, and a summary table
Summary
Runs of homozygosity (ROH) have become the state-of-the-art method for analysis of inbreeding in animal populations. We performed a ROH analysis on large medium-density SNP datasets in eight animal species (cat, cattle, dog, goat, horse, pig, sheep and water buffalo; 442 different populations) and make these results publicly available. Since 2010, analysis of ROH has become a standard approach to study inbreeding and detect signatures of selection in animal populations with the first reported studies in 2010 for cattle [5], in 2010 for dogs [6], in 2012 for pigs [7], in 2013 for horses [8], in 2014 for goats [9], in 2015 for sheep [10], in 2016 for cats [11] and in 2020 for water buffaloes [12]. It is commonly accepted that short ROH are indicators of distant
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