Transcription factor FveMYB117a inhibits axillary bud outgrowth by regulating cytokinin homeostasis in woodland strawberry.

Shoot branching affects plant architecture. In strawberry (Fragaria L.), short branches (crowns) develop from dormant axillary buds to form inflorescences and flowers. While this developmental transition contributes greatly to perenniality and yield in strawberry, its regulatory mechanism remains unclear and understudied. In the woodland strawberry (Fragaria vesca), we identified and characterized two independent mutants showing more crowns. Both mutant alleles reside in FveMYB117a, a R2R3-MYB transcription factor gene highly expressed in shoot apical meristems, axillary buds and young leaves. Transcriptome analysis revealed that the expression of several cytokinin pathway genes was altered in the fvemyb117a mutant. Consistently, active cytokinins were significantly increased in the axillary buds of the fvemyb117a mutant. Exogenous application of cytokinin enhanced crown outgrowth in the wild type, whereas the cytokinin inhibitors suppressed crown outgrowth in the fvemyb117a mutant. FveMYB117a binds directly to the promoters of the cytokinin homeostasis genes FveIPT2 encoding an isopentenyltransferase and FveCKX1 encoding a cytokinin oxidase to regulate their expression. Conversely, the type-B Arabidopsis response regulators FveARR1 and FveARR2b can directly inhibit the expression of FveMYB117a, indicative of a negative feedback regulation. In conclusion, we identified FveMYB117a as a key repressor of crown outgrowth by inhibiting cytokinin accumulation and provide a mechanistic basis for bud fate transition in an herbaceous perennial plant.

Multi-omics provide insights into the regulation of DNA methylation in pear fruit metabolism.

BACKGROUND: Extensive research has been conducted on fruit development in crops, but the metabolic regulatory networks underlying perennial fruit trees remain poorly understood. To address this knowledge gap, we conduct a comprehensive analysis of the metabolome, proteome, transcriptome, DNA methylome, and small RNAome profiles of pear fruit flesh at 11 developing stages, spanning from fruitlet to ripening. Here, we systematically investigate the metabolic landscape and regulatory network involved. RESULTS: We generate an association database consisting of 439 metabolites and 14,399 genes to elucidate the gene regulatory network of pear flesh metabolism. Interestingly, we detect increased DNA methylation in the promoters of most genes within the database during pear flesh development. Application of a DNA methylation inhibitor to the developing fruit represses chlorophyll degradation in the pericarp and promotes xanthophyll, ß-carotene, and abscisic acid (ABA) accumulation in the flesh. We find the gradual increase in ABA production during pear flesh development is correlated with the expression of several carotenoid pathway genes and multiple transcription factors. Of these transcription factors, the zinc finger protein PbZFP1 is identified as a positive mediator of ABA biosynthesis in pear flesh. Most ABA pathway genes and transcription factors are modified by DNA methylation in the promoters, although some are induced by the DNA methylation inhibitor. These results suggest that DNA methylation inhibits ABA accumulation, which may delay fruit ripening. CONCLUSION: Our findings provide insights into epigenetic regulation of metabolic regulatory networks during pear flesh development, particularly with regard to DNA methylation.

Leaf dissection and margin serration are independently regulated by two regulators converging on the CUC2-auxin module in strawberry.

