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Bud dormancy is an adaptive process that allows trees to survive the hard environmental conditions that they experience during the winter of temperate climates. Dormancy is characterized by the reduction in meristematic activity and the absence of visible growth. A prolonged exposure to cold temperatures is required to allow the bud resuming growth in response to warm temperatures. In fruit tree species, the dormancy cycle is believed to be regulated by a group of genes encoding MADS-box transcription factors. These genes are called ( ) and are phylogenetically related to the floral regulators ( ) and . The interest in and other orthologs of ( -like) genes has notably increased due to the publication of several reports suggesting their role in the control of bud dormancy in numerous fruit species, including apple, pear, peach, Japanese apricot, and kiwifruit among others. In this review, we briefly describe the physiological bases of the dormancy cycle and how it is genetically regulated, with a particular emphasis on and -like genes. We also provide a detailed report of the most recent advances about the transcriptional regulation of these genes by seasonal cues, epigenetics and plant hormones. From this information, we propose a tentative classification of and -like genes based on their seasonal pattern of expression. Furthermore, we discuss the potential biological role of and -like genes in bud dormancy in antagonizing the function of -like genes. Finally, we draw a global picture of the possible role of and -like genes in the bud dormancy cycle and propose a model that integrates these genes in a molecular network of dormancy cycle regulation in temperate fruit trees.

Background Auxin is an important phytohormone for fleshy fruit development, having been shown to be involved in the initial signal for fertilisation, fruit size through the control of cell division and cell expansion, and ripening related events. There is considerable knowledge of auxin-related genes, mostly from work in model species. With the apple genome now available, it is possible to carry out genomics studies on auxin-related genes to identify genes that may play roles in specific stages of apple fruit development. Results High amounts of auxin in the seed compared with the fruit cortex were observed in 'Royal Gala' apples, with amounts increasing through fruit development. Injection of exogenous auxin into developing apples at the start of cell expansion caused an increase in cell size. An expression analysis screen of auxin-related genes involved in auxin reception, homeostasis, and transcriptional regulation showed complex patterns of expression in each class of gene. Two mapping populations were phenotyped for fruit size over multiple seasons, and multiple quantitative trait loci (QTLs) were observed. One QTL mapped to a region containing an Auxin Response Factor ( ARF106 ). This gene is expressed during cell division and cell expansion stages, consistent with a potential role in the control of fruit size. Conclusions The application of exogenous auxin to apples increased cell expansion, suggesting that endogenous auxin concentrations are at least one of the limiting factors controlling fruit size. The expression analysis of ARF106 linked to a strong QTL for fruit weight suggests that the auxin signal regulating fruit size could partially be modulated through the function of this gene. One class of gene ( GH3 ) removes free auxin by conjugation to amino acids. The lower expression of these GH3 genes during rapid fruit expansion is consistent with the apple maximising auxin concentrations at this point.

Although flowering in mature fruit trees is recurrent, floral induction can be strongly inhibited by concurrent fruiting, leading to a pattern of irregular fruiting across consecutive years referred to as biennial bearing. The genetic determinants of biennial bearing in apple were investigated using the 114 flowering individuals from an F₁ population of 122 genotypes, from a ‘Starkrimson’ (strong biennial bearer)בGranny Smith’ (regular bearer) cross. The number of inflorescences, and the number and the mass of harvested fruit were recorded over 6 years and used to calculate 26 variables and indices quantifying yield, precocity of production, and biennial bearing. Inflorescence traits exhibited the highest genotypic effect, and three quantitative trait loci (QTLs) on linkage group (LG) 4, LG8, and LG10 explained 50% of the phenotypic variability for biennial bearing. Apple orthologues of flowering and hormone-related genes were retrieved from the whole-genome assembly of ‘Golden Delicious’ and their position was compared with QTLs. Four main genomic regions that contain floral integrator genes, meristem identity genes, and gibberellin oxidase genes co-located with QTLs. The results indicated that flowering genes are less likely to be responsible for biennial bearing than hormone-related genes. New hypotheses for the control of biennial bearing emerged from QTL and candidate gene co-locations and suggest the involvement of different physiological processes such as the regulation of flowering genes by hormones. The correlation between tree architecture and biennial bearing is also discussed.

