Improving the accuracy of genomic predictions in an outcrossing species with hybrid cultivars between heterozygote parents: A case study of oil palm (Elaeis guineensis Jacq.)

Nyouma Achille, Bell Joseph Martin, Jacob Florence, Riou Virginie, Manez Aurore, Pomiès Virginie, Domonhedo Hubert, Arifiyanto Deni, Cochard Benoît, Durand-Gasselin Tristan, Cros David. 2022. Improving the accuracy of genomic predictions in an outcrossing species with hybrid cultivars between heterozygote parents: A case study of oil palm (Elaeis guineensis Jacq.). Molecular Genetics and Genomics, 297 : 523-533.

Résumé : Genomic selection (GS) is a method of marker-assisted selection revolutionizing crop improvement, but it can still be optimized. For hybrid breeding between heterozygote parents of different populations or species, specific aspects can be considered to increase GS accuracy: (1) training population genotyping, i.e., only genotyping the hybrid parents or also a sample of hybrid individuals, and (2) marker effects modeling, i.e., using population-specific effects of single nucleotide polymorphism alleles model (PSAM) or across-population SNP genotype model (ASGM). Here, this was investigated empirically for the prediction of the performances of oil palm hybrids for yield traits. The GS model was trained on 352 hybrid crosses and validated on 213 independent hybrid crosses. The training and validation hybrid parents and 399 training hybrid individuals were genotyping by sequencing. Despite the small proportion of hybrid individuals genotyped and low parental heterozygosity, GS prediction accuracy increased on average by 5% (range 1.4–31.3%, depending on trait and model) when training was done using genomic data on hybrids and parents compared with only parental genomic data. With ASGM, GS prediction accuracy increased on average by 3% (− 10.2 to 40%, depending on trait and genotyping strategy) compared with PSAM. We conclude that the best GS strategy for oil palm is to aggregate genomic data of parents and hybrid individuals and to ignore the parental origin of marker alleles (ASGM). To gain a better insight into these results, future studies should examine the respective effect of capturing genetic variability within crosses and taking segregation distortion into account when genotyping hybrid individuals, and investigate the factors controlling the relative performances of ASGM and PSAM in hybrid crops.

Mots-clés Agrovoc : Elaeis guineensis, sélection assistée par marqueurs, hybride, génotype, modèle, méthode d'amélioration génétique, séquençage à haut débit, technique génétique

Mots-clés géographiques Agrovoc : Asie, Inde, Afrique, Angola, Côte d'Ivoire, République démocratique du Congo, Congo

Mots-clés libres : Sélection génomique, Genomic selection, Hybrid breeding, Oil Palm

Classification Agris : F30 - Génétique et amélioration des plantes

Champ stratégique Cirad : CTS 2 (2019-) - Transitions agroécologiques

Auteurs et affiliations

• Nyouma Achille, Université de Yaoundé 1 (CMR)
• Bell Joseph Martin, Université de Yaoundé 1 (CMR)
• Jacob Florence, PalmElit (FRA)
• Riou Virginie, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-6569-4363
• Manez Aurore, CIRAD-BIOS-UMR AGAP (FRA)
• Pomiès Virginie, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-5481-5120
• Domonhedo Hubert, INRAB (BEN)
• Arifiyanto Deni, SOCFINDO (IDN)
• Cochard Benoît, PalmElit (FRA)
• Durand-Gasselin Tristan, PalmElit (FRA)
• Cros David, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-8601-7991 - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/600292/)

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