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Genetic analysis of resistance to Pseudomonas syringae pv. actinidiae (Psa) in a kiwifruit progeny test: an application of generalised linear mixed models (GLMMs)
Linear Mixed models (LMMs) that incorporate genetic and spatial covariance structures have been used for many years to estimate genetic parameters and to predict breeding values in animal and plant breeding. Although the theoretical aspects for extending LMM to generalised linear mixed models (GLMMs...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer International Publishing
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4447754/ https://www.ncbi.nlm.nih.gov/pubmed/26034671 http://dx.doi.org/10.1186/2193-1801-3-547 |
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author | De Silva, Nihal H Gea, Luis Lowe, Russell |
author_facet | De Silva, Nihal H Gea, Luis Lowe, Russell |
author_sort | De Silva, Nihal H |
collection | PubMed |
description | Linear Mixed models (LMMs) that incorporate genetic and spatial covariance structures have been used for many years to estimate genetic parameters and to predict breeding values in animal and plant breeding. Although the theoretical aspects for extending LMM to generalised linear mixed models (GLMMs) have been around for some time, suitable software has been developed only within the last decade or so. The GLIMMIX procedure in SAS® is becoming popular for fitting GLMMs in various disciplines. Applications of GLMMs to genetic analysis have been limited, probably because of the complexity of the models used. This is particularly so for Proc GLIMMIX because, unlike ASReml software, it is not specifically tailored for analysis of breeding data and some pre-procedure coding is necessary. Binary data that fits the GLMM framework is commonly encountered in breeding experiments, such as when evaluating individuals for resistance by observing the presence or absence of disease. Bacterial canker (Psa) caused by Pseudomonas syringae pv. actinidiae is a serious disease of kiwifruit in New Zealand and other kiwifruit-producing countries. Data from a progeny test trial was available to identify parents with high breeding values for resistance. We successfully applied the GLIMMIX procedure for this purpose. Heritability for resistance was moderate, and we identified two parents and their family as having high potential for Psa resistance breeding. There are several potential pitfalls when using GLMMs with binary data and these are briefly discussed. |
format | Online Article Text |
id | pubmed-4447754 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Springer International Publishing |
record_format | MEDLINE/PubMed |
spelling | pubmed-44477542015-06-01 Genetic analysis of resistance to Pseudomonas syringae pv. actinidiae (Psa) in a kiwifruit progeny test: an application of generalised linear mixed models (GLMMs) De Silva, Nihal H Gea, Luis Lowe, Russell Springerplus Research Linear Mixed models (LMMs) that incorporate genetic and spatial covariance structures have been used for many years to estimate genetic parameters and to predict breeding values in animal and plant breeding. Although the theoretical aspects for extending LMM to generalised linear mixed models (GLMMs) have been around for some time, suitable software has been developed only within the last decade or so. The GLIMMIX procedure in SAS® is becoming popular for fitting GLMMs in various disciplines. Applications of GLMMs to genetic analysis have been limited, probably because of the complexity of the models used. This is particularly so for Proc GLIMMIX because, unlike ASReml software, it is not specifically tailored for analysis of breeding data and some pre-procedure coding is necessary. Binary data that fits the GLMM framework is commonly encountered in breeding experiments, such as when evaluating individuals for resistance by observing the presence or absence of disease. Bacterial canker (Psa) caused by Pseudomonas syringae pv. actinidiae is a serious disease of kiwifruit in New Zealand and other kiwifruit-producing countries. Data from a progeny test trial was available to identify parents with high breeding values for resistance. We successfully applied the GLIMMIX procedure for this purpose. Heritability for resistance was moderate, and we identified two parents and their family as having high potential for Psa resistance breeding. There are several potential pitfalls when using GLMMs with binary data and these are briefly discussed. Springer International Publishing 2014-09-22 /pmc/articles/PMC4447754/ /pubmed/26034671 http://dx.doi.org/10.1186/2193-1801-3-547 Text en © De Silva et al.; licensee Springer. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. |
spellingShingle | Research De Silva, Nihal H Gea, Luis Lowe, Russell Genetic analysis of resistance to Pseudomonas syringae pv. actinidiae (Psa) in a kiwifruit progeny test: an application of generalised linear mixed models (GLMMs) |
title | Genetic analysis of resistance to Pseudomonas syringae pv. actinidiae (Psa) in a kiwifruit progeny test: an application of generalised linear mixed models (GLMMs) |
title_full | Genetic analysis of resistance to Pseudomonas syringae pv. actinidiae (Psa) in a kiwifruit progeny test: an application of generalised linear mixed models (GLMMs) |
title_fullStr | Genetic analysis of resistance to Pseudomonas syringae pv. actinidiae (Psa) in a kiwifruit progeny test: an application of generalised linear mixed models (GLMMs) |
title_full_unstemmed | Genetic analysis of resistance to Pseudomonas syringae pv. actinidiae (Psa) in a kiwifruit progeny test: an application of generalised linear mixed models (GLMMs) |
title_short | Genetic analysis of resistance to Pseudomonas syringae pv. actinidiae (Psa) in a kiwifruit progeny test: an application of generalised linear mixed models (GLMMs) |
title_sort | genetic analysis of resistance to pseudomonas syringae pv. actinidiae (psa) in a kiwifruit progeny test: an application of generalised linear mixed models (glmms) |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4447754/ https://www.ncbi.nlm.nih.gov/pubmed/26034671 http://dx.doi.org/10.1186/2193-1801-3-547 |
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