Target enrichment sequencing coupled with GWAS identifies MdPRX10 as a candidate gene in the control of budbreak in apple

Watson Amy E., Guitton Baptiste, Soriano Alexandre, Rivallan Ronan, Vignes Hélène, Farrera Isabelle, Huettel Bruno, Arnaiz Catalina, da Silveira Falavigna Vítor, Coupel-Ledru Aude, Segura Vincent, Sarah Gautier, Dufayard Jean François, Sidibe-Bocs Stéphanie, Costes Evelyne, Andres Fernando. 2024. Target enrichment sequencing coupled with GWAS identifies MdPRX10 as a candidate gene in the control of budbreak in apple. Frontiers in Plant Science, 15:1352757, 19 p.

Url - jeu de données - Entrepôt autre : https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1023873

Résumé : The timing of floral budbreak in apple has a significant effect on fruit production and quality. Budbreak occurs as a result of a complex molecular mechanism that relies on accurate integration of external environmental cues, principally temperature. In the pursuit of understanding this mechanism, especially with respect to aiding adaptation to climate change, a QTL at the top of linkage group (LG) 9 has been identified by many studies on budbreak, but the genes underlying it remain elusive. Here, together with a dessert apple core collection of 239 cultivars, we used a targeted capture sequencing approach to increase SNP resolution in apple orthologues of known or suspected A. thaliana flowering time-related genes, as well as approximately 200 genes within the LG9 QTL interval. This increased the 275 223 SNP Axiom® Apple 480 K array dataset by an additional 40 857 markers. Robust GWAS analyses identified MdPRX10, a peroxidase superfamily gene, as a strong candidate that demonstrated a dormancy-related expression pattern and down-regulation in response to chilling. In-silico analyses also predicted the residue change resulting from the SNP allele associated with late budbreak could alter protein conformation and likely function. Late budbreak cultivars homozygous for this SNP allele also showed significantly up-regulated expression of C-REPEAT BINDING FACTOR (CBF) genes, which are involved in cold tolerance and perception, compared to reference cultivars, such as Gala. Taken together, these results indicate a role for MdPRX10 in budbreak, potentially via redox-mediated signaling and CBF gene regulation. Moving forward, this provides a focus for developing our understanding of the effects of temperature on flowering time and how redox processes may influence integration of external cues in dormancy pathways.

Mots-clés Agrovoc : expression des gènes, séquence nucléotidique, variété, Malus, changement climatique, polymorphisme génétique, Malus pumila, adaptation aux changements climatiques, génome, Transcription génique, phénotype, repos végétatif

Mots-clés géographiques Agrovoc : France

Mots-clés libres : Capture, Dormancy, Budbreak, Flowering, Peroxidase, Redox, CBF, Cold-perception

Agences de financement hors UE : ERA-NET, Agence Nationale de la Recherche, Agropolis Fondation

Projets sur financement : (FRA) Predicting and tuning seasonal responses of apple and peach to improve orchard yield and climate change resilience, (FRA) Labex Agro

Auteurs et affiliations

• Watson Amy E., INRAE (FRA)
• Guitton Baptiste, Université de Montpellier (FRA)
• Soriano Alexandre, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-1406-4606
• Rivallan Ronan, CIRAD-BIOS-UMR AGAP (FRA)
• Vignes Hélène, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-8725-2467
• Farrera Isabelle, Montpellier SupAgro (FRA)
• Huettel Bruno, MPIZ (DEU)
• Arnaiz Catalina, UPM (ESP)
• da Silveira Falavigna Vítor, Max Planck Institute for Plant Breeding Research (DEU)
• Coupel-Ledru Aude, Université de Montpellier (FRA)
• Segura Vincent, INRAE (FRA)
• Sarah Gautier, INRAE (FRA)
• Dufayard Jean François, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-7427-6822
• Sidibe-Bocs Stéphanie, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-7850-4426
• Costes Evelyne, INRAE (FRA) - auteur correspondant
• Andres Fernando, INRAE (FRA) - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/610025/)

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