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Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population
BACKGROUND: Improving yield prediction and selection efficiency is critical for tree breeding. This is vital for macadamia trees with the time from crossing to production of new cultivars being almost a quarter of a century. Genomic selection (GS) is a useful tool in plant breeding, particularly wit...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8139092/ https://www.ncbi.nlm.nih.gov/pubmed/34016055 http://dx.doi.org/10.1186/s12864-021-07694-z |
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author | OConnor, Katie M. Hayes, Ben J. Hardner, Craig M. Alam, Mobashwer Henry, Robert J. Topp, Bruce L. |
author_facet | OConnor, Katie M. Hayes, Ben J. Hardner, Craig M. Alam, Mobashwer Henry, Robert J. Topp, Bruce L. |
author_sort | OConnor, Katie M. |
collection | PubMed |
description | BACKGROUND: Improving yield prediction and selection efficiency is critical for tree breeding. This is vital for macadamia trees with the time from crossing to production of new cultivars being almost a quarter of a century. Genomic selection (GS) is a useful tool in plant breeding, particularly with perennial trees, contributing to an increased rate of genetic gain and reducing the length of the breeding cycle. We investigated the potential of using GS methods to increase genetic gain and accelerate selection efficiency in the Australian macadamia breeding program with comparison to traditional breeding methods. This study evaluated the prediction accuracy of GS in a macadamia breeding population of 295 full-sib progeny from 32 families (29 parents, reciprocals combined), along with a subset of parents. Historical yield data for tree ages 5 to 8years were used in the study, along with a set of 4113 SNP markers. The traits of focus were average nut yield from tree ages 5 to 8years and yield stability, measured as the standard deviation of yield over these 4 years. GBLUP GS models were used to obtain genomic estimated breeding values for each genotype, with a five-fold cross-validation method and two techniques: prediction across related populations and prediction across unrelated populations. RESULTS: Narrow-sense heritability of yield and yield stability was low (h(2)=0.30 and 0.04, respectively). Prediction accuracy for yield was 0.57 for predictions across related populations and 0.14 when predicted across unrelated populations. Accuracy of prediction of yield stability was high (r=0.79) for predictions across related populations. Predicted genetic gain of yield using GS in related populations was 474g/year, more than double that of traditional breeding methods (226g/year), due to the halving of generation length from 8 to 4years. CONCLUSIONS: The results of this study indicate that the incorporation of GS for yield into the Australian macadamia breeding program may accelerate genetic gain due to reduction in generation length, though the cost of genotyping appears to be a constraint at present. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-07694-z. |
format | Online Article Text |
id | pubmed-8139092 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-81390922021-05-21 Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population OConnor, Katie M. Hayes, Ben J. Hardner, Craig M. Alam, Mobashwer Henry, Robert J. Topp, Bruce L. BMC Genomics Research Article BACKGROUND: Improving yield prediction and selection efficiency is critical for tree breeding. This is vital for macadamia trees with the time from crossing to production of new cultivars being almost a quarter of a century. Genomic selection (GS) is a useful tool in plant breeding, particularly with perennial trees, contributing to an increased rate of genetic gain and reducing the length of the breeding cycle. We investigated the potential of using GS methods to increase genetic gain and accelerate selection efficiency in the Australian macadamia breeding program with comparison to traditional breeding methods. This study evaluated the prediction accuracy of GS in a macadamia breeding population of 295 full-sib progeny from 32 families (29 parents, reciprocals combined), along with a subset of parents. Historical yield data for tree ages 5 to 8years were used in the study, along with a set of 4113 SNP markers. The traits of focus were average nut yield from tree ages 5 to 8years and yield stability, measured as the standard deviation of yield over these 4 years. GBLUP GS models were used to obtain genomic estimated breeding values for each genotype, with a five-fold cross-validation method and two techniques: prediction across related populations and prediction across unrelated populations. RESULTS: Narrow-sense heritability of yield and yield stability was low (h(2)=0.30 and 0.04, respectively). Prediction accuracy for yield was 0.57 for predictions across related populations and 0.14 when predicted across unrelated populations. Accuracy of prediction of yield stability was high (r=0.79) for predictions across related populations. Predicted genetic gain of yield using GS in related populations was 474g/year, more than double that of traditional breeding methods (226g/year), due to the halving of generation length from 8 to 4years. CONCLUSIONS: The results of this study indicate that the incorporation of GS for yield into the Australian macadamia breeding program may accelerate genetic gain due to reduction in generation length, though the cost of genotyping appears to be a constraint at present. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-07694-z. BioMed Central 2021-05-20 /pmc/articles/PMC8139092/ /pubmed/34016055 http://dx.doi.org/10.1186/s12864-021-07694-z Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Article OConnor, Katie M. Hayes, Ben J. Hardner, Craig M. Alam, Mobashwer Henry, Robert J. Topp, Bruce L. Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population |
title | Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population |
title_full | Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population |
title_fullStr | Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population |
title_full_unstemmed | Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population |
title_short | Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population |
title_sort | genomic selection and genetic gain for nut yield in an australian macadamia breeding population |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8139092/ https://www.ncbi.nlm.nih.gov/pubmed/34016055 http://dx.doi.org/10.1186/s12864-021-07694-z |
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