Genomic dissection of inbreeding depression: a gate to new opportunities

ABSTRACT Inbreeding depression, reduction in performance of quantitative traits, including reproduction and survival, caused by inbreeding, is a well-known phenomenon observed in almost all experimental, domesticated, and natural populations. In spite of its importance to the fate of a small population and numerous research performed in the last century, the genetic basis of inbreeding depression is still unclear. Recent fast development of molecular techniques has enabled estimation of a genomic inbreeding coefficient (FROH), which reflects realized autozygosity and can be further partitioned to chromosomes and chromosomal segments. In this review, we first describe classical approach used in the estimation of inbreeding in livestock populations, followed by early concepts of replacing pedigree inbreeding coefficient by individual heterozygosity. Then, we explain runs of homozygosity as key approach in estimating realized autozygosity. Furthermore, we present two different concepts of analysing regions that substantially contribute to the inbreeding depression. Thus, we describe how to identify or map mutations that result in the reduction of performance and, in terms of quantitative genetics, how to analyse the architecture of inbreeding depression. At the end, we discuss future perspectives in eliminating deleterious mutations from livestock populations.