Leaf heteroblasty in Passiflora edulis as revealed by metabolic profiling and expression analyses of the microRNAs miR156 and miR172

Age-associated growth control modifies leaf proximodistal symmetry and enabled leaf shape diversification

Biological shape diversity is often manifested in modulation of organ symmetry and modification of the patterned elaboration of repeated shape elements.1,2,3,4,5 Whether and how these two aspects of shape determination are coordinately regulated is unclear.5,6,7 Plant leaves provide an attractive system to investigate this problem, because they often show asymmetries along the proximodistal (PD) axis of their blades, along which they can also produce repeated marginal outgrowths such as serrations or leaflets.1 One aspect of leaf shape diversity is heteroblasty, where the leaf form in a single genotype is modified with progressive plant age.8,9,10,11 In Arabidopsis thaliana, a plant with simple leaves, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9 (SPL9) controls heteroblasty by activating CyclinD3 expression, thereby sustaining proliferative growth and retarding differentiation in adult leaves.12,13 However, the precise significance of SPL9 action for leaf symmetry and marginal patterning is unknown. By combining genetics, quantitative shape analyses, and time-lapse imaging, we show that PD symmetry of the leaf blade in A. thaliana decreases in response to an age-dependent SPL9 expression gradient, and that SPL9 action coordinately regulates the distribution and shape of marginal serrations and overall leaf form. Using comparative analyses, we demonstrate that heteroblastic growth reprogramming in Cardamine hirsuta, a complex-leafed relative of A. thaliana, also involves prolonging the duration of cell proliferation and delaying differentiation. We further provide evidence that SPL9 enables species-specific action of homeobox genes that promote leaf complexity. In conclusion, we identified an age-dependent layer of organ PD growth regulation that modulates leaf symmetry and has enabled leaf shape diversification.

Leaf form diversity and evolution: a never-ending story in plant biology

Leaf form can vary at different levels, such as inter/intraspecies, and diverse leaf shapes reflect their remarkable ability to adapt to various environmental conditions. Over the past two decades, considerable progress has been made in unraveling the molecular mechanisms underlying leaf form diversity, particularly the regulatory mechanisms of leaf complexity. However, the mechanisms identified thus far are only part of the entire process, and numerous questions remain unanswered. This review aims to provide an overview of the current understanding of the molecular mechanisms driving leaf form diversity while highlighting the existing gaps in our knowledge. By focusing on the unanswered questions, this review aims to shed light on areas that require further research, ultimately fostering a more comprehensive understanding of leaf form diversity.

The Response and Evaluation of Morphology, Physiology, and Biochemistry Traits in Triploid Passiflora edulis Sims 'Mantianxing' to Drought Stress

As one of the most influential environmental factors, drought stress greatly impacts the development and production of plants. Triploid-induced Passiflora edulis Sims 'Mantianxing' is an important new cultivar for multi-resistance variety selective breeding, which is one of the P. edulis breeding essential targets. However, the performance of triploid 'Mantianxing' under drought stress is unknown. In order to study the drought resistance of triploid 'Mantianxing', our study compared drought-related indicators in diploids and triploids under natural drought experiments, including morphological, physiological, and biochemical characteristics. Results showed that triploid P. edulis 'Mantianxing' showed variable responses to drought treatment. Compared with diploids, triploids showed higher photosynthesis and chlorophyll fluorescence, osmotic adjustment substances, and antioxidant enzyme activity under drought stress and faster chlorophyll biosynthesis and growth recovery after rewatering. Generally speaking, these results indicate that the drought resistance of triploid P. edulis is superior to diploid. This study provides scientific information for breeding stress tolerance variety of P. edulis 'Mantianxing' new cultivar.

Unveiling the phenology and associated floral regulatory pathways of Humulus lupulus L. in subtropical conditions

MAIN CONCLUSION

The hop phenological cycle was described in subtropical condition of Brazil showing that flowering can happen at any time of year and this was related to developmental molecular pathways. Hops are traditionally produced in temperate regions, as it was believed that vernalization was necessary for flowering. Nevertheless, recent studies have revealed the potential for hops to flower in tropical and subtropical climates. In this work, we observed that hops in the subtropical climate of Minas Gerais, Brazil grow and flower multiple times throughout the year, independently of the season, contrasting with what happens in temperate regions. This could be due to the photoperiod consistently being inductive, with daylight hours below the described threshold (16.5 h critical). We observed that when the plants reached 7-9 nodes, the leaves began to transition from heart-shaped to trilobed-shaped, which could be indicative of the juvenile to adult transition. This could be related to the fact that the 5th node (in plants with 10 nodes) had the highest expression of miR156, while two miR172s increased in the 20th node (in plants with 25 nodes). Hop flowers appeared later, in the 25th or 28th nodes, and the expression of HlFT3 and HlFT5 was upregulated in plants between 15 and 20 nodes, while the expression of HlTFL3 was upregulated in plants with 20 nodes. These results indicate the role of axillary meristem age in regulating this process and suggest that the florigenic signal should be maintained until the hop plants bloom. In addition, it is possible that the expression of TFL is not sufficient to inhibit flowering in these conditions and promote branching. These findings suggest that the reproductive transition in hop under inductive photoperiodic conditions could occur in plants between 15 and 20 nodes. Our study sheds light on the intricate molecular mechanisms underlying hop floral development, paving the way for potential advancements in hop production on a global scale.

