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Link to original content: https://pubmed.ncbi.nlm.nih.gov/26313446
Accuracy of Genomic Selection in a Rice Synthetic Population Developed for Recurrent Selection Breeding - PubMed Skip to main page content
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. 2015 Aug 27;10(8):e0136594.
doi: 10.1371/journal.pone.0136594. eCollection 2015.

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

Cécile Grenier  1 , Tuong-Vi Cao  2 , Yolima Ospina  3 , Constanza Quintero  3 , Marc Henri Châtel  3 , Joe Tohme  3 , Brigitte Courtois  2 , Nourollah Ahmadi  2
Affiliations

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

Cécile Grenier et al. PLoS One. .

Erratum in

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.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Projection of the 343 S2:3 lines on the first plane of a factorial discriminant analysis using (A) phenotypic data and (B) genotypic data.
Fig 2
Fig 2. Mean correlation between GEBV obtained by cross validation of the training data set (Yp) and the observed BLUP values of the validation data sets (Yo).
Results presented for 2 traits, 9 incidence matrices and 3 k-fold cross validation experiments.
Fig 3
Fig 3. Mean correlation between GEBV obtained by cross validation of the training data set (Yp) and the observed BLUP values of the validation data sets (Yo).
The results of 4 different traits and 9 incidence matrices are presented.
Fig 4
Fig 4. Mean correlation between GEBV obtained by cross validation of the training data set (Yp) and the observed BLUP values of the validation data sets (Yo).
The results for flowering date (FL) and plant height (PH) and 15 incidence matrices are presented.
Fig 5
Fig 5. Mean correlation between GEBV obtained by cross validation of the training data set (Yp) and the observed BLUP values of the validation data sets (Yo).
The results for days to flowering (FL), plant height (PH), panicle weight (PW) and grain yield (YLD) and 35 incidence matrices are presented.
Fig 6
Fig 6. Mean correlation between GEBV obtained by cross validation of the training data set (Yp) and the observed BLUP values of the validation data sets (Yo).
Results for day to flowering (FL) are presented for different composition of the validation population (VP).
See this image and copyright information in PMC

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Grants and funding

The research activity was funded as part of the core budget of Cirad, and CIAT (Centro International de Agricultura Tropical) and specific funds from the Agropolis Foundation.