title: A simulation-based breeding design that uses whole-genome prediction in tomato.
abstract: Efficient plant breeding methods must be developed in order to increase yields and feed a growing world population, as well as to meet the demands of consumers with diverse preferences who require high-quality foods. We propose a strategy that integrates breeding simulations and phenotype prediction models using genomic information. The validity of this strategy was evaluated by the simultaneous genetic improvement of the yield and flavour of the tomato (Solanum lycopersicum), as an example. Reliable phenotype prediction models for the simulation were constructed from actual genotype and phenotype data. Our simulation predicted that selection for both yield and flavour would eventually result in morphological changes that would increase the total plant biomass and decrease the light extinction coefficient, an essential requirement for these improvements. This simulation-based genome-assisted approach to breeding will help to optimise plant breeding, not only in the tomato but also in other important agricultural crops.
authors.affiliation: NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan.
authors.forename: Eiji
authors.initials: E
authors.lastname: Yamamoto
authors.affiliation: NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Matsunaga
authors.affiliation: Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-8657, Japan.
authors.forename: Akio
authors.initials: A
authors.lastname: Onogi
authors.affiliation: Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-8657, Japan.
authors.forename: Hiromi
authors.initials: H
authors.lastname: Kajiya-Kanegae
authors.affiliation: Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-8657, Japan.
authors.forename: Mai
authors.initials: M
authors.lastname: Minamikawa
authors.affiliation: Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-8657, Japan.
authors.forename: Akinori
authors.initials: A
authors.lastname: Suzuki
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
authors.forename: Kenta
authors.initials: K
authors.lastname: Shirasawa
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
authors.forename: Hideki
authors.initials: H
authors.lastname: Hirakawa
authors.affiliation: NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan.
authors.forename: Tsukasa
authors.initials: T
authors.lastname: Nunome
authors.affiliation: NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan.
authors.forename: Hirotaka
authors.initials: H
authors.lastname: Yamaguchi
authors.affiliation: NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan.
authors.forename: Koji
authors.initials: K
authors.lastname: Miyatake
authors.affiliation: NARO Institute of Vegetable and Tea Science (NIVTS), 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8666, Japan.
authors.forename: Akio
authors.initials: A
authors.lastname: Ohyama
authors.affiliation: Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-8657, Japan.
authors.forename: Hiroyoshi
authors.initials: H
authors.lastname: Iwata
authors.affiliation: NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Fukuoka
mesh_terms: D001947:Breeding; D002874:Chromosome Mapping; D003198:Computer Simulation; D005828:Genetics, Population; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D015810:Linkage Disequilibrium; D018551:Solanum lycopersicum / Q000235:genetics*; D008957:Models, Genetic; D010641:Phenotype; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D012641:Selection, Genetic