, Volume 186, Issue 3, pp 655–669 | Cite as

Application of multi-phase experiments in plant pathology to identify genetic resistance to Diaporthe toxica in Lupinus albus

  • R. B. CowleyEmail author
  • G. J. Ash
  • J. D. I. Harper
  • A. B. Smith
  • B. R. Cullis
  • D. J. Luckett


Phenotyping assays in plant pathology using detached plant parts are multi-phase experimental processes. Such assays involve growing plants in field or controlled-environment trials (Phase 1) and then subjecting a sample removed from each plant to disease assessment, usually under laboratory conditions (Phase 2). Each phase may be subject to non-genetic sources of variation. To be able to separate these sources of variation in both phases from genetic sources of variation requires a multi-phase experiment with an appropriate experimental design and statistical analysis. To achieve this, a separate randomization is required for each phase, with additional replication in Phase 2. In this article, Phomopsis leaf and pod blight (caused by Diaporthe toxica) of Lupinus albus was used as a case study to apply a multi-phase experimental approach to identify genetic resistance to this pathogen, and demonstrate the principles of sound experimental design and analysis in detached plant part assays. In seven experiments, 250 breeding lines, cultivars, landraces, and recombinant in-bred lines from a mapping population of L. albus were screened using detached, inoculated leaves, and/or pods. The experimental, non-genetic variance in Phase 2 varied in magnitude compared to the Phase 1 experimental, non-genetic variance. The reliability of prediction for resistance to Phomopsis pod blight was high (mean of 0.70 in seven experiments), while reliability of prediction for leaf assays was lower (mean 0.35–0.51 depending on the scoring method used).


ASReml-R Broad-leaf lupin Detached leaf assay Detached pod assay Phomopsis leptostromiformis 



Detached leaf assay


Detached pod assay


New South Wales, Australia



This work was partly funded by the Grains Research & Development Corporation of Australia (GRDC). Neil Coombes is thanked for help with DiGGer. Mark Richards, David Roberts, and Cina Zachariah provided technical assistance, and Hua’an Yang (Department of Agriculture and Food Western Australia, Perth) provided seeds of the lupin recombinant in-bred lines in the mapping population. Thanks are extended to the anonymous reviewers whose constructive comments greatly aided this manuscript.


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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • R. B. Cowley
    • 1
    Email author
  • G. J. Ash
    • 1
  • J. D. I. Harper
    • 1
  • A. B. Smith
    • 2
  • B. R. Cullis
    • 3
  • D. J. Luckett
    • 1
  1. 1.EH Graham Centre for Agricultural Innovation (An Alliance Between NSW Department of Primary Industries and Charles Sturt University)Wagga WaggaAustralia
  2. 2.School of Mathematics and Applied StatisticsFaculty of Informatics University of WollongongWollongongAustralia
  3. 3.School of Mathematics and Applied StatisticsFaculty of Informatics University of Wollongong and Mathematics, Informatics and Statistics, CSIROWollongongAustralia

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