纯合子系作为血统同一性度量的性质。

IF 1.9 3区 农林科学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE
Oda B Wæge, Tom Druet, Peer Berg, Theo Meuwissen
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引用次数: 0

摘要

纯合子序列(ROH)通常用于量化个体或群体的自合子/血统同一性(IBD)。然而,该方法在牲畜种群分段水平上的准确性仅在少数研究中得到评估。因此,本研究的目的是确定ROH在多大程度上是真正的IBD,并估计在模拟牲畜种群中未被检测到的IBD片段的比例。我们模拟了一个随机交配100代的动物种群。基因组由一条染色体组成,SNP密度为每百万碱基46或92个SNP。此外,还记录了一组IBD的创始标记。使用四种不同的参数组合检测ROH。使用两组标记,我们计算了真阳性率、功率以及真(FIBD)和估计近交(FROH)之间的总体相关性。此外,引入了一种新的ROH内近交度量(f| ROH),并计算了与基因组中一般期望相比的ROH内纯合性水平。结果表明,长度大于2 Mb的ROH是IBD的可靠指标,所有ROH长度和参数组合的f| ROH均大于0.9。对于超过9 Mb的ROH,真实阳性率仅持续超过0.9,这表明许多已确定的ROH可能与比基础人群更古老的共同祖先有关。功率主要由参数的严密性来控制,即允许较短的ROH增加功率。基于roh的近交FROH个体测量值与FIBD高度相关,同时回归系数接近1(即FROH变异1%对应FIBD变异1%)。使用严格的ROH参数导致低估了种群的近交率。增加标记密度可以改善预测,包括更高的真阳性率、功率、更高的相关性和更少的近交率低估。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Properties of Runs of Homozygosity as a Measure of Identity by Descent.

Runs of Homozygosity (ROH) are commonly used to quantify autozygosity/identity-by-descent (IBD) in an individual or population. However, the method's accuracy at the segment level in livestock populations has only been evaluated in a few studies. Thus, the aim of this study was to determine to what extent ROH are truly IBD and estimate the proportion of IBD segments that go undetected in a simulated livestock population. We simulated a population of randomly mating animals for 100 generations. The genome consisted of a single chromosome with a SNP density of either 46 or 92 SNPs per mega base (Mb). In addition, a set of founder markers tracing IBD was recorded. ROH were detected using four different parameter combinations. Using the two sets of markers, we calculated the true positive rate, power, and overall correlation between true (FIBD) and estimated inbreeding (FROH). Additionally, a new measure for within-ROH inbreeding (F|ROH) was introduced and calculated the level of homozygosity within a ROH compared to the general expectation in the genome. The results indicate that ROH longer than 2 Mb are a reliable indicator of IBD, with the F|ROH being over 0.9 for all ROH lengths and parameter combinations. True positive rates only exceeded 0.9 consistently for ROH over 9 Mb, indicating that many of the identified ROH may be associated with common ancestors more ancient than the base population. The power was mainly controlled by the parameter stringency, that is, allowing for shorter ROH increased the power. The ROH-based individual measure of inbreeding FROH was highly correlated to FIBD while also having regression coefficients close to 1 (i.e., a 1% variation in FROH corresponded to a 1% variation in FIBD). Using stringent ROH parameters resulted in underestimation of the rate of inbreeding in the population. Increasing marker density improved predictions, including a higher true positive rate, power, higher correlations, and less underestimation of inbreeding rates.

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来源期刊
Journal of Animal Breeding and Genetics
Journal of Animal Breeding and Genetics 农林科学-奶制品与动物科学
CiteScore
5.20
自引率
3.80%
发文量
58
审稿时长
12-24 weeks
期刊介绍: The Journal of Animal Breeding and Genetics publishes original articles by international scientists on genomic selection, and any other topic related to breeding programmes, selection, quantitative genetic, genomics, diversity and evolution of domestic animals. Researchers, teachers, and the animal breeding industry will find the reports of interest. Book reviews appear in many issues.
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