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Expected benefit of genomic selection over forward selection in conifer breeding and deployment

Genomic selection is a proven technology in animal and plant breeding to accelerate genetic gain, but as yet is to be fully realised in forest tree breeding. This paper examines, through stochastic simulation, the potential benefits of genomic selection (GS) over forward selection (FS) in a typical...

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Autores principales: Li, Yongjun, Dungey, Heidi S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6287808/
https://www.ncbi.nlm.nih.gov/pubmed/30532178
http://dx.doi.org/10.1371/journal.pone.0208232
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author Li, Yongjun
Dungey, Heidi S.
author_facet Li, Yongjun
Dungey, Heidi S.
author_sort Li, Yongjun
collection PubMed
description Genomic selection is a proven technology in animal and plant breeding to accelerate genetic gain, but as yet is to be fully realised in forest tree breeding. This paper examines, through stochastic simulation, the potential benefits of genomic selection (GS) over forward selection (FS) in a typical conifer breeding program. Methods of speeding the deployment of selected material were also considered, including top-grafting onto mature seed orchard ortets, using additional replicates of clones in archives for crossing, and embryogenesis and clonal propagation. Genetic gain per generation was found to increase considerably when the size of the training population was larger (800 c.f. 3000 clones), or when the heritability was higher (0.2 c.f. 0.5). The largest genetic gain, of 24% was achieved where large training populations (3000 clones) and high heritability traits (0.5) were combined. The accuracy of genomic breeding values (GEBVs) increased with the increase in the number of clones in the training population, the heritability of the trait and the density of the SNP markers. Calculated accuracies of simulated GEBVs and genetic gain per unit of time suggested that 2000 clones in the training population is the minimum size for effective genomic selection for conifers. Compared with forward selection, genomic selection with 2000 clones in the training population, and a 60K SNP panel, an increase of 1.58 mm per year in diameter-at-breast-height (DBH) and 2.44 kg/m(3) per year for wood density can be expected. After one generation (9-years), this would be equivalent to 14.23 mm and 21.97 kg/m(3) for DBH and wood density respectively. Deploying clones of the selected individuals always resulted in higher additional genetic gain than deploying progeny/seedlings. Deploying genetic material selected from genomic selection with top-grafting for early coning appeared to be the best option. Application of genomic selection to conifer breeding programs, combined with deployment tools such as top-grafting and embryogenesis are powerful tools to speed the delivery of genetic gain to the forest.
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spelling pubmed-62878082018-12-28 Expected benefit of genomic selection over forward selection in conifer breeding and deployment Li, Yongjun Dungey, Heidi S. PLoS One Research Article Genomic selection is a proven technology in animal and plant breeding to accelerate genetic gain, but as yet is to be fully realised in forest tree breeding. This paper examines, through stochastic simulation, the potential benefits of genomic selection (GS) over forward selection (FS) in a typical conifer breeding program. Methods of speeding the deployment of selected material were also considered, including top-grafting onto mature seed orchard ortets, using additional replicates of clones in archives for crossing, and embryogenesis and clonal propagation. Genetic gain per generation was found to increase considerably when the size of the training population was larger (800 c.f. 3000 clones), or when the heritability was higher (0.2 c.f. 0.5). The largest genetic gain, of 24% was achieved where large training populations (3000 clones) and high heritability traits (0.5) were combined. The accuracy of genomic breeding values (GEBVs) increased with the increase in the number of clones in the training population, the heritability of the trait and the density of the SNP markers. Calculated accuracies of simulated GEBVs and genetic gain per unit of time suggested that 2000 clones in the training population is the minimum size for effective genomic selection for conifers. Compared with forward selection, genomic selection with 2000 clones in the training population, and a 60K SNP panel, an increase of 1.58 mm per year in diameter-at-breast-height (DBH) and 2.44 kg/m(3) per year for wood density can be expected. After one generation (9-years), this would be equivalent to 14.23 mm and 21.97 kg/m(3) for DBH and wood density respectively. Deploying clones of the selected individuals always resulted in higher additional genetic gain than deploying progeny/seedlings. Deploying genetic material selected from genomic selection with top-grafting for early coning appeared to be the best option. Application of genomic selection to conifer breeding programs, combined with deployment tools such as top-grafting and embryogenesis are powerful tools to speed the delivery of genetic gain to the forest. Public Library of Science 2018-12-10 /pmc/articles/PMC6287808/ /pubmed/30532178 http://dx.doi.org/10.1371/journal.pone.0208232 Text en © 2018 Li, Dungey http://creativecommons.org/licenses/by/4.0/ 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 author and source are credited.
spellingShingle Research Article
Li, Yongjun
Dungey, Heidi S.
Expected benefit of genomic selection over forward selection in conifer breeding and deployment
title Expected benefit of genomic selection over forward selection in conifer breeding and deployment
title_full Expected benefit of genomic selection over forward selection in conifer breeding and deployment
title_fullStr Expected benefit of genomic selection over forward selection in conifer breeding and deployment
title_full_unstemmed Expected benefit of genomic selection over forward selection in conifer breeding and deployment
title_short Expected benefit of genomic selection over forward selection in conifer breeding and deployment
title_sort expected benefit of genomic selection over forward selection in conifer breeding and deployment
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6287808/
https://www.ncbi.nlm.nih.gov/pubmed/30532178
http://dx.doi.org/10.1371/journal.pone.0208232
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