title: 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 (FROH) is more accurate for estimating autozygosity and for detecting both past and more recent inbreeding effects than are estimates from pedigree data (FPED). The better results of FROHsuggest that FROHcan 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.
authors.affiliation: Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.
authors.forename: E
authors.initials: E
authors.lastname: Peripolli
authors.affiliation: Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.|Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil.
authors.forename: D P
authors.initials: DP
authors.lastname: Munari
authors.affiliation: Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil.|Embrapa Gado de Leite, Juiz de Fora, 36038-330, Brazil.
authors.forename: M V G B
authors.initials: MVGB
authors.lastname: Silva
authors.affiliation: Departamento de Zootecnia e Desenvolvimento Rural, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Florianópolis, 88034-000, Brazil.
authors.forename: A L F
authors.initials: ALF
authors.lastname: Lima
authors.affiliation: Departamento de Zootecnia e Desenvolvimento Rural, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Florianópolis, 88034-000, Brazil.
authors.forename: R
authors.initials: R
authors.lastname: Irgang
authors.affiliation: Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.|Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil.
authors.forename: F
authors.initials: F
authors.lastname: Baldi
mesh_terms: D000818:Animals; D002417:Cattle; D014644:Genetic Variation; D005828:Genetics, Population; D006041:Goats; D006720:Homozygote; D006736:Horses; D007178:Inbreeding; D015810:Linkage Disequilibrium; D058751:Livestock / Q000235:genetics*; D017422:Sequence Analysis, DNA; D034561:Sheep, Domestic; D013552:Swine
keywords: autozygosity; genetic diversity; homozygosity; inbreeding; livestock