Run of Homozygosity a Procedure to Detecting Inbreeding in Farm Animals

Abstract

Inbreeding depression is a harmful phenomenon in livestock which is outcome of inbreeding. Inbreeding is consequence mating between two individuals who are more related to each other than average relatedness in population, which results in reducing in fitness of progenies and genetic variability in populations. Development of high-density genome-wide single nucleotide polymorphism (SNP) array facilitated inbreeding measurement as molecular data through calculating autozygosity region in individual genome. Autozygosity refer to chromosomal fragments that are identical-by-descent (IBD) and can be measured using runs of homozygosity (ROH). ROH is therefore defined as contiguous homozygous regions of the genome where two haplotypes inherited from the parents are IBD. The length and frequency of ROH may describe the history and recent bottlenecks in population and also revealed signatures of positive selection in population. Inbreeding coefficient can be derived from ROH (F_ROH), which is defined as total lengths of all ROH divided by the total autosomal genome length. A lot of studies calculated inbreeding level as F_ROH in human, cattle, pig, sheep, chicken and other farm animals through SNP array. In most of them, accuracy and preciseness of F_ROHwere confirmed in comparing to F_PED, Some of them calculated inbreeding depression by using F_ROH and some other evaluated the relationship between ROH location with gene and quantitative trait locus (QTL) position on genome. These studies indicated that inbreeding levels in bovine and porcine populations are much higher than those in human populations. Even though most of researches concluded that F_ROHcan precisely calculated Inbreeding and it can be useful for estimating inbreeding coefficient in absent of pedigree, but some concern were exist in about of panel density, genotyping errors and undetected heterozygosity within continuous ROH which complicated identifying and quantifying ROH. In this review, run of homozygosity is defined and discussed in detail in human and livestock.