The remarkable diversity of leaf forms allows plants to adapt to their living environment. In general, leaf diversity is shaped by leaf complexity (compound or simple) and leaf margin pattern (entire, serrated, or lobed). Prior studies in multiple species have uncovered a conserved module of CUC2-auxin that regulates both leaf complexity and margin serration. How this module is regulated in different species to contribute to the species-specific leaf form is unclear. Furthermore, the mechanistic connection between leaf complexity and leaf serration regulation is not well studied. Strawberry has trifoliate compound leaves with serrations at the margin. In the wild strawberry Fragaria vesca, a mutant named salad was isolated that showed deeper leaf serrations but normal leaf complexity. SALAD encodes a single-Myb domain protein and is expressed at the leaf margin. Genetic analysis showed that cuc2a is epistatic to salad, indicating that SALAD normally limits leaf serration depth by repressing CUC2a expression. When both Arabidopsis homologs of SALAD were knocked out, deeper serrations were observed in Arabidopsis rosette leaves, supporting a conserved function of SALAD in leaf serration regulation. We incorporated the analysis of a third strawberry mutant simple leaf 1 (sl1) with reduced leaf complexity but normal leaf serration. We showed that SL1 and SALAD independently regulate CUC2a at different stages of leaf development to, respectively, regulate leaf complexity and leaf serration. Our results provide a clear and simple mechanism of how leaf complexity and leaf serration are coordinately as well as independently regulated to achieve diverse leaf forms.

FvDFR2 rather than FvDFR1 play key roles for anthocyanin synthesis in strawberry petioles.

The accumulation of anthocyanins can be found in both the fruit and petioles of strawberries, but the fruit appears red while the petioles appear purple-red. Additionally, in the white-fruited diploid strawberries, the petioles can accumulate anthocyanins normally, suggesting a different synthesis pattern between the petioles and fruits. We screened the EMS mutagenized population of a red-fruited diploid strawberry 'Ruegen' and discovered a mutant which showed no anthocyanin accumulation in the petioles but normal accumulation in the fruit. Through BSA sequencing and allelic test, it was found that a mutation in FvDFR2 was responsible for this phenotype. Furthermore, the complex formed by the interaction between the petiole-specific FvMYB10L and FvTT8 only binds the promoter of FvDFR2 but not FvDFR1, resulting in the expression of only FvDFR2 in the petiole. FvDFR2 can catalyze the conversion of DHQ and eventually the formation of cyanidin and peonidin, giving the petiole a purplish-red color. In the fruit, however, both FvDFR1 and FvDFR2 can be expressed, which can mediate the synthesis of cyanidin and pelargonidin. Our study clearly reveals different regulation of FvDFR1 and FvDFR2 in mediating anthocyanin synthesis in petioles and fruits.

The red/far-red light photoreceptor FvePhyB regulates tissue elongation and anthocyanin accumulation in woodland strawberry.

Light is an important environmental signal that influences plant growth and development. Among the photoreceptors, phytochromes can sense red/far-red light to coordinate various biological processes. However, their functions in strawberry are not yet known. In this study, we identified an EMS mutant, named P8, in woodland strawberry (Fragaria vesca) that showed greatly increased plant height and reduced anthocyanin content. Mapping-by-sequencing revealed that the causal mutation in FvePhyB leads to premature termination of translation. The light treatment assay revealed that FvePhyB is a bona fide red/far-red light photoreceptor, as it specifically inhibits hypocotyl length under red light. Transcriptome analysis showed that the FvePhyB mutation affects the expression levels of genes involved in hormone synthesis and signaling and anthocyanin biosynthesis in petioles and fruits. The srl mutant with a longer internode is caused by a mutation in the DELLA gene FveRGA1 (Repressor of GA1) in the gibberellin pathway. We found that the P8 srl double mutant has much longer internodes than srl, suggesting a synergistic role of FvePhyB and FveRGA1 in this process. Taken together, these results demonstrate the important role of FvePhyB in regulating plant architecture and anthocyanin content in woodland strawberry.

Transcriptional reprogramming of nucleotide metabolism in response to altered pyrimidine availability in Arabidopsis seedlings.

