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Multi-Trait Genomic Prediction Improves Predictive Ability for Dry Matter Yield and Water-Soluble Carbohydrates in Perennial Ryegrass

In perennial ryegrass (Lolium perenne L), annual and seasonal dry matter yield (DMY) and nutritive quality of herbage are high-priority traits targeted for improvement through selective breeding. Genomic prediction (GP) has proven to be a valuable tool for improving complex traits and may be further...

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Autores principales: Arojju, Sai Krishna, Cao, Mingshu, Trolove, Michael, Barrett, Brent A., Inch, Courtney, Eady, Colin, Stewart, Alan, Faville, Marty J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7426495/
https://www.ncbi.nlm.nih.gov/pubmed/32849742
http://dx.doi.org/10.3389/fpls.2020.01197
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author Arojju, Sai Krishna
Cao, Mingshu
Trolove, Michael
Barrett, Brent A.
Inch, Courtney
Eady, Colin
Stewart, Alan
Faville, Marty J.
author_facet Arojju, Sai Krishna
Cao, Mingshu
Trolove, Michael
Barrett, Brent A.
Inch, Courtney
Eady, Colin
Stewart, Alan
Faville, Marty J.
author_sort Arojju, Sai Krishna
collection PubMed
description In perennial ryegrass (Lolium perenne L), annual and seasonal dry matter yield (DMY) and nutritive quality of herbage are high-priority traits targeted for improvement through selective breeding. Genomic prediction (GP) has proven to be a valuable tool for improving complex traits and may be further enhanced through the use of multi-trait (MT) prediction models. In this study, we evaluated the relative performance of MT prediction models to improve predictive ability for DMY and key nutritive quality traits, using two different training populations (TP1, n = 463 and TP2, n = 517) phenotyped at multiple locations. MT models outperformed single-trait (ST) models by 24% to 59% for DMY and 67% to 105% for nutritive quality traits, such as low, high, and total WSC, when a correlated secondary trait was included in both the training and test set (MT-CV2) or in the test set alone (MT-CV3) (trait-assisted genomic selection). However, when a secondary trait was included in training set and not the test set (MT-CV1), the predictive ability was not statistically significant (p > 0.05) compared to the ST model. We evaluated the impact of training set size when using a MT-CV2 model. Using a highly correlated trait (r(g) = 0.88) as the secondary trait in the MT-CV2 model, there was no loss in predictive ability for DMY even when the training set was reduced to 50% of its original size. In contrast, using a weakly correlated secondary trait (r(g) = 0.56) in the MT-CV2 model, predictive ability began to decline when the training set size was reduced by only 11% from its original size. Using a ST model, genomic predictive ability in a population unrelated to the training set was poor (r(p) = −0.06). However, when using an MT-CV2 model, the predictive ability was positive and high (r(p) = 0.76) for the same population. Our results demonstrate the first assessment of MT models in forage species and illustrate the prospects of using MT genomic selection in forages, and other outcrossing plant species, to accelerate genetic gains for complex agronomical traits, such as DMY and nutritive quality characteristics.
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spelling pubmed-74264952020-08-25 Multi-Trait Genomic Prediction Improves Predictive Ability for Dry Matter Yield and Water-Soluble Carbohydrates in Perennial Ryegrass Arojju, Sai Krishna Cao, Mingshu Trolove, Michael Barrett, Brent A. Inch, Courtney Eady, Colin Stewart, Alan Faville, Marty J. Front Plant Sci Plant Science In perennial ryegrass (Lolium perenne L), annual and seasonal dry matter yield (DMY) and nutritive quality of herbage are high-priority traits targeted for improvement through selective breeding. Genomic prediction (GP) has proven to be a valuable tool for improving complex traits and may be further enhanced through the use of multi-trait (MT) prediction models. In this study, we evaluated the relative performance of MT prediction models to improve predictive ability for DMY and key nutritive quality traits, using two different training populations (TP1, n = 463 and TP2, n = 517) phenotyped at multiple locations. MT models outperformed single-trait (ST) models by 24% to 59% for DMY and 67% to 105% for nutritive quality traits, such as low, high, and total WSC, when a correlated secondary trait was included in both the training and test set (MT-CV2) or in the test set alone (MT-CV3) (trait-assisted genomic selection). However, when a secondary trait was included in training set and not the test set (MT-CV1), the predictive ability was not statistically significant (p > 0.05) compared to the ST model. We evaluated the impact of training set size when using a MT-CV2 model. Using a highly correlated trait (r(g) = 0.88) as the secondary trait in the MT-CV2 model, there was no loss in predictive ability for DMY even when the training set was reduced to 50% of its original size. In contrast, using a weakly correlated secondary trait (r(g) = 0.56) in the MT-CV2 model, predictive ability began to decline when the training set size was reduced by only 11% from its original size. Using a ST model, genomic predictive ability in a population unrelated to the training set was poor (r(p) = −0.06). However, when using an MT-CV2 model, the predictive ability was positive and high (r(p) = 0.76) for the same population. Our results demonstrate the first assessment of MT models in forage species and illustrate the prospects of using MT genomic selection in forages, and other outcrossing plant species, to accelerate genetic gains for complex agronomical traits, such as DMY and nutritive quality characteristics. Frontiers Media S.A. 2020-08-07 /pmc/articles/PMC7426495/ /pubmed/32849742 http://dx.doi.org/10.3389/fpls.2020.01197 Text en Copyright © 2020 Arojju, Cao, Trolove, Barrett, Inch, Eady, Stewart and Faville http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Arojju, Sai Krishna
Cao, Mingshu
Trolove, Michael
Barrett, Brent A.
Inch, Courtney
Eady, Colin
Stewart, Alan
Faville, Marty J.
Multi-Trait Genomic Prediction Improves Predictive Ability for Dry Matter Yield and Water-Soluble Carbohydrates in Perennial Ryegrass
title Multi-Trait Genomic Prediction Improves Predictive Ability for Dry Matter Yield and Water-Soluble Carbohydrates in Perennial Ryegrass
title_full Multi-Trait Genomic Prediction Improves Predictive Ability for Dry Matter Yield and Water-Soluble Carbohydrates in Perennial Ryegrass
title_fullStr Multi-Trait Genomic Prediction Improves Predictive Ability for Dry Matter Yield and Water-Soluble Carbohydrates in Perennial Ryegrass
title_full_unstemmed Multi-Trait Genomic Prediction Improves Predictive Ability for Dry Matter Yield and Water-Soluble Carbohydrates in Perennial Ryegrass
title_short Multi-Trait Genomic Prediction Improves Predictive Ability for Dry Matter Yield and Water-Soluble Carbohydrates in Perennial Ryegrass
title_sort multi-trait genomic prediction improves predictive ability for dry matter yield and water-soluble carbohydrates in perennial ryegrass
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7426495/
https://www.ncbi.nlm.nih.gov/pubmed/32849742
http://dx.doi.org/10.3389/fpls.2020.01197
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