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Genomic selection in rubber tree breeding: A comparison of models and methods for managing G×E interactions

Souza Livia Moura, Francisco Felipe O., Gonçalves Paulo De Souza, Scaloppi Junior Erivaldo José, Le Guen Vincent, Fritsche-Neto Roberto, Souza Anete Pereira. 2019. Genomic selection in rubber tree breeding: A comparison of models and methods for managing G×E interactions. Frontiers in Plant Science, 10:1353, 14 p.

Journal article ; Article de recherche ; Article de revue à facteur d'impact Revue en libre accès total
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Quartile : Q1, Sujet : PLANT SCIENCES

Abstract : Several genomic prediction models combining genotype × environment (G×E) interactions have recently been developed and used for genomic selection (GS) in plant breeding programs. G×E interactions reduce selection accuracy and limit genetic gains in plant breeding. Two data sets were used to compare the prediction abilities of multienvironment G×E genomic models and two kernel methods. Specifically, a linear kernel, or GB (genomic best linear unbiased predictor [GBLUP]), and a nonlinear kernel, or Gaussian kernel (GK), were used to compare the prediction accuracies (PAs) of four genomic prediction models: 1) a single-environment, main genotypic effect model (SM); 2) a multienvironment, main genotypic effect model (MM); 3) a multienvironment, single-variance G×E deviation model (MDs); and 4) a multienvironment, environment-specific variance G×E deviation model (MDe). We evaluated the utility of genomic selection (GS) for 435 individual rubber trees at two sites and genotyped the individuals via genotyping-by-sequencing (GBS) of single-nucleotide polymorphisms (SNPs). Prediction models were used to estimate stem circumference (SC) during the first 4 years of tree development in conjunction with a broad-sense heritability (H2) of 0.60. Applying the model (SM, MM, MDs, and MDe) and kernel method (GB and GK) combinations to the rubber tree data revealed that the multienvironment models were superior to the single-environment genomic models, regardless of the kernel (GB or GK) used, suggesting that introducing interactions between markers and environmental conditions increases the proportion of variance explained by the model and, more importantly, the PA. Compared with the classic breeding method (CBM), methods in which GS is incorporated resulted in a 5-fold increase in response to selection for SC with multienvironment GS (MM, MDe, or MDs). Furthermore, GS resulted in a more balanced selection response for SC and contributed to a reduction in selection time when used in conjunction with traditional genetic breeding programs. Given the rapid advances in genotyping methods and their declining costs and given the overall costs of large-scale progeny testing and shortened breeding cycles, we expect GS to be implemented in rubber tree breeding programs.

Mots-clés Agrovoc : Hevea brasiliensis, Sélection, Intéraction génotype environnement

Mots-clés géographiques Agrovoc : Brésil

Mots-clés libres : Hevea brasiliensis, Breeding, Multienvironment trials (MET), Single nucleotide, Genotyping by sequencing

Classification Agris : K10 - Forestry production
F30 - Plant genetics and breeding

Champ stratégique Cirad : CTS 1 (2019-) - Biodiversité

Auteurs et affiliations

  • Souza Livia Moura, UNICAMP (BRA) - auteur correspondant
  • Francisco Felipe O., UNICAMP (BRA) - auteur correspondant
  • Gonçalves Paulo De Souza, IAC (BRA)
  • Scaloppi Junior Erivaldo José, IAC (BRA)
  • Le Guen Vincent, CIRAD-BIOS-UMR AGAP (FRA)
  • Fritsche-Neto Roberto, ESALQ (BRA)
  • Souza Anete Pereira, UNICAMP (BRA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/594116/)

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