In Arabidopsis seedlings, inhibition of aspartate transcarbamoylase (ATC) and de novo pyrimidine synthesis resulted in pyrimidine starvation and developmental arrest a few days after germination. Synthesis of pyrimidine nucleotides by salvaging of exogenous uridine (Urd) restored normal seedling growth and development. We used this experimental system and transcriptional profiling to investigate genome-wide responses to changes in pyrimidine availability. Gene expression changes at different times after Urd supplementation of pyrimidine-starved seedlings were mapped to major pathways of nucleotide metabolism, in order to better understand potential coordination of pathway activities, at the level of transcription. Repression of de novo synthesis genes and induction of intracellular and extracellular salvaging genes were early and sustained responses to pyrimidine limitation. Since de novo synthesis is energetically more costly than salvaging, this may reflect a reduced energy status of the seedlings, as has been shown in recent studies for seedlings growing under pyrimidine limitation. The unexpected induction of pyrimidine catabolism genes under pyrimidine starvation may result from induction of nucleoside hydrolase NSH1 and repression of genes in the plastid salvaging pathway, diverting uracil (Ura) to catabolism. Identification of pyrimidine-responsive transcription factors with enriched binding sites in highly coexpressed genes of nucleotide metabolism and modeling of potential transcription regulatory networks provided new insights into possible transcriptional control of key enzymes and transporters that regulate nucleotide homeostasis in plants.

Molecular bases of strawberry fruit quality traits: Advances, challenges, and opportunities.

The strawberry is one of the world's most popular fruits, providing humans with vitamins, fibers, and antioxidants. Cultivated strawberry (Fragaria × ananassa) is an allo-octoploid and highly heterozygous, making it a challenge for breeding, quantitative trait locus (QTL) mapping, and gene discovery. Some wild strawberry relatives, such as Fragaria vesca, have diploid genomes and are becoming laboratory models for the cultivated strawberry. Recent advances in genome sequencing and CRISPR-mediated genome editing have greatly improved the understanding of various aspects of strawberry growth and development in both cultivated and wild strawberries. This review focuses on fruit quality traits that are most relevant to the consumers, including fruit aroma, sweetness, color, firmness, and shape. Recently available phased-haplotype genomes, single nucleotide polymorphism (SNP) arrays, extensive fruit transcriptomes, and other big data have made it possible to locate key genomic regions or pinpoint specific genes that underlie volatile synthesis, anthocyanin accumulation for fruit color, and sweetness intensity or perception. These new advances will greatly facilitate marker-assisted breeding, the introgression of missing genes into modern varieties, and precise genome editing of selected genes and pathways. Strawberries are poised to benefit from these recent advances, providing consumers with fruit that is tastier, longer-lasting, healthier, and more beautiful.

Comparison of red raspberry and wild strawberry fruits reveals mechanisms of fruit type specification.

Belonging to Rosaceae, red raspberry (Rubus idaeus) and wild strawberry (Fragaria vesca) are closely related species with distinct fruit types. While the numerous ovaries become the juicy drupelet fruits in raspberry, their strawberry counterparts become dry and tasteless achenes. In contrast, while the strawberry receptacle, the stem tip, enlarges to become a red fruit, the raspberry receptacle shrinks and dries. The distinct fruit-forming ability of homologous organs in these 2 species allows us to investigate fruit type determination. We assembled and annotated the genome of red raspberry (R. idaeus) and characterized its fruit development morphologically and physiologically. Subsequently, transcriptomes of dissected and staged raspberry fruit tissues were compared to those of strawberry from a prior study. Class B MADS box gene expression was negatively associated with fruit-forming ability, which suggested a conserved inhibitory role of class B heterodimers, PISTILLATA/TM6 or PISTILLATA/APETALA3, for fruit formation. Additionally, the inability of strawberry ovaries to develop into fruit flesh was associated with highly expressed lignification genes and extensive lignification of the ovary pericarp. Finally, coexpressed gene clusters preferentially expressed in the dry strawberry achenes were enriched in "cell wall biosynthesis" and "ABA signaling," while coexpressed clusters preferentially expressed in the fleshy raspberry drupelets were enriched in "protein translation." Our work provides extensive genomic resources as well as several potential mechanisms underlying fruit type specification. These findings provide the framework for understanding the evolution of different fruit types, a defining feature of angiosperms.

