Genomic predictions improve clonal selection in oil palm (Elaeis guineensis Jacq.) hybrids

Nyouma Achille, Bell Joseph Martin, Jacob Florence, Riou Virginie, Manez Aurore, Pomiès Virginie, Nodichao Leifi, Syahputra Indra, Affandi Dadang, Cochard Benoît, Durand-Gasselin Tristan, Cros David. 2020. Genomic predictions improve clonal selection in oil palm (Elaeis guineensis Jacq.) hybrids. Plant Science, 299:110547, 12 p.

Quartile : Q1, Sujet : PLANT SCIENCES / Quartile : Q2, Sujet : BIOCHEMISTRY & MOLECULAR BIOLOGY

Résumé : The prediction of clonal genetic value for yield is challenging in oil palm (Elaeis guineensis Jacq.). Currently, clonal selection involves two stages of phenotypic selection (PS): ortet preselection on traits with sufficient heritability among a small number of individuals in the best crosses in progeny tests, and final selection on performance in clonal trials. The present study evaluated the efficiency of genomic selection (GS) for clonal selection. The training set comprised almost 300 Deli × La Mé crosses phenotyped for eight palm oil yield components and the validation set 42 Deli × La Mé ortets. Genotyping-by-sequencing (GBS) revealed 15,054 single nucleotide polymorphisms (SNP). The effects of the SNP dataset (density and percentage of missing data) and two GS modeling approaches, ignoring (ASGM) and considering (PSAM) the parental origin of alleles, were assessed. The results showed prediction accuracies ranging from 0.08 to 0.70 for ortet candidates without data records, depending on trait, SNP dataset and modeling. ASGM was better (on average slightly more accurate, less sensitive to SNP dataset and simpler), although PSAM appeared interesting for a few traits. With ASGM, the number of SNPs had to reach 7,000, while the percentage of missing data per SNP was of secondary importance, and GS prediction accuracies were higher than those of PS for most of the traits. Finally, this makes possible two practical applications of GS, that will increase genetic progress by improving ortet preselection before clonal trials: (1) preselection at the mature stage on all yield components jointly using ortet genotypes and phenotypes, and (2) genomic preselection on more yield components than PS, among a large population of the best possible crosses at nursery stage.

Mots-clés Agrovoc : Elaeis guineensis, sélection, marqueur génétique, hybride, clone, sélection assistée par marqueurs

Mots-clés géographiques Agrovoc : Indonésie

Mots-clés complémentaires : Sélection clonale

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

Classification Agris : F30 - Génétique et amélioration des plantes

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

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
• Nodichao Leifi, INRAB (BEN)
• Syahputra Indra, SOCFINDO (IDN)
• Affandi Dadang, 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/596315/)

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