利用高密度标记图谱估计中性基因组的遗传多样性。

Estimating genetic diversity across the neutral genome with the use of dense marker maps.

机构信息

Wageningen UR Livestock Research, Animal Breeding and Genomics Centre, PO Box 65, 8200 AB Lelystad, The Netherlands.

出版信息

Genet Sel Evol. 2010 May 10;42(1):12. doi: 10.1186/1297-9686-42-12.

DOI:10.1186/1297-9686-42-12

PMID:20459708

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2882900/

Abstract

BACKGROUND

With the advent of high throughput DNA typing, dense marker maps have become available to investigate genetic diversity on specific regions of the genome. The aim of this paper was to compare two marker based estimates of the genetic diversity in specific genomic regions lying in between markers: IBD-based genetic diversity and heterozygosity.

METHODS

A computer simulated population was set up with individuals containing a single 1-Morgan chromosome and 1665 SNP markers and from this one, an additional population was produced with a lower marker density i.e. 166 SNP markers. For each marker interval based on adjacent markers, the genetic diversity was estimated either by IBD probabilities or heterozygosity. Estimates were compared to each other and to the true genetic diversity. The latter was calculated for a marker in the middle of each marker interval that was not used to estimate genetic diversity.

RESULTS

The simulated population had an average minor allele frequency of 0.28 and an LD (r(2)) of 0.26, comparable to those of real livestock populations. Genetic diversities estimated by IBD probabilities and by heterozygosity were positively correlated, and correlations with the true genetic diversity were quite similar for the simulated population with a high marker density, both for specific regions (r = 0.19-0.20) and large regions (r = 0.61-0.64) over the genome. For the population with a lower marker density, the correlation with the true genetic diversity turned out to be higher for the IBD-based genetic diversity.

CONCLUSIONS

Genetic diversities of ungenotyped regions of the genome (i.e. between markers) estimated by IBD-based methods and heterozygosity give similar results for the simulated population with a high marker density. However, for a population with a lower marker density, the IBD-based method gives a better prediction, since variation and recombination between markers are missed with heterozygosity.

摘要

背景

随着高通量 DNA 分型技术的出现，已经可以获得用于研究基因组特定区域遗传多样性的密集标记图谱。本文的目的是比较两种基于标记的遗传多样性估计方法，即基于 IBD 的遗传多样性和杂合性，用于研究特定基因组区域内标记之间的遗传多样性。

方法

使用包含单个 1-Morgan 染色体和 1665 个 SNP 标记的个体创建了一个计算机模拟群体，并在此基础上，生成了一个标记密度较低的群体，即 166 SNP 标记。对于基于相邻标记的每个标记区间，通过 IBD 概率或杂合性来估计遗传多样性。将这些估计值相互比较，并与真实遗传多样性进行比较。后者是通过计算每个标记区间中间的标记来计算的，这些标记未用于估计遗传多样性。

结果

模拟群体的平均次要等位基因频率为 0.28，LD（r(2)）为 0.26，与真实家畜群体相似。基于 IBD 概率和杂合性估计的遗传多样性呈正相关，对于具有高密度标记的模拟群体，两者与真实遗传多样性的相关性非常相似，无论是特定区域（r = 0.19-0.20）还是基因组上的大区域（r = 0.61-0.64）。对于标记密度较低的群体，基于 IBD 的遗传多样性与真实遗传多样性的相关性更高。