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.

摘要：近交衰退——即近交导致的包括繁殖与存活在内的数量性状表现降低——是几乎所有实验、驯化及自然种群中均已观测到的公认现象。尽管近交衰退对小种群的存续至关重要，且上个世纪已开展大量相关研究，但其遗传基础仍未明确。近年来分子技术的飞速发展使得基因组近交系数（FROH）的估算成为可能，该系数可反映实际同源纯合性，还能进一步按染色体及染色体片段进行拆分。本综述首先介绍了畜禽种群近交估算的经典方法，随后阐述了以个体杂合性替代系谱近交系数的早期思路。接着，本文解释了作为估算实际同源纯合性核心方法的纯合子片段（runs of homozygosity）。此外，本文提出了两种分析对近交衰退具有显著贡献的基因组区域的不同思路，进而阐明了如何识别或定位导致性状表现下降的突变，并从数量遗传学角度分析近交衰退的遗传架构。最后，本文探讨了从畜禽种群中清除有害突变的未来研究方向。