A simulation-based breeding design that uses whole-genome prediction in tomato

Scientific Reports
Eiji YamamotoHiroyuki Fukuoka

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.

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Citations

May 16, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Dandan WangPeiwu Li
Mar 2, 2019·G3 : Genes - Genomes - Genetics·Osval A Montesinos-LópezJosé Crossa
Apr 2, 2017·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Zibei LinHans D Daetwyler
Nov 30, 2019·Biology·Juhi ChaudharyRupesh Deshmukh
Sep 24, 2020·Plants·Elisa CappettaMaria Raffaella Ercolano
May 10, 2017·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Akio OhyamaTakeshi Hayashi
Aug 21, 2020·G3 : Genes - Genomes - Genetics·Christopher O HernandezMichael R Mazourek
Feb 10, 2021·Genes·Matteo MartinaArnaud G Bovy
Mar 23, 2021·Frontiers in Plant Science·Eiji YamamotoSachiko Isobe
Jun 2, 2021·Genetics, Selection, Evolution : GSE·Emre KaramanMogens S Lund
Jun 3, 2021·Genes·Andrés J Cortés, Felipe López-Hernández
Apr 20, 2021·G3 : Genes - Genomes - Genetics·Eiji Yamamoto, Hiroshi Matsunaga

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Datasets Mentioned

BETA
DRA003755

Methods Mentioned

BETA
PCA
genotyping

Software Mentioned

randomForest
rrBLUP
BEAGLE
STRUCTURE HARVESTER
R package KernSmooth
STRUCTER
R
CLUMPP
R package genetics

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