Abstract
Flower development and budbreak timing are key determinants of final crop yield in apple but their genetic underpinnings are not well understood. Furthermore, they are greatly influenced by climatic conditions, rendering them vulnerable to the effects of seasonal temperature shifts. Improved understanding of their genetic regulation could help in limiting this potential damage to fruit production. Curated collections of diverse cultivars are an invaluable tool in identifying genes controlling important traits. A 242-cultivar French dessert apple (Malus domestica) core collection, representing 90% of the total allelic variability of this apple type, was derived from a large germplasm collection. The diverse floral phenotypes evident in the collection make it ideal for quantitative analyses. In addition, all cultivars were genotyped with both the Axiom® Apple 480K array and targeted capture sequencing of known or suspected flowering-related genes. This population, located near Montpellier in France, is the focus of two projects, FruitFlow (SusCrop ERA-NET) and FlowCODE (MSCA Fellowship), which aim to exploit this diversity to explore the genetics of flowering time and floral induction, respectively. FruitFlow, enabled by high SNP resolution within flowering-related genes and nine years of phenology data from the core collection, identified a strong candidate within a well-known QTL on chromosome 9 associated with flowering time, using a GWAS approach. This candidate, MdPEROXIDASE 10 (MdPRX10), may be involved in regulating redox status, which has been linked to budbreak in several fruit species. Furthermore, previously published RNAseq data indicated an expression pattern linked to cold-induced dormancy and in-silico analyses predicted the SNP allele associated with late flowering would likely disrupt MdPRX10 function. In addition, cultivars homozygous forthis ‘late’ allele showed significantly up-regulated expression of C-REPEATBINDING FACTOR (CBF) genes, which are involved in cold tolerance and perception. Taken together, these results indicate a role for MdPRX10 in budbreak, potentially via redox-mediated signalling and CBF gene regulation. Moving forward, the project FlowCODE aims to characterise transcriptional regulation of floral induction (FI) in apple, the decision enabling a meristem to produce a floral bud. The central FI mechanism appears highly conserved in annual species, but as it is the regulation of this process that enables environmental adaptation, it is likely very different within a perennial lifecycle with dormancy requirements, such as in apple. In Arabidopsis, FI is activated via multiple environmental and internal cues within various flowering pathways that converge at the highly homologous genes, FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1 (TFL1), an FI promoter and inhibitor, respectively. FlowCODE will decipher the molecular control of FI in apple by combining molecular and quantitative approaches to discover cis and trans loci associated to the gene transcription of the apple FT and TFL1 orthologues, MdFT and MdTFL1. For this, leaves and meristems from short shoots were sampled from all core collection cultivars in the period during which FI occurs. Expression levels of MdFT and MdTFL1 genes will be measured using qPCR and an expression QTL (eQTL) analysis performed. Any detected cis elements will be examined for known binding motifs. In parallel, yeast one-hybrid and dual luciferase reporter assays will be used to reveal interactions between any eQTL-detected TFs or flowering-related TFs from the capture sequence library and the regulatory regions of MdFT and MdTFL1 genes. These two projects demonstrate the utility of diversity panels like the core collection to better understand the molecular mechanisms underlying important traits and will enable development of more resilient varieties of apple.