Auxin biosynthesis gene FveYUC4 is critical for leaf and flower morphogenesis in woodland strawberry.

Auxin plays an essential role in plant growth and development, particularly in fruit development. The YUCCA (YUC) genes encode flavin monooxygenases that catalyze a rate-limiting step in auxin biosynthesis. Mutations that disrupt YUC gene function provide useful tools for dissecting general and specific functions of auxin during plant development. In woodland strawberry (Fragaria vesca), two ethyl methanesulfonate mutants, Y422 and Y1011, have been identified that exhibit severe defects in leaves and flowers. In particular, the width of the leaf blade is greatly reduced, and each leaflet in the mutants has fewer and deeper serrations. In addition, the number and shape of the floral organs are altered, resulting in smaller fruits. Mapping by sequencing revealed that both mutations reside in the FveYUC4 gene, and were therefore renamed as yuc4-1 and yuc4-2. Consistent with a role for FveYUC4 in auxin synthesis, free auxin and its metabolites are significantly reduced in the yuc4 leaves and flowers. This role of FveYUC4 in leaf and flower development is supported by its high and specific expression in young leaves and flower buds using GUS reporters. Furthermore, germline transformation of pYUC4::YUC4, which resulted in elevated expression of FveYUC4 in yuc4 mutants, not only rescued the leaf and flower defects but also produced parthenocarpic fruits. Taken together, our data demonstrate that FveYUC4 is essential for leaf and flower morphogenesis in woodland strawberry by providing auxin hormone at the proper time and in the right tissues.

Roles and evolution of four LEAFY homologs in floral patterning and leaf development in woodland strawberry.

The plant-specific transcription factor LEAFY (LFY), generally maintained as a single-copy gene in most angiosperm species, plays critical roles in flower development. The woodland strawberry (Fragaria vesca) possesses four LFY homologs in the genome; however, their respective functions and evolution remain unknown. Here, we identified and validated that mutations in one of the four LFY homologs, FveLFYa, cause homeotic conversion of floral organs and reiterative outgrowth of ectopic flowers. In contrast to FveLFYa, FveLFYb/c/d appear dispensable under normal growth conditions, as fvelfyc mutants are indistinguishable from wild type and FveLFYb and FveLFYd are barely expressed. Transgenic analysis and yeast one-hybrid assay showed that FveLFYa and FveLFYb, but not FveLFYc and FveLFYd, are functionally conserved with AtLFY in Arabidopsis (Arabidopsis thaliana). Unexpectedly, LFY-binding site prediction and yeast one-hybrid assay revealed that the transcriptional links between LFY and the APETALA1 (AP1) promoter/the large AGAMOUS (AG) intron are missing in F. vesca, which is due to the loss of LFY-binding sites. The data indicate that mutations in cis-regulatory elements could contribute to LFY evolution. Moreover, we showed that FveLFYa is involved in leaf development, as approximately 30% of mature leaves have smaller or fewer leaflets in fvelfya. Phylogenetic analysis indicated that LFY homologs in Fragaria species may arise from recent duplication events in their common ancestor and are undergoing convergent gene loss. Together, these results provide insight into the role of LFY in flower and leaf development in strawberry and have important implications for the evolution of LFY.

Cyclin A participates in the TSO1-MYB3R1 regulatory module to maintain shoot meristem size and fertility in Arabidopsis.

The stem cell pools at the shoot apex and root tip give rise to all the above- and below-ground tissues of a plant. Previous studies in Arabidopsis identified a TSO1-MYB3R1 transcriptional module that controls the number and size of the stem cell pools at the shoot apex and root tip. As TSO1 and MYB3R1 are homologous to components of an animal cell cycle regulatory complex, DREAM, Arabidopsis mutants of TSO1 and MYB3R1 provide valuable tools for investigations into the link between cell cycle regulation and stem cell maintenance in plants. In this study, an Arabidopsis cyclin A gene, CYCA3;4, was identified as a member of the TSO1-MYB3R1 regulatory module and cyca3;4 mutations suppressed the tso1-1 mutant phenotype specifically in the shoot. The work reveals how the TSO1-MYB3R1 module is integrated with the cell cycle machinery to control cell division at the shoot meristem.

