Centre for the Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada; Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland.
Centre for the Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
J Dairy Sci. 2019 Mar;102(3):2807-2817. doi: 10.3168/jds.2018-15520. Epub 2019 Jan 17.
Inbreeding depression is a growing concern in livestock because it can detrimentally affect animal fitness, health, and production levels. Genomic information can be used to more effectively capture variance in Mendelian sampling, thereby enabling more accurate estimation of inbreeding, but further progress is still required. The calculation of inbreeding for herd management purposes is largely still done using pedigree information only, although inbreeding coefficients calculated in this manner have been shown to be less accurate than genomic inbreeding measures. Continuous stretches of homozygous genotypes, so called runs of homozygosity, have been shown to provide a better estimate of autozygosity at the genomic level than conventional measures based on inbreeding coefficients calculated through conventional pedigree information or even genomic relationship matrices. For improved and targeted management of genomic inbreeding at the population level, the development of methods that incorporate genomic information in mate selection programs may provide a more precise tool for reducing the detrimental effects of inbreeding in dairy herds. Additionally, a better understanding of the genomic architecture of inbreeding and incorporating that knowledge into breeding programs could significantly refine current practices. Opportunities to maintain high levels of genetic progress in traits of interest while managing homozygosity and sustaining acceptable levels of heterozygosity in highly selected dairy populations exist and should be examined more closely for continued sustainability of both the dairy cattle population as well as the dairy industry. The inclusion of precise genomic measures of inbreeding, such as runs of homozygosity, inbreeding, and mating programs, may provide a path forward. In this symposium review article, we describe traditional measures of inbreeding and the recent developments made toward more precise measures of homozygosity using genomic information. The effects of homozygosity resulting from inbreeding on phenotypes, the identification and mapping of detrimental homozygosity haplotypes, management of inbreeding with genomic data, and areas in need of further research are discussed.
近交衰退是家畜领域日益关注的问题，因为它会对动物的适应性、健康和生产水平产生不利影响。基因组信息可用于更有效地捕捉孟德尔抽样中的方差，从而更准确地估计近交程度，但仍需要进一步的进展。尽管以这种方式计算的近交系数不如基于基因组关系矩阵或传统系谱信息计算的基因组近交度量准确，但为了进行群体管理，仍主要使用系谱信息来计算近交。连续的纯合基因型（称为纯合子延伸）已被证明在基因组水平上比基于传统近交系数的常规方法更好地估计自交，甚至比基于传统系谱信息或甚至基因组关系矩阵计算的近交系数更好。为了在群体水平上改进和有针对性地管理基因组近交，可以开发将基因组信息纳入选配计划的方法，为减少奶牛群体中近交的不利影响提供更精确的工具。此外，更好地了解基因组近交的结构，并将这些知识纳入选种计划，可能会显著改进当前的实践。在高度选择的奶牛群体中，存在维持感兴趣的性状高水平遗传进展的机会，同时管理同型性并维持可接受的杂合度水平。应该更密切地研究这些机会，以维持奶牛群体和奶牛业的可持续性。包含近交的精确基因组度量，如纯合子延伸、近交和选配计划，可能是一种前进的方向。在本次研讨会综述文章中，我们描述了传统的近交度量方法，以及使用基因组信息更精确地度量同型性的最新进展。讨论了由近交引起的同型性对表型的影响、有害同型性单倍型的鉴定和定位、利用基因组数据管理近交以及需要进一步研究的领域。
