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
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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.

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来源期刊
Molecular Breeding
Molecular Breeding 农林科学-农艺学
CiteScore
5.60
自引率
6.50%
发文量
67
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.
期刊最新文献
Using genomic selection to correct pedigree errors in kiwiberry breeding. Genomic selection in a kiwiberry breeding programme: integrating intra- and inter-specific crossing. Rapid development of naked malting barley germplasm through targeted mutagenesis. CsKIP1.7A, a gene involved in fruit development, contributes to the yield heterosis formation of hybrid F1 in cucumber. A novel trait to reduce the mechanical damage of peach fruits at harvest: The first genetic dissection study for peduncle length.
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