Natural variations in the PbCPK28 promoter regulate sugar content through interaction with PbTST4 and PbVHA-A1 in pear.

Soluble sugars play an important role in plant growth, development and fruit quality. Pear fruits have demonstrated a considerable improvement in sugar quality during their long history of selection. However, little is known about the underlying molecular mechanisms accompanying the changes in fruit sugar content as a result of selection by horticulturists. Here, we identified a calcium-dependent protein kinase (PbCPK28), which is located on LG15 and is present within a selective sweep region, thus linked to the quantitative trait loci for soluble solids. Association analysis indicates that a single nucleotide polymorphism-13 variation (SNP13T/C ) in the PbCPK28 regulatory region led to fructose content diversity in pear. Elevated expression of PbCPK28 resulted in significantly increased fructose levels in pear fruits. Furthermore, PbCPK28 interacts with and phosphorylates PbTST4, a proton antiporter, thereby coupling the sugar import into the vacuole with proton export. We demonstrated that residues S277 and S314 of PbTST4 are crucial for its function. Additionally, PbCPK28 interacts with and phosphorylates the vacuolar hydrogen proton pump PbVHA-A1, which could provide proton motive forces for PbTST4. We also found that the T11 and Y120 phosphorylation sites in PbVHA-A1 are essential for its function. Evolution analysis and yeast-two-hybrid results support that the CPK-TST/CPK-VHA-A regulatory network is highly conserved in plants, especially the corresponding phosphorylation sites. Together, our work identifies an agriculturally important natural variation and an important regulatory network, allowing genetic improvement of fruit sugar contents in pears through modulation of PbCPK28 expression and phosphorylation of PbTST4 and PbVHA-A1.

Factor of DNA methylation 1 affects woodland strawberry plant stature and organ size via DNA methylation.

RNA-directed DNA methylation (RdDM) is an epigenetic process that directs silencing to specific genomic regions and loci. The biological functions of RdDM are not well studied in horticultural plants. Here, we isolated the ethyl methane-sulfonate-induced mutant reduced organ size (ros) producing small leaves, flowers, and fruits in woodland strawberry (Fragaria vesca) due to reduced cell numbers compared with that in the wild-type (WT). The candidate mutation causes a premature stop codon in FvH4_6g28780, which shares high similarity to Arabidopsis (Arabidopsis thaliana) Factor of DNA Methylation1 (FDM1) encoding an RdDM pathway component and was named FveFDM1. Consistently, the fvefdm1CR mutants generated by CRISPR/Cas9 also produced smaller organs. Overexpressing FveFDM1 in an Arabidopsis fdm1-1 fdm2-1 double mutant restored DNA methylation at the RdDM target loci. FveFDM1 acts in a protein complex with its homolog Involved in De Novo 2 (FveIDN2). Furthermore, whole-genome bisulfite sequencing revealed that DNA methylation, especially in the CHH context, was remarkably reduced throughout the genome in fvefdm1. Common and specific differentially expressed genes were identified in different tissues of fvefdm1 compared to in WT tissues. DNA methylation and expression levels of several gibberellic acid (GA) biosynthesis and cell cycle genes were validated. Moreover, the contents of GA and auxin were substantially reduced in the young leaves of fvefdm1 compared to in the WT. However, exogenous application of GA and auxin could not recover the organ size of fvefdm1. In addition, expression levels of FveFDM1, FveIDN2, Nuclear RNA Polymerase D1 (FveNRPD1), Domains Rearranged Methylase 2 (FveDRM2), and cell cycle genes were greatly induced by GA treatment. Overall, our work demonstrated the critical roles of FveFDM1 in plant growth and development via RdDM-mediated DNA methylation in horticultural crops.