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.

Irregular flowering over years is commonly observed in fruit trees. The early prediction of tree behavior is highly desirable in breeding programmes. This study aims at performing such predictions, combining simplified phenotyping and statistics methods. Sequences of vegetative vs. floral annual shoots (AS) were observed along axes in trees belonging to five apple related full-sib families. Sequences were analyzed using Markovian and linear mixed models including year and site effects. Indices of flowering irregularity, periodicity and synchronicity were estimated, at tree and axis scales. They were used to predict tree behavior and detect QTL with a Bayesian pedigree-based analysis, using an integrated genetic map containing 6,849 SNPs. The combination of a Biennial Bearing Index (BBI) with an autoregressive coefficient (γ ) efficiently predicted and classified the genotype behaviors, despite few misclassifications. Four QTLs common to BBIs and γ and one for synchronicity were highlighted and revealed the complex genetic architecture of the traits. Irregularity resulted from high AS synchronism, whereas regularity resulted from either asynchronous locally alternating or continual regular AS flowering. A relevant and time-saving method, based on sampling of axes and statistical indices is proposed, which is efficient to evaluate the tree breeding values for flowering regularity and could be transferred to other species.

Background The transition from vegetative to floral state in shoot apical meristems (SAM) is a key event in plant development and is of crucial importance for reproductive success. In perennial plants, this event is recurrent during tree life and subject to both within-tree and between-years heterogeneity. In the present study, our goal was to identify candidate processes involved in the repression or induction of flowering in apical buds of adult apple trees. Results Genes differentially expressed (GDE) were examined between trees artificially set in either ‘ON’ or ‘OFF’ situation, and in which floral induction (FI) was shown to be inhibited or induced in most buds, respectively, using qRT-PCR and microarray analysis. From the period of FI through to flower differentiation, GDE belonged to four main biological processes (i) response to stimuli, including response to oxidative stress; (ii) cellular processes, (iii) cell wall biogenesis, and (iv) metabolic processes including carbohydrate biosynthesis and lipid metabolic process. Several key regulator genes, especially TEMPRANILLO ( TEM ), FLORAL TRANSITION AT MERISTEM ( FTM1 ) and SQUAMOSA PROMOTER BINDING PROTEIN-LIKE ( SPL ) were found differentially expressed. Moreover, homologs of SPL and Leucine-Rich Repeat proteins were present under QTL zones previously detected for biennial bearing. Conclusions This data set suggests that apical buds of ‘ON’ and ‘OFF’ trees were in different physiological states, resulting from different metabolic, hormonal and redox status which are likely to contribute to FI control in adult apple trees. Investigations on carbohydrate and hormonal fluxes from sources to SAM and on cell detoxification process are expected to further contribute to the identification of the underlying physiological mechanisms of FI in adult apple trees.

Linkage maps are needed for genetic studies and molecular breeding of taro ( Colocasia esculenta ). In this study, we used genotyping-by-sequencing (GBS) to identify single nucleotide polymorphism (SNP) loci on two mapping populations: F31 (HLB11 × VU006) composed of 266 progenies and F32 [HLB01 × (VU370×ID316)] composed of 292 progenies. SNP calling generated an initial set of 22,734 SNPs for F31 and 16,744 for F32. A large proportion of individuals and loci were later removed by filtering on the proportion of missing data and segregation distortions. Linkage maps were constructed with filtered SNPs in association with 14 simple sequence repeat (SSR) markers, using the maximum likelihood method. In both populations, loci were successfully grouped into 14 linkage groups (LGs) with an independence logarithm of odds (LOD) threshold of 11.0 and 8.0 for F31 and F32, respectively. LGs ranged in size from 90 to 15 markers for F31 and from 92 to 12 markers for F32. Bridge markers (459 SNPs and 9 SSRs) were identified and revealed homologous groups between families. Although our maps presented unprecedented chromosome coverage, the colinearity between homologous groups was low (except for LG07), and map lengths were globally inflated. Putative effects of missing data, segregation distortion, and genotyping errors on map accuracy are discussed. This research work led to the identification of a reliable set of SNPs potentially useful as a tool for a wide range of genetic studies in taro.

