Prediction of additive genetic variances of descendants for complex families based on Mendelian sampling variances.

IF 2.1 3区 生物学 Q3 GENETICS & HEREDITY
Tobias A M Niehoff, Jan Ten Napel, Mario P L Calus
{"title":"Prediction of additive genetic variances of descendants for complex families based on Mendelian sampling variances.","authors":"Tobias A M Niehoff, Jan Ten Napel, Mario P L Calus","doi":"10.1093/g3journal/jkae205","DOIUrl":null,"url":null,"abstract":"<p><p>The ability to predict the outcome of selection and mating decisions enables breeders to make strategically better selection decisions. To improve genetic progress, those individuals need to be selected whose offspring can be expected to show high genetic variance next to high breeding values. Previously published approaches enable to predict the variance of descendants of 2 future generations for up to 4 founding haplotypes, or 2 outbred individuals, based on phased genotypes, allele effects, and recombination frequencies. The purpose of this study was to develop a general approach for the analytical calculation of the genetic variance in any future generation. The core development is an equation for the prediction of the variance of double haploid lines, under the assumption of no selection and negligible drift, stemming from an arbitrary number of founder haplotypes. This double haploid variance can be decomposed into gametic Mendelian sampling variances (MSVs) of ancestors of the double haploid lines allowing usage for non-double haploid genotypes that enables application in animal breeding programs as well as in plant breeding programs. Together with the breeding values of the founders, the gametic MSV may be used in new selection criteria. We present our idea of such a criterion that describes the genetic level of selected individuals in 4 generations. Since breeding programs do select, the assumption made for predicting variances is clearly violated, which decreases the accuracy of predicted gametic MSV caused by changes in allele frequency and linkage disequilibrium. Despite violating the assumption, we found high predictive correlations of our criterion to the true genetic level that was obtained by means of simulation for the \"corn\" and \"cattle\" genome models tested in this study (0.90 and 0.97). In practice, the genotype phases, genetic map, and allele effects all need to be estimated meaning inaccuracies in their estimation will lead to inaccurate variance prediction. Investigation of variance prediction accuracy when input parameters are estimated was not part of this study.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1000,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540313/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"G3: Genes|Genomes|Genetics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/g3journal/jkae205","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 0

Abstract

The ability to predict the outcome of selection and mating decisions enables breeders to make strategically better selection decisions. To improve genetic progress, those individuals need to be selected whose offspring can be expected to show high genetic variance next to high breeding values. Previously published approaches enable to predict the variance of descendants of 2 future generations for up to 4 founding haplotypes, or 2 outbred individuals, based on phased genotypes, allele effects, and recombination frequencies. The purpose of this study was to develop a general approach for the analytical calculation of the genetic variance in any future generation. The core development is an equation for the prediction of the variance of double haploid lines, under the assumption of no selection and negligible drift, stemming from an arbitrary number of founder haplotypes. This double haploid variance can be decomposed into gametic Mendelian sampling variances (MSVs) of ancestors of the double haploid lines allowing usage for non-double haploid genotypes that enables application in animal breeding programs as well as in plant breeding programs. Together with the breeding values of the founders, the gametic MSV may be used in new selection criteria. We present our idea of such a criterion that describes the genetic level of selected individuals in 4 generations. Since breeding programs do select, the assumption made for predicting variances is clearly violated, which decreases the accuracy of predicted gametic MSV caused by changes in allele frequency and linkage disequilibrium. Despite violating the assumption, we found high predictive correlations of our criterion to the true genetic level that was obtained by means of simulation for the "corn" and "cattle" genome models tested in this study (0.90 and 0.97). In practice, the genotype phases, genetic map, and allele effects all need to be estimated meaning inaccuracies in their estimation will lead to inaccurate variance prediction. Investigation of variance prediction accuracy when input parameters are estimated was not part of this study.

基于孟德尔抽样方差预测复杂家系后代的加性遗传方差。
预测选育和交配决策结果的能力使育种者能够做出战略性更强的选育决策。为了提高遗传进展,需要选择那些后代可望表现出高遗传变异和高育种价值的个体。以前发表的方法可以根据相位基因型、等位基因效应和重组频率,预测多达 4 个创始单倍型或 2 个外源个体的后代遗传变异。本研究的目的是开发一种分析计算任何后代遗传变异的通用方法。研究的核心是在无选择和漂移可忽略不计的假设条件下,预测由任意数量的创始单倍型产生的双单倍体品系方差的方程。这种双单倍体方差可分解为双单倍体品系祖先的配子孟德尔抽样方差(MSV),并可用于非双单倍体基因型,从而在动物育种计划和植物育种计划中得到应用。配子 MSV 与祖先的育种值一起,可用于新的选择标准。我们提出了这种标准的概念,它描述了四代中被选个体的遗传水平。由于育种计划确实会进行选择,因此预测变异的假设显然被违反了,这就降低了等位基因频率和连锁不平衡变化所导致的配子 MSV 预测的准确性。尽管违反了这一假设,但我们发现我们的标准与真实遗传水平的预测相关性很高,这是在本研究测试的 "玉米 "和 "牛 "基因组模型中通过模拟得到的(0.90 和 0.97)。在实践中,基因型阶段、遗传图谱和等位基因效应都需要估算,这意味着估算不准确将导致方差预测不准确。对输入参数进行估计时的方差预测准确性的调查不在本研究范围内。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
G3: Genes|Genomes|Genetics
G3: Genes|Genomes|Genetics GENETICS & HEREDITY-
CiteScore
5.10
自引率
3.80%
发文量
305
审稿时长
3-8 weeks
期刊介绍: G3: Genes, Genomes, Genetics provides a forum for the publication of high‐quality foundational research, particularly research that generates useful genetic and genomic information such as genome maps, single gene studies, genome‐wide association and QTL studies, as well as genome reports, mutant screens, and advances in methods and technology. The Editorial Board of G3 believes that rapid dissemination of these data is the necessary foundation for analysis that leads to mechanistic insights. G3, published by the Genetics Society of America, meets the critical and growing need of the genetics community for rapid review and publication of important results in all areas of genetics. G3 offers the opportunity to publish the puzzling finding or to present unpublished results that may not have been submitted for review and publication due to a perceived lack of a potential high-impact finding. G3 has earned the DOAJ Seal, which is a mark of certification for open access journals, awarded by DOAJ to journals that achieve a high level of openness, adhere to Best Practice and high publishing standards.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信