Using genomic selection to correct pedigree errors in kiwiberry breeding.

IF 2.6 3区农林科学 Q1 AGRONOMY

Molecular Breeding Pub Date : 2025-03-11 eCollection Date: 2025-03-01 DOI:10.1007/s11032-025-01552-6

Daniel Mertten, Catherine M McKenzie, Susan Thomson, John McCallum, Dave Andersen, Samantha Baldwin, Michael Lenhard, Paul M Datson

{"title":"Using genomic selection to correct pedigree errors in kiwiberry breeding.","authors":"Daniel Mertten, Catherine M McKenzie, Susan Thomson, John McCallum, Dave Andersen, Samantha Baldwin, Michael Lenhard, Paul M Datson","doi":"10.1007/s11032-025-01552-6","DOIUrl":null,"url":null,"abstract":"In breeding programmes, accurate estimation of breeding values is crucial for selecting superior genotypes. Traditional methods rely on phenotypic observations and pedigree information to estimate variance components and heritability. However, pedigree errors can significantly affect the accuracy of these estimates, especially in long-lived perennial vines. This study evaluates the effect of pedigree errors on breeding value predictions in kiwiberry breeding and explores the benefits of using genomic selection. We applied Best Linear Unbiased Prediction (BLUP) to estimate breeding values for each genotype for a given trait. Four scenarios with varying degrees of alteration in pedigree-based relationship matrices were used to represent inaccurate relationships between genotypes. Pedigree-based breeding values were compared with genomic estimated breeding values for one vine-related and four fruit-related quantitative traits. The results showed that as the degree of altered population structure increased, the prediction accuracy of pedigree-based breeding values decreased. In contrast, genomic selection, which uses marker inheritance, maintained realised relationships between genotypes, making it a more robust method for predicting genetic merit. In kiwiberries, as in all species of the genus Actinidia, only female vines bear fruit. The genotypic merit of fruit-related traits in male genotypes can only be estimated indirectly. Marker-based predictions outperformed pedigree-based predictions, especially for genotypes without phenotypic observations, such as male siblings. This study reviewed the induced population structures and introduced genomic selection into the kiwiberry breeding programme. We demonstrated that genomic selection provides more accurate breeding values by capturing true genetic relationships and reducing the effects of misidentified relationships between individuals.Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01552-6.","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"45 3","pages":"33"},"PeriodicalIF":2.6000,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11896956/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecular Breeding","FirstCategoryId":"97","ListUrlMain":"https://doi.org/10.1007/s11032-025-01552-6","RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/3/1 0:00:00","PubModel":"eCollection","JCR":"Q1","JCRName":"AGRONOMY","Score":null,"Total":0}

引用次数: 0

Abstract

In breeding programmes, accurate estimation of breeding values is crucial for selecting superior genotypes. Traditional methods rely on phenotypic observations and pedigree information to estimate variance components and heritability. However, pedigree errors can significantly affect the accuracy of these estimates, especially in long-lived perennial vines. This study evaluates the effect of pedigree errors on breeding value predictions in kiwiberry breeding and explores the benefits of using genomic selection. We applied Best Linear Unbiased Prediction (BLUP) to estimate breeding values for each genotype for a given trait. Four scenarios with varying degrees of alteration in pedigree-based relationship matrices were used to represent inaccurate relationships between genotypes. Pedigree-based breeding values were compared with genomic estimated breeding values for one vine-related and four fruit-related quantitative traits. The results showed that as the degree of altered population structure increased, the prediction accuracy of pedigree-based breeding values decreased. In contrast, genomic selection, which uses marker inheritance, maintained realised relationships between genotypes, making it a more robust method for predicting genetic merit. In kiwiberries, as in all species of the genus Actinidia, only female vines bear fruit. The genotypic merit of fruit-related traits in male genotypes can only be estimated indirectly. Marker-based predictions outperformed pedigree-based predictions, especially for genotypes without phenotypic observations, such as male siblings. This study reviewed the induced population structures and introduced genomic selection into the kiwiberry breeding programme. We demonstrated that genomic selection provides more accurate breeding values by capturing true genetic relationships and reducing the effects of misidentified relationships between individuals.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01552-6.

查看原文本刊更多论文

利用基因组选择纠正猕猴桃育种中的家系错误。

在育种规划中，准确估计育种值对于选择优良基因型至关重要。传统的方法依靠表型观察和系谱信息来估计方差成分和遗传力。然而，谱系误差会显著影响这些估计的准确性，特别是在长寿命的多年生葡萄藤中。本研究评估了家系误差对猕猴桃育种育种价值预测的影响，并探讨了使用基因组选择的好处。我们应用最佳线性无偏预测（BLUP）来估计给定性状的每个基因型的育种值。在基于家系的关系矩阵中有不同程度改变的四种情况被用来表示基因型之间不准确的关系。对1个葡萄相关性状和4个果实相关性状的家系育种值与基因组育种估计值进行了比较。结果表明，随着种群结构变异程度的增加，基于家系的育种值预测精度降低。相比之下，使用标记遗传的基因组选择维持了基因型之间的关系，使其成为预测遗传优点的更可靠的方法。猕猴桃和猕猴桃属的所有种类一样，只有雌性藤蔓果实。雄性基因型中果实相关性状的基因型优势只能间接估计。基于标记的预测优于基于系谱的预测，特别是对于没有表型观察的基因型，例如男性兄弟姐妹。本研究综述了猕猴桃诱导群体结构，并将基因组选择引入猕猴桃育种计划。我们证明，基因组选择通过捕捉真实的遗传关系和减少个体之间错误识别关系的影响，提供了更准确的育种价值。补充资料：在线版本包含补充资料，下载地址：10.1007/s11032-025-01552-6。

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

Molecular Breeding 农林科学-农艺学

CiteScore

5.60

自引率

6.50%

发文量

审稿时长

1.5 months

期刊介绍： Molecular Breeding is an international journal publishing papers on applications of plant molecular biology, i.e., research most likely leading to practical applications. The practical applications might relate to the Developing as well as the industrialised World and have demonstrable benefits for the seed industry, farmers, processing industry, the environment and the consumer. All papers published should contribute to the understanding and progress of modern plant breeding, encompassing the scientific disciplines of molecular biology, biochemistry, genetics, physiology, pathology, plant breeding, and ecology among others. Molecular Breeding welcomes the following categories of papers: full papers, short communications, papers describing novel methods and review papers. All submission will be subject to peer review ensuring the highest possible scientific quality standards. Molecular Breeding core areas: Molecular Breeding will consider manuscripts describing contemporary methods of molecular genetics and genomic analysis, structural and functional genomics in crops, proteomics and metabolic profiling, abiotic stress and field evaluation of transgenic crops containing particular traits. Manuscripts on marker assisted breeding are also of major interest, in particular novel approaches and new results of marker assisted breeding, QTL cloning, integration of conventional and marker assisted breeding, and QTL studies in crop plants.