Because irregular bearing generates major agronomic issues in fruit-tree species, particularly in apple, the selection of regular cultivars is desirable. Here, we aimed to define methods and descriptors allowing a diagnostic for bearing behaviour during the first years of tree maturity, when tree production is increasing. Flowering occurrences were collected at whole-tree and (annual) shoot scales on a segregating apple population. At both scales, the number of inflorescences over the years was modelled. Two descriptors were derived from model residuals: a new biennial bearing index, based on deviation around yield trend over years and an autoregressive coefficient, which represents dependency between consecutive yields. At the shoot scale, entropy was also considered to represent the within-tree flowering synchronicity. Clusters of genotypes with similar bearing behaviours were built. Both descriptors at the whole-tree and shoot scales were consistent for most genotypes and were used to discriminate regular from biennial and irregular genotypes. Quantitative trait loci were detected for the new biennial bearing index at both scales. Combining descriptors at a local scale with entropy showed that regular bearing at the tree scale may result from different strategies of synchronization in flowering at the local scale. The proposed methods and indices open an avenue to quantify bearing behaviour during the first years of tree maturity and to capture genetic variations. Their extension to other progenies and species, possible variants of descriptors, and their use in breeding programmes considering a limited number of years or fruit yields are discussed.

Background: Auxin is an important phytohormone for fleshy fruit development, having been shown to be involved in the initial signal for fertilisation, fruit size through the control of cell division and cell expansion, and ripening related events. There is considerable knowledge of auxin-related genes, mostly from work in model species. With the apple genome now available, it is possible to carry out genomics studies on auxin-related genes to identify genes that may play roles in specific stages of apple fruit development. Results: High amounts of auxin in the seed compared with the fruit cortex were observed in ‘Royal Gala’ apples, with amounts increasing through fruit development. Injection of exogenous auxin into developing apples at the start of cell expansion caused an increase in cell size. An expression analysis screen of auxin-related genes involved in auxin reception, homeostasis, and transcriptional regulation showed complex patterns of expression in each class of gene. Two mapping populations were phenotyped for fruit size over multiple seasons, and multiple quantitative trait loci (QTLs) were observed. One QTL mapped to a region containing an Auxin Response Factor (ARF106). This gene is expressed during cell division and cell expansion stages, consistent with a potential role in the control of fruit size. Conclusions: The application of exogenous auxin to apples increased cell expansion, suggesting that endogenous auxin concentrations are at least one of the limiting factors controlling fruit size. The expression analysis of ARF106 linked to a strong QTL for fruit weight suggests that the auxin signal regulating fruit size could partially be modulated through the function of this gene. One class of gene (GH3) removes free auxin by conjugation to amino acids. The lower expression of these GH3 genes during rapid fruit expansion is consistent with the apple maximising auxin concentrations at this point.

Linkage maps are needed for genetic studies and molecular breeding of taro (Colocasia esculenta). In this study, we used genotyping-by-sequencing (GBS) to identify single nucleotide polymorphism (SNP) loci on two mapping populations: F31 (HLB11 × VU006) composed of 266 progenies and F32 [HLB01 × (VU370×ID316)] composed of 292 progenies. SNP calling generated an initial set of 22,734 SNPs for F31 and 16,744 for F32. A large proportion of individuals and loci were later removed by filtering on the proportion of missing data and segregation distortions. Linkage maps were constructed with filtered SNPs in association with 14 simple sequence repeat (SSR) markers, using the maximum likelihood method. In both populations, loci were successfully grouped into 14 linkage groups (LGs) with an independence logarithm of odds (LOD) threshold of 11.0 and 8.0 for F31 and F32, respectively. LGs ranged in size from 90 to 15 markers for F31 and from 92 to 12 markers for F32. Bridge markers (459 SNPs and 9 SSRs) were identified and revealed homologous groups between families. Although our maps presented unprecedented chromosome coverage, the colinearity between homologous groups was low (except for LG07), and map lengths were globally inflated. Putative effects of missing data, segregation distortion, and genotyping errors on map accuracy are discussed. This research work led to the identification of a reliable set of SNPs potentially useful as a tool for a wide range of genetic studies in taro.