title: Selection on Optimal Haploid Value Increases Genetic Gain and Preserves More Genetic Diversity Relative to Genomic Selection.
abstract: Doubled haploids are routinely created and phenotypically selected in plant breeding programs to accelerate the breeding cycle. Genomic selection, which makes use of both phenotypes and genotypes, has been shown to further improve genetic gain through prediction of performance before or without phenotypic characterization of novel germplasm. Additional opportunities exist to combine genomic prediction methods with the creation of doubled haploids. Here we propose an extension to genomic selection, optimal haploid value (OHV) selection, which predicts the best doubled haploid that can be produced from a segregating plant. This method focuses selection on the haplotype and optimizes the breeding program toward its end goal of generating an elite fixed line. We rigorously tested OHV selection breeding programs, using computer simulation, and show that it results in up to 0.6 standard deviations more genetic gain than genomic selection. At the same time, OHV selection preserved a substantially greater amount of genetic diversity in the population than genomic selection, which is important to achieve long-term genetic gain in breeding populations.
authors.affiliation: AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources (DEDJTR), Bundoora, Victoria 3083, Australia School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3086, Australia hans.daetwyler@ecodev.vic.gov.au.
authors.forename: Hans D
authors.identifier: http://orcid.org/0000-0002-3018-3640
authors.initials: HD
authors.lastname: Daetwyler
authors.affiliation: AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources (DEDJTR), Bundoora, Victoria 3083, Australia School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3086, Australia.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Hayden
authors.affiliation: AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources (DEDJTR), Bundoora, Victoria 3083, Australia School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3086, Australia.
authors.forename: German C
authors.initials: GC
authors.lastname: Spangenberg
authors.affiliation: AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources (DEDJTR), Bundoora, Victoria 3083, Australia School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3086, Australia.
authors.forename: Ben J
authors.initials: BJ
authors.lastname: Hayes
mesh_terms: D001947:Breeding / Q000379:methods*; D014644:Genetic Variation; D023281:Genomics; D006238:Haploidy; D008957:Models, Genetic
keywords: GenPred; doubled haploid; genetic diversity; genetic gain; genomic selection; haplotype; shared data resource