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Molecular Breeding for Complex Adaptive Traits: How Integrating Crop Ecophysiology and Modelling Can Enhance Efficiency

  • Graeme Hammer
  • Charlie Messina
  • Erik van Oosterom
  • Scott Chapman
  • Vijaya Singh
  • Andrew Borrell
  • David Jordan
  • Mark Cooper

Abstract

Progress in crop improvement is limited by the ability to identify favourable combinations of genotypes (G) and management practices (M) in relevant target environments (E) given the resources available to search among the myriad of possible combinations. To underpin yield advance we require prediction of phenotype based on genotype. In plant breeding, traditional phenotypic selection methods have involved measuring phenotypic performance of large segregating populations in multi-environment trials and applying rigorous statistical procedures based on quantitative genetic theory to identify superior individuals. Recent developments in the ability to inexpensively and densely map/sequence genomes have facilitated a shift from the level of the individual (genotype) to the level of the genomic region. Molecular breeding strategies using genome wide prediction and genomic selection approaches have developed rapidly. However, their applicability to complex traits remains constrained by gene-gene and gene-environment interactions, which restrict the predictive power of associations of genomic regions with phenotypic responses. Here it is argued that crop ecophysiology and functional whole plant modelling can provide an effective link between molecular and organism scales and enhance molecular breeding by adding value to genetic prediction approaches. A physiological framework that facilitates dissection and modelling of complex traits can inform phenotyping methods for marker/gene detection and underpin prediction of likely phenotypic consequences of trait and genetic variation in target environments. This approach holds considerable promise for more effectively linking genotype to phenotype for complex adaptive traits. Specific examples focused on drought adaptation are presented to highlight the concepts.

Keywords

Genotype-to-phenotype Phenotypic prediction Trait physiology QTL Functional genomics Crop improvement 

Notes

Acknowledgements

This paper summarises the research of a team of people, which would not have been possible without their enthusiasm and dedication nor without the financial support of a number of funders including Australian Research Council, Grains Research and Development Corporation, DuPont Pioneer, European Union FP7, and Australian Centre for International Agricultural Research. The authors acknowledge Crop and Pasture Science (CSIRO Publishing) and Journal of Experimental Botany (Oxford Journals) for permissions to re-use figures.

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Graeme Hammer
    • 1
  • Charlie Messina
    • 2
  • Erik van Oosterom
    • 1
  • Scott Chapman
    • 3
  • Vijaya Singh
    • 1
  • Andrew Borrell
    • 4
  • David Jordan
    • 4
  • Mark Cooper
    • 2
  1. 1.Centre for Plant Science, Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandBrisbaneAustralia
  2. 2.DuPont-PioneerJohnstonUSA
  3. 3.CSIRO Plant Industry and Climate Adaptation FlagshipQueensland Bioscience PrecinctSt LuciaAustralia
  4. 4.Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, Hermitage Research FacilityThe University of QueenslandWarwickAustralia

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