杂种遗传和基因组模型中品种间和本地品种比例的隔离。

Segregation between breeds and local breed proportions in genetic and genomic models for crossbreds.

机构信息

Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus C, Denmark.

Faculty of Agricultural Sciences, Agricultural University of Iceland, 311, Borgarnes, Iceland.

出版信息

Genet Sel Evol. 2023 Jul 5;55(1):45. doi: 10.1186/s12711-023-00810-5.

DOI:10.1186/s12711-023-00810-5

PMID:37407936

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10320957/

Abstract

BACKGROUND

The breeding value of a crossbred individual can be expressed as the sum of the contributions from each of the contributing pure breeds. In theory, the breeding value should account for segregation between breeds, which results from the difference in the mean contribution of loci between breeds, which in turn is caused by differences in allele frequencies between breeds. However, with multiple generations of crossbreeding, how to account for breed segregation in genomic models that split the breeding value of crossbreds based on breed origin of alleles (BOA) is not known. Furthermore, local breed proportions (LBP) have been modelled based on BOA and is a concept related to breed segregation. The objectives of this study were to explore the theoretical background of the effect of LBP and how it relates to breed segregation and to investigate how to incorporate breed segregation (co)variance in genomic BOA models.

RESULTS

We showed that LBP effects result from the difference in the mean contribution of loci between breeds in an additive genetic model, i.e. breed segregation effects. We found that the (co)variance structure for BS effects in genomic BOA models does not lead to relationship matrices that are positive semi-definite in all cases. However, by setting one breed as a reference breed, a valid (co)variance structure can be constructed by including LBP effects for all other breeds and assuming them to be correlated. We successfully estimated variance components for a genomic BOA model with LBP effects in a simulated example.

CONCLUSIONS

Breed segregation effects and LBP effects are two alternative ways to account for the contribution of differences in the mean effects of loci between breeds. When the covariance between LBP effects across breeds is included in the model, a valid (co)variance structure for LBP effects can be constructed by setting one breed as reference breed and fitting an LBP effect for each of the other breeds.

摘要

背景

杂交个体的育种值可以表示为每个贡献纯品种贡献的总和。从理论上讲，育种值应该考虑品种间的分离，这是由于品种间平均贡献的差异造成的，而这种差异又是由品种间等位基因频率的差异造成的。然而，经过多代杂交，如何在基于等位基因起源（BOA）将杂种的育种值分割的基因组模型中考虑品种间的分离尚不清楚。此外，基于 BOA 已经对局部品种比例（LBP）进行了建模，这是一个与品种间分离有关的概念。本研究的目的是探讨 LBP 效应的理论背景及其与品种间分离的关系，并研究如何在基因组 BOA 模型中纳入品种间分离（协）方差。

结果

我们表明，LBP 效应是由加性遗传模型中品种间平均贡献的差异产生的，即品种间分离效应。我们发现，BS 效应在基因组 BOA 模型中的（协）方差结构并不总是导致所有情况下的关系矩阵为半正定的。然而，通过将一个品种设定为参考品种，可以通过包括所有其他品种的 LBP 效应并假设它们是相关的来构建有效的（协）方差结构。我们在一个模拟示例中成功地估计了包含 LBP 效应的基因组 BOA 模型的方差分量。