Plant age-dependent dynamics of annatto pigment (bixin) biosynthesis in Bixa orellana

Age affects the production of secondary metabolites, but how developmental cues regulate secondary metabolism remains poorly understood. The achiote tree (Bixa orellana L.) is a source of bixin, an apocarotenoid used in diverse industries worldwide. Understanding how age-dependent mechanisms control bixin biosynthesis is of great interest for plant biology and for economic reasons. Here we overexpressed miRNA156 (miR156) in B. orellana to comprehensively study the effects of the miR156-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) module on age-dependent bixin biosynthesis in leaves. Overexpression of miR156 in annatto plants (miR156ox) reduced BoSPL transcript levels, impacted leaf ontogeny, lessened bixin production, and increased abscisic acid levels. Modulation of expression of BoCCD4-4 and BoCCD1, key genes in carotenoid biosynthesis, was associated with diverting the carbon flux from bixin to abscisic acid in miR156ox leaves. Proteomic analyses revealed an overall low accumulation of most secondary metabolite-related enzymes in miR156ox leaves, suggesting that miR156-targeted BoSPLs may be required to activate several secondary metabolic pathways. Our findings suggest that the conserved BomiR156-BoSPL module is deployed to regulate leaf dynamics of bixin biosynthesis, and may create novel opportunities to fine-tune bixin output in B. orellana breeding programs.

Topological data analysis reveals core heteroblastic and ontogenetic programs embedded in leaves of grapevine (Vitaceae) and maracuyá (Passifloraceae)

Leaves are often described in language that evokes a single shape. However, embedded in that descriptor is a multitude of latent shapes arising from evolutionary, developmental, environmental, and other effects. These confounded effects manifest at distinct developmental time points and evolve at different tempos. Here, revisiting datasets comprised of thousands of leaves of vining grapevine (Vitaceae) and maracuyá (Passifloraceae) species, we apply a technique from the mathematical field of topological data analysis to comparatively visualize the structure of heteroblastic and ontogenetic effects on leaf shape in each group. Consistent with a morphologically closer relationship, members of the grapevine dataset possess strong core heteroblasty and ontogenetic programs with little deviation between species. Remarkably, we found that most members of the maracuyá family also share core heteroblasty and ontogenetic programs despite dramatic species-to-species leaf shape differences. This conservation was not initially detected using traditional analyses such as principal component analysis or linear discriminant analysis. We also identify two morphotypes of maracuyá that deviate from the core structure, suggesting the evolution of new developmental properties in this phylogenetically distinct sub-group. Our findings illustrate how topological data analysis can be used to disentangle previously confounded developmental and evolutionary effects to visualize latent shapes and hidden relationships, even ones embedded in complex, high-dimensional datasets.

Advances in Tissue Culture and Transformation Studies in Non-model Species: Passiflora spp. (Passifloraceae)

In this chapter, we report advances in tissue culture applied to Passiflora. We present reproducible protocols for somatic embryogenesis, endosperm-derived triploid production, and genetic transformation for such species knowledge generated by our research team and collaborators in the last 20 years. Our research group has pioneered the work on passion fruit somatic embryogenesis, and we directed efforts to characterize several aspects of this morphogenic pathway. Furthermore, we expanded the possibilities of understanding the molecular mechanism related to developmental phase transitions of Passiflora edulis Sims. and P. cincinnata Mast., and a transformation protocol is presented for the overexpression of microRNA156.

Expression divergence of expansin genes drive the heteroblasty in Ceratopteris chingii

BACKGROUND

Sterile-fertile heteroblasty is a common phenomenon observed in ferns, where the leaf shape of a fern sporophyll, responsible for sporangium production, differs from that of a regular trophophyll. However, due to the large size and complexity of most fern genomes, the molecular mechanisms that regulate the formation of these functionally different heteroblasty have remained elusive. To shed light on these mechanisms, we generated a full-length transcriptome of Ceratopteris chingii with PacBio Iso-Seq from five tissue samples. By integrating Illumina-based sequencing short reads, we identified the genes exhibiting the most significant differential expression between sporophylls and trophophylls.

RESULTS

The long reads were assembled, resulting in a total of 24,024 gene models. The differential expressed genes between heteroblasty primarily involved reproduction and cell wall composition, with a particular focus on expansin genes. Reconstructing the phylogeny of expansin genes across 19 plant species, ranging from green algae to seed plants, we identified four ortholog groups for expansins. The observed high expression of expansin genes in the young sporophylls of C. chingii emphasizes their role in the development of heteroblastic leaves. Through gene coexpression analysis, we identified highly divergent expressions of expansin genes both within and between species.

CONCLUSIONS

The specific regulatory interactions and accompanying expression patterns of expansin genes are associated with variations in leaf shapes between sporophylls and trophophylls.

