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Selection of trait-specific markers and multi-environment models improve genomic predictive ability in rice

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  • Aditi Bhandari
  • Jérôme Bartholomé
  • Tuong-Vi Cao-Hamadoun
  • Nilima Kumari
  • Julien Frouin
  • Arvind Kumar
  • Nourollah Ahmadi

Abstract

Developing high yielding rice varieties that are tolerant to drought stress is crucial for the sustainable livelihood of rice farmers in rainfed rice cropping ecosystems. Genomic selection (GS) promises to be an effective breeding option for these complex traits. We evaluated the effectiveness of two rather new options in the implementation of GS: trait and environment-specific marker selection and the use of multi-environment prediction models. A reference population of 280 rainfed lowland accessions endowed with 215k SNP markers data was phenotyped under a favorable and two managed drought environments. Trait-specific SNP subsets (28k) were selected for each trait under each environment, using results of GWAS performed with the complete genotype dataset. Performances of single-environment and multi-environment genomic prediction models were compared using kernel regression based methods (GBLUP and RKHS) under two cross validation scenarios: availability (CV2) or not (CV1) of phenotypic data for the validation set, in one of the environments. Trait-specific marker selection strategy achieved predictive ability (PA) of genomic prediction up to 22% higher than markers selected on the bases of neutral linkage disequilibrium (LD). Tolerance to drought stress was up to 32% better predicted by multi-environment models (especially RKHS based models) under CV2 strategy. Under the less favorable CV1 strategy, the multi-environment models achieved similar PA than the single-environment predictions. We also showed that reasonable PA could be obtained with as few as 3,000 SNP markers, even in a population of low LD extent, provided marker selection is based on pairwise LD. The implications of these findings for breeding for drought tolerance are discussed. The most resource sparing option would be accurate phenotyping of the reference population in a favorable environment and under a managed drought, while the candidate population would be phenotyped only under one of those environments.

Suggested Citation

  • Aditi Bhandari & Jérôme Bartholomé & Tuong-Vi Cao-Hamadoun & Nilima Kumari & Julien Frouin & Arvind Kumar & Nourollah Ahmadi, 2019. "Selection of trait-specific markers and multi-environment models improve genomic predictive ability in rice," PLOS ONE, Public Library of Science, vol. 14(5), pages 1-21, May.
    • Handle: RePEc:plo:pone00:0208871
    DOI: 10.1371/journal.pone.0208871
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    References listed on IDEAS

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    1. Pandey, S. & Bhandari, H. & Hardy, B., 2007. "Economic Costs of Drought and Rice Farmers’ Coping Mechanisms: A Cross-Country Comparative Analysis," IRRI Books, International Rice Research Institute (IRRI), number 281814.
    2. Cécile Grenier & Tuong-Vi Cao & Yolima Ospina & Constanza Quintero & Marc Henri Châtel & Joe Tohme & Brigitte Courtois & Nourollah Ahmadi, 2015. "Accuracy of Genomic Selection in a Rice Synthetic Population Developed for Recurrent Selection Breeding," PLOS ONE, Public Library of Science, vol. 10(8), pages 1-25, August.
    3. Jennifer Spindel & Hasina Begum & Deniz Akdemir & Parminder Virk & Bertrand Collard & Edilberto Redoña & Gary Atlin & Jean-Luc Jannink & Susan R McCouch, 2015. "Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic," PLOS Genetics, Public Library of Science, vol. 11(2), pages 1-25, February.
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