A genome-wide assessment of the genetic diversity, evolution and relationships with allied species of the clonally propagated crop Vanilla planifolia Jacks. ex Andrews

Favre Félicien, Jourda Cyril, Grisoni Michel, Piet Quentin, Rivallan Ronan, Dijoux Jean-Bernard, Hascoat Jérémy, Lepers-Andrzejewski Sandra, Besse Pascale, Charron Carine. 2022. A genome-wide assessment of the genetic diversity, evolution and relationships with allied species of the clonally propagated crop Vanilla planifolia Jacks. ex Andrews. Genetic Resources and Crop Evolution, 69 : 2125-2139.

Note générale : The raw sequence data have been deposited in the Short Read Archive under NCBI BioProject ID PRJNA756864. Biological samples used in this study have been deposited in the BioSamples Database under the accession identifier SAMN 20,927,883 to 20,928,015, and SAMN20981991 to SAMN20981994.

Résumé : The Vanilla genus is a complex taxonomic group characterized by a vegetative reproduction mode combined with intra- and inter-specific hybridizations, and polyploidy events. These factors strongly impact the diversification of the genus and complicate the delimitation of taxa. Among the hundred Vanilla species, Vanilla planifolia Jacks. ex Andrews and Vanilla × tahitensis J. W. Moore are the main cultivated aromatic species. We applied Genotyping-by-Sequencing to explore the genetic diversity of these two cultivated vanilla species, seven closely related species and nineteen interspecific hybrids. The inter- and intra-specific relationships of 133 vanilla accessions were examined based on 2004 filtered SNPs. Our results showed a strong genetic structuring between the nine species studied, with wild species showing much lower heterozygosity levels than cultivated ones. Moreover, using Bayesian clustering analyses, the kinship of several hybrids could be verified. We evidenced in particular that Vanilla sotoarenasii and Vanilla odorata C.Presl may be the parental species of V. x tahitensis. The analysis of 1129 SNPs for 84 V. planifolia accessions showed a clear genetic demarcation between the vegetatively propagated traditional vanilla cultivars compared to the accessions derived from sexual reproduction, and a higher genetic diversity and lower heterozygosity of the latter (Ho = 0.206) compared to the former (Ho = 0.362). Our data are consistent with a single-step domestication for V. planifolia in accordance with the recent history of its cultivation. It also opens avenues to breed new V. planifolia varieties adapted to biotic and abiotic constraints and to reduce mutational load induced by clonal propagation.

Mots-clés Agrovoc : phytogénétique, diversité génétique (comme ressource), domestication des plantes, génotype, Vanilla planifolia

Mots-clés libres : Breeding, Domestication, Vanilla, GBS

Classification Agris : F30 - Génétique et amélioration des plantes
F40 - Écologie végétale

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

Agences de financement européennes : European Regional Development Fund

Agences de financement hors UE : Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Université de La Réunion, Conseil Régional de La Réunion, Consejo Nacional de Ciencia y Tecnología

Projets sur financement : (MEX) Estrategias para la adaptacion y mitigacion al cambio climatico necesarias para el rescate del cultivo de la vainilla en Mexico

Auteurs et affiliations

• Favre Félicien, Université de la Réunion (REU)
• Jourda Cyril, CIRAD-BIOS-UMR PVBMT (REU) ORCID: 0000-0002-7799-3501
• Grisoni Michel, CIRAD-BIOS-UMR PVBMT (MDG) ORCID: 0000-0001-9867-9098
• Piet Quentin, CIRAD-BIOS-UMR PVBMT (REU)
• Rivallan Ronan, CIRAD-BIOS-UMR AGAP (FRA)
• Dijoux Jean-Bernard, CIRAD-BIOS-UMR PVBMT (REU)
• Hascoat Jérémy, CIRAD-BIOS-UMR PVBMT (REU)
• Lepers-Andrzejewski Sandra, Etablissement vanille de Tahiti (PYF)
• Besse Pascale, Université de la Réunion (REU)
• Charron Carine, CIRAD-BIOS-UMR PVBMT (REU) ORCID: 0000-0003-0281-9936 - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/600684/)

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