Redefining and interpreting genomic relationships of metafounders

IF 3.6 1区 农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE Genetics Selection Evolution Pub Date : 2024-05-02 DOI:10.1186/s12711-024-00891-w
Andres Legarra, Matias Bermann, Quanshun Mei, Ole F. Christensen
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Abstract

Metafounders are a useful concept to characterize relationships within and across populations, and to help genetic evaluations because they help modelling the means and variances of unknown base population animals. Current definitions of metafounder relationships are sensitive to the choice of reference alleles and have not been compared to their counterparts in population genetics—namely, heterozygosities, FST coefficients, and genetic distances. We redefine the relationships across populations with an arbitrary base of a maximum heterozygosity population in Hardy–Weinberg equilibrium. Then, the relationship between or within populations is a cross-product of the form $${\Gamma }_{\left(b,{b}^{\prime}\right)}=\left(\frac{2}{n}\right)\left(2{\mathbf{p}}_{b}-\mathbf{1}\right)\left(2{\mathbf{p}}_{{b}^{\prime}}-\mathbf{1}\right)^{\prime}$$ with $$\mathbf{p}$$ being vectors of allele frequencies at $$n$$ markers in populations $$b$$ and $$b^{\prime}$$ . This is simply the genomic relationship of two pseudo-individuals whose genotypes are equal to twice the allele frequencies. We also show that this coding is invariant to the choice of reference alleles. In addition, standard population genetics metrics (inbreeding coefficients of various forms; FST differentiation coefficients; segregation variance; and Nei’s genetic distance) can be obtained from elements of matrix $${\varvec{\Gamma}}$$ .
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重新定义和解释元创始人的基因组关系
元基因是一个有用的概念,可用于描述种群内和种群间的关系,并有助于遗传评估,因为元基因有助于模拟未知基础种群动物的均值和方差。目前的元始祖关系定义对参考等位基因的选择很敏感,而且还没有与群体遗传学中的对应关系--即杂合度、FST系数和遗传距离--进行过比较。我们以处于哈代-温伯格平衡状态的最大杂合度种群为基础,重新定义种群间的关系。然后,种群之间或种群内部的关系是一个形式为 $${\Gamma }_{\left(b.)的交叉积、{b}^{\prime}\right)}=\left(\frac{2}{n}\right)\left(2{\mathbf{p}}_{b}-\mathbf{1}\right)\left(2{\mathbf{p}}_{{b}^{\prime}}-\$$mathbf{p}$$是种群 $$b$ 和 $$b^{prime}$ 中 $$n$ 标记的等位基因频率向量。这就是基因型等于等位基因频率两倍的两个假个体的基因组关系。我们还证明,这种编码与参考等位基因的选择无关。此外,标准种群遗传学指标(各种形式的近交系数、FST 分化系数、分离方差和内氏遗传距离)可以从矩阵 $${varvec{\Gamma}}$ 的元素中获得。
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来源期刊
Genetics Selection Evolution
Genetics Selection Evolution 生物-奶制品与动物科学
CiteScore
6.50
自引率
9.80%
发文量
74
审稿时长
1 months
期刊介绍: Genetics Selection Evolution invites basic, applied and methodological content that will aid the current understanding and the utilization of genetic variability in domestic animal species. Although the focus is on domestic animal species, research on other species is invited if it contributes to the understanding of the use of genetic variability in domestic animals. Genetics Selection Evolution publishes results from all levels of study, from the gene to the quantitative trait, from the individual to the population, the breed or the species. Contributions concerning both the biological approach, from molecular genetics to quantitative genetics, as well as the mathematical approach, from population genetics to statistics, are welcome. Specific areas of interest include but are not limited to: gene and QTL identification, mapping and characterization, analysis of new phenotypes, high-throughput SNP data analysis, functional genomics, cytogenetics, genetic diversity of populations and breeds, genetic evaluation, applied and experimental selection, genomic selection, selection efficiency, and statistical methodology for the genetic analysis of phenotypes with quantitative and mixed inheritance.
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