Genomic prediction of crown rust resistance in Lolium perenne
Abstract Background Genomic selection (GS) can accelerate genetic gains in breeding programmes by reducing the time it takes to complete a cycle of selection. Puccinia coronata f. sp lolli (crown rust) is one of the most widespread diseases of perennial ryegrass and can lead to reductions in yield,...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BioMed Central
2018-05-01
|
| Series: | BMC Genetics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12863-018-0613-z |
| id |
doaj-art-e0a2dc26565d4cb48d07366261ff87b3 |
|---|---|
| recordtype |
oai_dc |
| spelling |
doaj-art-e0a2dc26565d4cb48d07366261ff87b32018-08-20T16:32:07ZengBioMed CentralBMC Genetics1471-21562018-05-0119111010.1186/s12863-018-0613-zGenomic prediction of crown rust resistance in Lolium perenneSai Krishna Arojju0Patrick Conaghan1Susanne Barth2Dan Milbourne3Michael D. Casler4Trevor R. Hodkinson5Thibauld Michel6Stephen L. Byrne7Teagasc, Crop Science DepartmentTeagasc, Grassland Science Research Department, Animal and Grassland Research and Innovation CentreTeagasc, Crop Science DepartmentTeagasc, Crop Science DepartmentDepartment of Agronomy, University of Wisconsin-MadisonDepartment of Botany, School of Natural Sciences, Trinity College DublinTeagasc, Crop Science DepartmentTeagasc, Crop Science DepartmentAbstract Background Genomic selection (GS) can accelerate genetic gains in breeding programmes by reducing the time it takes to complete a cycle of selection. Puccinia coronata f. sp lolli (crown rust) is one of the most widespread diseases of perennial ryegrass and can lead to reductions in yield, persistency and nutritional value. Here, we used a large perennial ryegrass population to assess the accuracy of using genome wide markers to predict crown rust resistance and to investigate the factors affecting predictive ability. Results Using these data, predictive ability for crown rust resistance in the complete population reached a maximum of 0.52. Much of the predictive ability resulted from the ability of markers to capture genetic relationships among families within the training set, and reducing the marker density had little impact on predictive ability. Using permutation based variable importance measure and genome wide association studies (GWAS) to identify and rank markers enabled the identification of a small subset of SNPs that could achieve predictive abilities close to those achieved using the complete marker set. Conclusion Using a GWAS to identify and rank markers enabled a small panel of markers to be identified that could achieve higher predictive ability than the same number of randomly selected markers, and predictive abilities close to those achieved with the entire marker set. This was particularly evident in a sub-population characterised by having on-average higher genome-wide linkage disequilibirum (LD). Higher predictive abilities with selected markers over random markers suggests they are in LD with QTL. Accuracy due to genetic relationships will decay rapidly over generations whereas accuracy due to LD will persist, which is advantageous for practical breeding applications.http://link.springer.com/article/10.1186/s12863-018-0613-zGenomic selectionCrown rustPerennial ryegrassGenetic relationshipGWAS |
| institution |
Open Data Bank |
| collection |
Open Access Journals |
| building |
Directory of Open Access Journals |
| language |
English |
| format |
Article |
| author |
Sai Krishna Arojju Patrick Conaghan Susanne Barth Dan Milbourne Michael D. Casler Trevor R. Hodkinson Thibauld Michel Stephen L. Byrne |
| spellingShingle |
Sai Krishna Arojju Patrick Conaghan Susanne Barth Dan Milbourne Michael D. Casler Trevor R. Hodkinson Thibauld Michel Stephen L. Byrne Genomic prediction of crown rust resistance in Lolium perenne BMC Genetics Genomic selection Crown rust Perennial ryegrass Genetic relationship GWAS |
| author_facet |
Sai Krishna Arojju Patrick Conaghan Susanne Barth Dan Milbourne Michael D. Casler Trevor R. Hodkinson Thibauld Michel Stephen L. Byrne |
| author_sort |
Sai Krishna Arojju |
| title |
Genomic prediction of crown rust resistance in Lolium perenne |
| title_short |
Genomic prediction of crown rust resistance in Lolium perenne |
| title_full |
Genomic prediction of crown rust resistance in Lolium perenne |
| title_fullStr |
Genomic prediction of crown rust resistance in Lolium perenne |
| title_full_unstemmed |
Genomic prediction of crown rust resistance in Lolium perenne |
| title_sort |
genomic prediction of crown rust resistance in lolium perenne |
| publisher |
BioMed Central |
| series |
BMC Genetics |
| issn |
1471-2156 |
| publishDate |
2018-05-01 |
| description |
Abstract Background Genomic selection (GS) can accelerate genetic gains in breeding programmes by reducing the time it takes to complete a cycle of selection. Puccinia coronata f. sp lolli (crown rust) is one of the most widespread diseases of perennial ryegrass and can lead to reductions in yield, persistency and nutritional value. Here, we used a large perennial ryegrass population to assess the accuracy of using genome wide markers to predict crown rust resistance and to investigate the factors affecting predictive ability. Results Using these data, predictive ability for crown rust resistance in the complete population reached a maximum of 0.52. Much of the predictive ability resulted from the ability of markers to capture genetic relationships among families within the training set, and reducing the marker density had little impact on predictive ability. Using permutation based variable importance measure and genome wide association studies (GWAS) to identify and rank markers enabled the identification of a small subset of SNPs that could achieve predictive abilities close to those achieved using the complete marker set. Conclusion Using a GWAS to identify and rank markers enabled a small panel of markers to be identified that could achieve higher predictive ability than the same number of randomly selected markers, and predictive abilities close to those achieved with the entire marker set. This was particularly evident in a sub-population characterised by having on-average higher genome-wide linkage disequilibirum (LD). Higher predictive abilities with selected markers over random markers suggests they are in LD with QTL. Accuracy due to genetic relationships will decay rapidly over generations whereas accuracy due to LD will persist, which is advantageous for practical breeding applications. |
| topic |
Genomic selection Crown rust Perennial ryegrass Genetic relationship GWAS |
| url |
http://link.springer.com/article/10.1186/s12863-018-0613-z |
| _version_ |
1612686374873333760 |