Two MYB activators of anthocyanin biosynthesis exhibit specialized activities in petiole and fruit of diploid strawberry.

The R2R3-MYB transcription factor FveMYB10 is a major regulator of anthocyanin pigmentation in the red fruits of strawberry. fvemyb10 loss-of-function mutants form yellow fruits but still accumulate purple-colored anthocyanins in the petioles, suggesting that anthocyanin biosynthesis is under distinct regulation in fruits and petioles. From chemical mutagenesis in the diploid wild strawberry Fragaria vesca, we identified a green petioles (gp)-1 mutant that lacks anthocyanins in petioles. Using mapping-by-sequencing and transient functional assays, we confirmed that the causative mutation resides in a FveMYB10-Like (FveMYB10L) gene and that FveMYB10 and FveMYB10L function independently in the fruit and petiole, respectively. In addition to their tissue-specific regulation, FveMYB10 and FveMYB10L respond differently to changes in light quality, produce distinct anthocyanin compositions, and preferentially activate different downstream anthocyanin biosynthesis genes in their respective tissues. This work identifies a new regulator of anthocyanin synthesis and demonstrates that two paralogous MYB genes with specialized functions enable tissue-specific regulation of anthocyanin biosynthesis in fruit and petiole tissues.

A GT-1 and PKc domain-containing transcription regulator SIMPLE LEAF1 controls compound leaf development in woodland strawberry.

Leaves are strikingly diverse in terms of shapes and complexity. The wild and cultivated strawberry plants mostly develop trifoliate compound leaves, yet the underlying genetic basis remains unclear in this important fruit crop in Rosaceae. Here, we identified two EMS mutants designated simple leaf1 (sl1-1 and sl1-2) and one natural simple-leafed mutant monophylla in Fragaria vesca. Their causative mutations all reside in SL1 (FvH4_7g28640) causing premature stop codon at different positions in sl1-1 and sl1-2 and an eight-nucleotide insertion (GTTCATCA) in monophylla. SL1 encodes a transcription regulator with the conserved DNA-binding domain GT-1 and the catalytic domain of protein kinases PKc. Expression of SL1pro::SL1 in sl1-1 completely restored compound leaf formation. The 35S::SL1 lines developed palmate-like leaves with four or five leaflets at a low penetrance. However, overexpressing the truncated SL1ΔPK caused no phenotypes, probably due to the disruption of homodimerization. SL1 is preferentially expressed at the tips of leaflets and serrations. Moreover, SL1 is closely associated with the auxin pathway and works synergistically with FveLFYa in leaf morphogenesis. Overall, our work uncovered a new type of transcription regulator that promotes compound leaf formation in the woodland strawberry and shed new lights on the diversity of leaf complexity control.

Rosaceae fruit transcriptome database (ROFT)-a useful genomic resource for comparing fruits of apple, peach, strawberry, and raspberry.

Rosaceae is a large plant family consisting of many economically important fruit crops including peach, apple, pear, strawberry, raspberry, plum, and others. Investigations into their growth and development will promote both basic understanding and progress toward increasing fruit yield and quality. With the ever-increasing high-throughput sequencing data of Rosaceae, comparative studies are hindered by inconsistency of sample collection with regard to tissue, stage, growth conditions, and by vastly different handling of the data. Therefore, databases that enable easy access and effective utilization of directly comparable transcript data are highly desirable. Here, we describe a database for comparative analysis, ROsaceae Fruit Transcriptome database (ROFT), based on RNA-seq data generated from the same laboratory using similarly dissected and staged fruit tissues of four important Rosaceae fruit crops: apple, peach, strawberry, and red raspberry. Hence, the database is unique in allowing easy and robust comparisons among fruit gene expression across the four species. ROFT enables researchers to query orthologous genes and their expression patterns during different fruit developmental stages in the four species, identify tissue-specific and tissue-/stage-specific genes, visualize and compare ortholog expression in different fruit types, explore consensus co-expression networks, and download different data types. The database provides users access to vast amounts of RNA-seq data across the four economically important fruits, enables investigations of fruit type specification and evolution, and facilitates the selection of genes with critical roles in fruit development for further studies.

