Investigating pedigree- and SNP-associated components of heritability in a wild population of Soay sheep

Caelinn James, J. Pemberton, P. Navarro, S. Knott
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Abstract

Estimates of narrow sense heritability derived from genomic data that contain related individuals may be biased due to the within-family effects such as dominance, epistasis and common environmental factors. However, for many wild populations, removal of related individuals from the data would result in small sample sizes. In 2013, Zaitlen et al. proposed a method to estimate heritability in populations that include close relatives by simultaneously fitting an identity-by-state genomic relatedness matrix (GRM) and an identity-by-descent GRM. The IBD GRM is identical to the IBS GRM, except relatedness estimates below a specified threshold are set to 0. We applied this method to a sample of 8557 wild Soay sheep from St. Kilda, with genotypic information for 419,281 single nucleotide polymorphisms to investigate polygenic and monogenic traits. We also implemented a variant of the model in which the IBD GRM was replaced by a GRM constructed from SNPs with low minor allele frequency to examine whether any additive genetic variance is captured by rare alleles. Each model was compared to an animal model with a single GRM based on all genotyped markers (the IBS GRM) using a log likelihood ratio test. Whilst the inclusion of the IBD GRM did not significantly improve the fit of the model for the monogenic traits, it improved the fit for some of the polygenic traits, suggesting that dominance, epistasis and/or common environment not already captured by the non-genetic random effects fitted in our models may influence these traits.
研究苏伊羊野生种群遗传力的系谱和snp相关成分
从包含相关个体的基因组数据中得出的狭义遗传力估计可能由于家族内效应(如显性、上位性和共同环境因素)而存在偏差。然而,对于许多野生种群来说,从数据中删除相关个体将导致样本量小。2013年,Zaitlen等人提出了一种方法,通过同时拟合身份-状态基因组相关性矩阵(GRM)和身份-血统GRM来估计包括近亲在内的群体的遗传力。IBD GRM与IBS GRM完全相同,除了低于指定阈值的相关性估计被设置为0。本研究采用该方法对圣基尔达地区8557只野生索伊羊进行了多基因和单基因性状分析,获得了419281个单核苷酸多态性基因型信息。我们还实现了该模型的一个变体,其中IBD GRM被由低次要等位基因频率的SNPs构建的GRM取代,以检查是否有任何加性遗传变异被罕见等位基因捕获。使用对数似然比检验将每个模型与基于所有基因型标记的单一GRM (IBS GRM)的动物模型进行比较。虽然纳入IBD GRM并没有显著提高模型对单基因性状的拟合,但它提高了对一些多基因性状的拟合,这表明我们模型中拟合的非遗传随机效应尚未捕获的显性、上位性和/或共同环境可能会影响这些性状。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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