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Focused identification of germplasm strategy (FIGS) detects wheat stem rust resistance linked to environmental variables

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Abstract

Recent studies have shown that novel genetic variation for resistance to pests and diseases can be detected in plant genetic resources originating from locations with an environmental profile similar to the collection sites of a reference set of accessions with known resistance, based on the Focused Identification of Germplasm Strategy (FIGS) approach. FIGS combines both the development of a priori information based on the quantification of the trait-environment relationship and the use of this information to define a best bet subset of accessions with a higher probability of containing new variation for the sought after trait(s). The present study investigates the development strategy of the a priori information using different modeling techniques including learning-based techniques as a follow up to previous work where parametric approaches were used to quantify the stem rust resistance and climate variables relationship. The results show that the predictive power, derived from the accuracy parameters and cross-validation, varies depending on whether the models are based on linear or non-linear approaches. The prediction based on learning techniques are relatively higher indicating that the non-linear approaches, in particular support vector machine and neural networks, outperform both principal component logistic regression and generalized partial least squares. Overall there are indications that the trait distribution of resistance to stem rust is confined to certain environments or areas, whereas the susceptible types appear to be limited to other areas with some degree of overlapping of the two classes. The results also point to a number of issues to consider for improving the predictive performance of the models.

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Abbreviations

AUC:

Area under the ROC curve

GPLS:

Generalized partial least squares

GIS:

Geographic information systems

NN:

Neural networks

PCA:

Principal component analysis

PCLR:

Principal component logistic regression

PLS:

Partial least squares

RF:

Random forest

ROC:

Receiver operating characteristics

SVM:

Support vector machine

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Authors and Affiliations

  1. International Center for Agricultural Research in the Dry Areas (ICARDA), Aleppo, Syria

    Abdallah Bari, Kenneth Street, Eddy De Pauw & Ahmed Amri

  2. Bioversity International, Rome, Italy

    Michael Mackay

  3. Nordic Genetic Resources Center (NordGen), Alnarp, Sweden

    Dag Terje Filip Endresen

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  1. Abdallah Bari
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  2. Kenneth Street
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  3. Michael Mackay
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  4. Dag Terje Filip Endresen
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  5. Eddy De Pauw
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Correspondence to Kenneth Street.

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Bari, A., Street, K., Mackay, M. et al. Focused identification of germplasm strategy (FIGS) detects wheat stem rust resistance linked to environmental variables. Genet Resour Crop Evol 59, 1465–1481 (2012). https://doi.org/10.1007/s10722-011-9775-5

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