CW198 acts as a genetic insulator to block enhancer-promoter interaction in plants.

Insulators in vertebrates play a role in genome architecture and orchestrate temporo-spatial enhancer-promoter interactions. In plants, insulators and their associated binding factors have not been documented as of yet, largely as a result of a lack of characterized insulators. In this study, we took a comprehensive strategy to identify and validate the enhancer-blocking insulator CW198. We show that a 1.08-kb CW198 fragment from Arabidopsis can, when interposed between an enhancer and a promoter, efficiently abrogate the activation function of both constitutive and floral organ-specific enhancers in transgenic Arabidopsis and tobacco plants. In plants, both transcriptional crosstalk and spreading of histone modifications were rarely detectable across CW198, which resembles the insulation property observed across the CTCF insulator in the mammalian genome. Taken together, our findings support that CW198 acts as an enhancer-blocking insulator in both Arabidopsis and tobacco. The significance of the present findings and their relevance to the mitigation of mutual interference between enhancers and promoters, as well as multiple promoters in transgenes, is discussed.

Mechanism of fertilization-induced auxin synthesis in the endosperm for seed and fruit development.

The dominance of flowering plants on earth is owed largely to the evolution of maternal tissues such as fruit and seedcoat that protect and disseminate the seeds. The mechanism of how fertilization triggers the development of these specialized maternal tissues is not well understood. A key event is the induction of auxin synthesis in the endosperm, and the mobile auxin subsequently stimulates seedcoat and fruit development. However, the regulatory mechanism of auxin synthesis in the endosperm remains unknown. Here, we show that a type I MADS box gene AGL62 is required for the activation of auxin synthesis in the endosperm in both Fragaria vesca, a diploid strawberry, and in Arabidopsis. Several strawberry FveATHB genes were identified as downstream targets of FveAGL62 and act to repress auxin biosynthesis. In this work, we identify a key mechanism for auxin induction to mediate fertilization success, a finding broadly relevant to flowering plants.

Plant development: Unveiling cytokinin's role in the end of flowering.

Plant reproductive duration is defined by the onset as well as the end of flowering. A new study characterizes the little-known process of flowering cessation by imaging cellular and molecular dynamics at the shoot apical meristem, revealing a critical role of cytokinin.

Comparative transcriptomic analysis of apple and peach fruits: insights into fruit type specification.

Fruits represent key evolutionary innovations in angiosperms and exhibit diverse types adapted for seed dissemination. However, the mechanisms that underlie fruit type diversity are not understood. The Rosaceae family comprises many different fruit types, including 'pome' and 'drupe' fruits, and hence is an excellent family for investigating the genetic basis of fruit type specification. Using comparative transcriptomics, we investigated the molecular events that correlate with pome (apple) and drupe (peach) fleshy fruit development, focusing on the earliest stages of fruit initiation. We identified PI and TM6, MADS box genes whose expression negatively correlates with fruit flesh-forming tissues irrespective of fruit type. In addition, the MADS box gene FBP9 is expressed in fruit-forming tissues in both species, and was lost multiple times in the genomes of dry-fruit-forming eudicots including Arabidopsis. Network analysis reveals co-expression between FBP9 and photosynthesis genes in both apple and peach, suggesting that FBP9 and photosynthesis may both promote fleshy fruit development. The large transcriptomic datasets at the earliest stages of pome and drupe fruit development provide rich resources for comparative studies, and the work provides important insights into fruit-type specification.