Genome properties of key oil palm (Elaeis guineensis Jacq.) breeding populations

Seyum Essubalew Getachew, Ngalle Bille Hermine, Abtew Wosene Gebreselassie, Rastas Pasi, Arifianto Deni, Domonhedo Hubert, Cochard Benoît, Jacob Florence, Riou Virginie, Pomies Virginie, Lopez David, Bell Joseph Martin, Cros David. 2022. Genome properties of key oil palm (Elaeis guineensis Jacq.) breeding populations. Journal of Applied Genetics, 63 : 633-650.

Résumé : A good knowledge of the genome properties of the populations makes it possible to optimize breeding methods, in particular genomic selection (GS). In oil palm (Elaeis guineensis Jacq), the world's main source of vegetable oil, this would provide insight into the promising GS results obtained so far. The present study considered two complex breeding populations, Deli and La Mé, with 943 individuals and 7324 single-nucleotide polymorphisms (SNPs) from genotyping-by-sequencing. Linkage disequilibrium (LD), haplotype sharing, effective size (Ne), and fixation index (Fst) were investigated. A genetic linkage map spanning 1778.52 cM and with a recombination rate of 2.85 cM/Mbp was constructed. The LD at r2=0.3, considered the minimum to get reliable GS results, spanned over 1.05 cM/0.22 Mbp in Deli and 0.9 cM/0.21 Mbp in La Mé. The significant degree of differentiation existing between Deli and La Mé was confirmed by the high Fst value (0.53), the pattern of correlation of SNP heterozygosity and allele frequency among populations, and the decrease of persistence of LD and of haplotype sharing among populations with increasing SNP distance. However, the level of resemblance between the two populations over short genomic distances (correlation of r values between populations >0.6 for SNPs separated by <0.5 cM/1 kbp and percentage of common haplotypes >40% for haplotypes <3600 bp/0.20 cM) likely explains the superiority of GS models ignoring the parental origin of marker alleles over models taking this information into account. The two populations had low Ne (<5). Population-specific genetic maps and reference genomes are recommended for future studies.

Mots-clés Agrovoc : phytogénétique, génétique des populations, Elaeis guineensis, génome, sélection, carte génétique, amélioration des cultures

Mots-clés libres : Palmier à huile, Oil Palm, Linkage disequilibrium, Population genetics, Haplotypes

Classification Agris : F30 - Génétique et amélioration des plantes
F02 - Multiplication végétative des plantes

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

Agences de financement européennes : European Commission

Auteurs et affiliations

• Seyum Essubalew Getachew, University of Yaounde 1 (CMR)
• Ngalle Bille Hermine, University of Yaounde 1 (CMR)
• Abtew Wosene Gebreselassie, Jimma University College of Agriculture and Veterinary Medicine (ETH)
• Rastas Pasi, University of Helsinki (FIN)
• Arifianto Deni, SOCFINDO (IDN)
• Domonhedo Hubert, INRAB (BEN)
• Cochard Benoît, PalmElit (FRA)
• Jacob Florence, PalmElit (FRA)
• Riou Virginie, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-6569-4363
• Pomies Virginie, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-5481-5120
• Lopez David, CIRAD-BIOS-UMR AGAP (FRA)
• Bell Joseph Martin, Université de Yaoundé 1 (CMR)
• Cros David, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-8601-7991 - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/601137/)

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