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Implementation of different relationship estimate methodologies in breeding value prediction in kiwiberry (Actinidia arguta)

In dioecious crops such as Actinidia arguta (kiwiberries), some of the main challenges when breeding for fruit characteristics are the selection of potential male parents and the long juvenile period. Currently, breeding values of male parents are estimated through progeny tests, which makes the bre...

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Autores principales: Mertten, Daniel, Baldwin, Samantha, Cheng, Canhong H., McCallum, John, Thomson, Susan, Ashton, David T., McKenzie, Catherine M., Lenhard, Michael, Datson, Paul M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Netherlands 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10584781/
https://www.ncbi.nlm.nih.gov/pubmed/37868140
http://dx.doi.org/10.1007/s11032-023-01419-8
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author Mertten, Daniel
Baldwin, Samantha
Cheng, Canhong H.
McCallum, John
Thomson, Susan
Ashton, David T.
McKenzie, Catherine M.
Lenhard, Michael
Datson, Paul M.
author_facet Mertten, Daniel
Baldwin, Samantha
Cheng, Canhong H.
McCallum, John
Thomson, Susan
Ashton, David T.
McKenzie, Catherine M.
Lenhard, Michael
Datson, Paul M.
author_sort Mertten, Daniel
collection PubMed
description In dioecious crops such as Actinidia arguta (kiwiberries), some of the main challenges when breeding for fruit characteristics are the selection of potential male parents and the long juvenile period. Currently, breeding values of male parents are estimated through progeny tests, which makes the breeding of new kiwiberry cultivars time-consuming and costly. The application of best linear unbiased prediction (BLUP) would allow direct estimation of sex-related traits and speed up kiwiberry breeding. In this study, we used a linear mixed model approach to estimate narrow sense heritability for one vine-related trait and five fruit-related traits for two incomplete factorial crossing designs. We obtained BLUPs for all genotypes, taking into consideration whether the relationship was pedigree-based or marker-based. Owing to the high cost of genome sequencing, it is important to understand the effects of different sources of relationship matrices on estimating breeding values across a breeding population. Because of the increasing implementation of genomic selection in crop breeding, we compared the effects of incorporating different sources of information in building relationship matrices and ploidy levels on the accuracy of BLUPs’ heritability and predictive ability. As kiwiberries are autotetraploids, multivalent chromosome formation and occasionally double reduction can occur during meiosis, and this can affect the accuracy of prediction. This study innovates the breeding programme of autotetraploid kiwiberries. We demonstrate that the accuracy of BLUPs of male siblings, without phenotypic observations, strongly improved when a tetraploid marker-based relationship matrix was used rather than parental BLUPs and female siblings with phenotypic observations. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11032-023-01419-8.
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spelling pubmed-105847812023-10-20 Implementation of different relationship estimate methodologies in breeding value prediction in kiwiberry (Actinidia arguta) Mertten, Daniel Baldwin, Samantha Cheng, Canhong H. McCallum, John Thomson, Susan Ashton, David T. McKenzie, Catherine M. Lenhard, Michael Datson, Paul M. Mol Breed Article In dioecious crops such as Actinidia arguta (kiwiberries), some of the main challenges when breeding for fruit characteristics are the selection of potential male parents and the long juvenile period. Currently, breeding values of male parents are estimated through progeny tests, which makes the breeding of new kiwiberry cultivars time-consuming and costly. The application of best linear unbiased prediction (BLUP) would allow direct estimation of sex-related traits and speed up kiwiberry breeding. In this study, we used a linear mixed model approach to estimate narrow sense heritability for one vine-related trait and five fruit-related traits for two incomplete factorial crossing designs. We obtained BLUPs for all genotypes, taking into consideration whether the relationship was pedigree-based or marker-based. Owing to the high cost of genome sequencing, it is important to understand the effects of different sources of relationship matrices on estimating breeding values across a breeding population. Because of the increasing implementation of genomic selection in crop breeding, we compared the effects of incorporating different sources of information in building relationship matrices and ploidy levels on the accuracy of BLUPs’ heritability and predictive ability. As kiwiberries are autotetraploids, multivalent chromosome formation and occasionally double reduction can occur during meiosis, and this can affect the accuracy of prediction. This study innovates the breeding programme of autotetraploid kiwiberries. We demonstrate that the accuracy of BLUPs of male siblings, without phenotypic observations, strongly improved when a tetraploid marker-based relationship matrix was used rather than parental BLUPs and female siblings with phenotypic observations. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11032-023-01419-8. Springer Netherlands 2023-10-18 /pmc/articles/PMC10584781/ /pubmed/37868140 http://dx.doi.org/10.1007/s11032-023-01419-8 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Mertten, Daniel
Baldwin, Samantha
Cheng, Canhong H.
McCallum, John
Thomson, Susan
Ashton, David T.
McKenzie, Catherine M.
Lenhard, Michael
Datson, Paul M.
Implementation of different relationship estimate methodologies in breeding value prediction in kiwiberry (Actinidia arguta)
title Implementation of different relationship estimate methodologies in breeding value prediction in kiwiberry (Actinidia arguta)
title_full Implementation of different relationship estimate methodologies in breeding value prediction in kiwiberry (Actinidia arguta)
title_fullStr Implementation of different relationship estimate methodologies in breeding value prediction in kiwiberry (Actinidia arguta)
title_full_unstemmed Implementation of different relationship estimate methodologies in breeding value prediction in kiwiberry (Actinidia arguta)
title_short Implementation of different relationship estimate methodologies in breeding value prediction in kiwiberry (Actinidia arguta)
title_sort implementation of different relationship estimate methodologies in breeding value prediction in kiwiberry (actinidia arguta)
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10584781/
https://www.ncbi.nlm.nih.gov/pubmed/37868140
http://dx.doi.org/10.1007/s11032-023-01419-8
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