An evaluation of inbreeding measures using a whole-genome sequenced cattle pedigree.
An evaluation of inbreeding measures using a whole-genome sequenced cattle pedigree.
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利用全基因组测序的牛系谱评估近交措施。
DOI：
10.1038/s41437-020-00383-9
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发表时间：
2021-03
期刊：
影响因子：
3.8
通讯作者：
Druet T
中科院分区：
文献类型：
--
作者：
Alemu SW;Kadri NK;Harland C;Faux P;Charlier C;Caballero A;Druet T
近交系数F的估计对于研究近交衰退和保护种群的管理是必不可少的。已经提出了几种方法来估计实现的F使用遗传标记，但它仍然不清楚应该使用哪一个。在这里，我们使用的全基因组序列数据的245个个体从荷斯坦牛谱系经验评估估计最好捕捉纯合性的变异导致ID，如罕见的有害等位基因或基因座杂合子优势和分离在中频。估计依赖于联合配子（FUNI）或基因组关系（FGRM）之间的相关性提出了最高的相关性与这些变种。然而，在罕见的等位基因的纯合性仍然很难捕捉。第二组依赖于过量纯合性（FHOM）、血统纯合片段（FHBD）、纯合性运行（FROH）或已知系谱（FPED）的估计值在捕获全基因组纯合性方面更好，反映了近亲繁殖对所有变体的影响，并且对于具有低至中等频率（0.10 <0.10）的年轻等位基因。< 0.25）。结果表明，FUNI和FGRM可能与ID呈现更强的关联。然而，当隐性有害等位基因达到较高频率时，例如在有效群体规模较小的群体中，情况可能有所不同。对于基因座特异性近交措施或在低标记密度下，方法的排名也可以改变，因为FHBD更好地利用了来自相邻标记的信息。最后，我们证实，基因组措施一般是上级基于谱系的估计。特别是，FPED与基因座特异性纯合性无关。
The estimation of the inbreeding coefficient (F) is essential for the study of inbreeding depression (ID) or for the management of populations under conservation. Several methods have been proposed to estimate the realized F using genetic markers, but it remains unclear which one should be used. Here we used whole-genome sequence data for 245 individuals from a Holstein cattle pedigree to empirically evaluate which estimators best capture homozygosity at variants causing ID, such as rare deleterious alleles or loci presenting heterozygote advantage and segregating at intermediate frequency. Estimators relying on the correlation between uniting gametes (FUNI) or on the genomic relationships (FGRM) presented the highest correlations with these variants. However, homozygosity at rare alleles remained poorly captured. A second group of estimators relying on excess homozygosity (FHOM), homozygous-by-descent segments (FHBD), runs-of-homozygosity (FROH) or on the known genealogy (FPED) was better at capturing whole-genome homozygosity, reflecting the consequences of inbreeding on all variants, and for young alleles with low to moderate frequencies (0.10 < . < 0.25). The results indicate that FUNI and FGRM might present a stronger association with ID. However, the situation might be different when recessive deleterious alleles reach higher frequencies, such as in populations with a small effective population size. For locus-specific inbreeding measures or at low marker density, the ranking of the methods can also change as FHBD makes better use of the information from neighboring markers. Finally, we confirmed that genomic measures are in general superior to pedigree-based estimates. In particular, FPED was uncorrelated with locus-specific homozygosity.
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作者：
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