Toward integration of genomic selection with crop modelling: the development of an integrated approach to predicting rice heading dates

Akio Onogi, Maya Watanabe, Toshihiro Mochizuki, Takeshi Hayashi, Hiroshi Nakagawa, Toshihiro Hasegawa, Hiroyoshi Iwata

Research output: Contribution to journalArticle

20 Citations (Scopus)

Abstract

Key message: It is suggested that accuracy in predicting plant phenotypes can be improved by integrating genomic prediction with crop modelling in a single hierarchical model. Abstract: Accurate prediction of phenotypes is important for plant breeding and management. Although genomic prediction/selection aims to predict phenotypes on the basis of whole-genome marker information, it is often difficult to predict phenotypes of complex traits in diverse environments, because plant phenotypes are often influenced by genotype–environment interaction. A possible remedy is to integrate genomic prediction with crop/ecophysiological modelling, which enables us to predict plant phenotypes using environmental and management information. To this end, in the present study, we developed a novel method for integrating genomic prediction with phenological modelling of Asian rice (Oryza sativa, L.), allowing the heading date of untested genotypes in untested environments to be predicted. The method simultaneously infers the phenological model parameters and whole-genome marker effects on the parameters in a Bayesian framework. By cultivating backcross inbred lines of Koshihikari × Kasalath in nine environments, we evaluated the potential of the proposed method in comparison with conventional genomic prediction, phenological modelling, and two-step methods that applied genomic prediction to phenological model parameters inferred from Nelder–Mead or Markov chain Monte Carlo algorithms. In predicting heading dates of untested lines in untested environments, the proposed and two-step methods tended to provide more accurate predictions than the conventional genomic prediction methods, particularly in environments where phenotypes from environments similar to the target environment were unavailable for training genomic prediction. The proposed method showed greater accuracy in prediction than the two-step methods in all cross-validation schemes tested, suggesting the potential of the integrated approach in the prediction of phenotypes of plants.

Original languageEnglish
Pages (from-to)805-817
Number of pages13
JournalTheoretical and Applied Genetics
Volume129
Issue number4
DOIs
Publication statusPublished - Apr 1 2016

Fingerprint

heading
marker-assisted selection
Phenotype
rice
prediction
crops
genomics
phenotype
Genome
methodology
Markov Chains
Information Management
Oryza
information management
genome
Genotype
plant breeding
inbred lines
Oryza sativa

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Agronomy and Crop Science
  • Genetics

Cite this

Toward integration of genomic selection with crop modelling : the development of an integrated approach to predicting rice heading dates. / Onogi, Akio; Watanabe, Maya; Mochizuki, Toshihiro; Hayashi, Takeshi; Nakagawa, Hiroshi; Hasegawa, Toshihiro; Iwata, Hiroyoshi.

In: Theoretical and Applied Genetics, Vol. 129, No. 4, 01.04.2016, p. 805-817.

Research output: Contribution to journalArticle

Onogi, Akio ; Watanabe, Maya ; Mochizuki, Toshihiro ; Hayashi, Takeshi ; Nakagawa, Hiroshi ; Hasegawa, Toshihiro ; Iwata, Hiroyoshi. / Toward integration of genomic selection with crop modelling : the development of an integrated approach to predicting rice heading dates. In: Theoretical and Applied Genetics. 2016 ; Vol. 129, No. 4. pp. 805-817.
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