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Accuracy of Genomic Selection in a Rice Synthetic Population Developed for Recurrent Selection Breeding

Author

Listed:
  • Cécile Grenier
  • Tuong-Vi Cao
  • Yolima Ospina
  • Constanza Quintero
  • Marc Henri Châtel
  • Joe Tohme
  • Brigitte Courtois
  • Nourollah Ahmadi

Abstract

Genomic selection (GS) is a promising strategy for enhancing genetic gain. We investigated the accuracy of genomic estimated breeding values (GEBV) in four inter-related synthetic populations that underwent several cycles of recurrent selection in an upland rice-breeding program. A total of 343 S2:4 lines extracted from those populations were phenotyped for flowering time, plant height, grain yield and panicle weight, and genotyped with an average density of one marker per 44.8 kb. The relative effect of the linkage disequilibrium (LD) and minor allele frequency (MAF) thresholds for selecting markers, the relative size of the training population (TP) and of the validation population (VP), the selected trait and the genomic prediction models (frequentist and Bayesian) on the accuracy of GEBVs was investigated in 540 cross validation experiments with 100 replicates. The effect of kinship between the training and validation populations was tested in an additional set of 840 cross validation experiments with a single genomic prediction model. LD was high (average r2 = 0.59 at 25 kb) and decreased slowly, distribution of allele frequencies at individual loci was markedly skewed toward unbalanced frequencies (MAF average value 15.2% and median 9.6%), and differentiation between the four synthetic populations was low (FST ≤0.06). The accuracy of GEBV across all cross validation experiments ranged from 0.12 to 0.54 with an average of 0.30. Significant differences in accuracy were observed among the different levels of each factor investigated. Phenotypic traits had the biggest effect, and the size of the incidence matrix had the smallest. Significant first degree interaction was observed for GEBV accuracy between traits and all the other factors studied, and between prediction models and LD, MAF and composition of the TP. The potential of GS to accelerate genetic gain and breeding options to increase the accuracy of predictions are discussed.

Suggested Citation

  • 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.
    • Handle: RePEc:plo:pone00:0136594
    DOI: 10.1371/journal.pone.0136594
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    References listed on IDEAS

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    Cited by:

    1. 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.
    2. Muhammad Junaid Zaghum & Kashir Ali & Sheng Teng, 2022. "Integrated Genetic and Omics Approaches for the Regulation of Nutritional Activities in Rice ( Oryza sativa L.)," Agriculture, MDPI, vol. 12(11), pages 1-17, October.
    3. Julien Frouin & Axel Labeyrie & Arnaud Boisnard & Gian Attilio Sacchi & Nourollah Ahmadi, 2019. "Genomic prediction offers the most effective marker assisted breeding approach for ability to prevent arsenic accumulation in rice grains," PLOS ONE, Public Library of Science, vol. 14(6), pages 1-22, June.

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