Vegetative phase change causes age-dependent changes in phenotypic plasticity

Phenotypic plasticity allows organisms to optimize traits for their environment. As organisms age, they experience diverse environments that benefit from varying degrees of phenotypic plasticity. Developmental transitions can control these age-dependent changes in plasticity, and as such, the timing of these transitions can determine when plasticity changes in an organism. Here, we investigate how the transition from juvenile-to adult-vegetative development known as vegetative phase change (VPC) contributes to age-dependent changes in phenotypic plasticity and how the timing of this transition responds to environment using both natural accessions and mutant lines in the model plant Arabidopsis thaliana. We found that the adult phase of vegetative development has greater plasticity in leaf morphology than the juvenile phase and confirmed that this difference in plasticity is caused by VPC using mutant lines. Furthermore, we found that the timing of VPC, and therefore the time when increased plasticity is acquired, varies significantly across genotypes and environments. The consistent age-dependent changes in plasticity caused by VPC suggest that VPC may be adaptive. This genetic and environmental variation in the timing of VPC indicates the potential for population-level adaptive evolution of VPC.

Transcriptomic and targeted metabolomic unravelling the molecular mechanism of sugar metabolism regulating heteroblastic changes in Pinus massoniana seedlings

Pine seedling leaf characteristics show a distinct transition from primary to secondary needles, known as heteroblastic change. However, the underlying regulatory mechanism is poorly understood. The molecular mechanism of sugar metabolism involved in regulating heteroblastic changes in Pinus massoniana seedlings was investigated via transcriptomics and targeted metabolomics. The results identified 12 kinds of sugar metabolites in the foliage. Three types of sugar accumulated at the highest levels: sucrose, glucose and fructose. Compared to seedlings with only primary needles (PN), the contents of these soluble sugars were lower in seedlings with developing secondary needle buds (SNB). RNA-seq analysis highlighted 1086 DEGs between PN and SNB seedlings, revealing significant enrichment in KEGG pathways including starch and sucrose metabolism, plant hormone signal transduction and amino sugar and nucleic acid sugar metabolism. Combined transcriptomic and metabolomic analysis revealed that HK, MDH, and ATPase could potentially enhance sugar availability by stimulating the glycolytic/TCA cycle and oxidative phosphorylation. These processes may lead to a reduced sugar content in the foliage of SNB seedlings. We also identified 72 transcription factors, among which the expression levels of MYB, WRKY, NAC and C2H2 family genes were closely related to those of DEGs in the sugar metabolism pathway. In addition, we identified alternative splicing (AS) events in one NAC gene leading to two isoforms, PmNAC5L and PmNAC5S. PmNAC5L was significantly upregulated, while PmNAC5S was significantly downregulated in SNB seedlings. Overall, our results provide new insights into how sugar metabolism is involved in regulating heteroblastic changes in pine seedlings.

Molecular mechanisms of miR172a and its target gene LbrTOE3 regulating maturation in Lilium

MAIN CONCLUSION

Lbr-miR172a could promote the growth phase transition and shorten maturation in Lilium, while LbrTOE3 inhibited this process and prolonged the growth period. Lilium is an ornamental flower with high economic value for both food and medicinal purposes. However, under natural conditions, Lilium bulbs take a long time and cost more to grow to commercial size. This research was conducted to shorten the maturation time by subjecting Lilium bulbs to alternating temperature treatment. To explore the molecular mechanism of the vegetative phase change (VPC) in Lilium after variable temperature treatment, the key module miR172a-TOE3 was selected based on a combined omics analysis. Gene cloning and transgene functional validation showed that overexpression of Lbr-mir172a promoted a phase change, while overexpression of LbrTOE3 inhibited this process. Subcellular localization and transcriptional activation assays indicated that LbrTOE3 was predominantly localized in the nucleus and showed transcriptional activity. In situ hybridization showed that LbrTOE3 expression was significantly downregulated after alternating temperature treatment. This study elucidates the molecular mechanisms of the phase transition of Lilium and provides a scientific basis for the phase transition in other plants.

Convergent evolution of the annual life history syndrome from perennial ancestors

Despite most angiosperms being perennial, once-flowering annuals have evolved multiple times independently, making life history traits among the most labile trait syndromes in flowering plants. Much research has focused on discerning the adaptive forces driving the evolution of annual species, and in pinpointing traits that distinguish them from perennials. By contrast, little is known about how 'annual traits' evolve, and whether the same traits and genes have evolved in parallel to affect independent origins of the annual syndrome. Here, we review what is known about the distribution of annuals in both phylogenetic and environmental space and assess the evidence for parallel evolution of annuality through similar physiological, developmental, and/or genetic mechanisms. We then use temperate grasses as a case study for modeling the evolution of annuality and suggest future directions for understanding annual-perennial transitions in other groups of plants. Understanding how convergent life history traits evolve can help predict species responses to climate change and allows transfer of knowledge between model and agriculturally important species.

QTL and candidate genes for heterophylly in soybean based on two populations of recombinant inbred lines

Heterophylly, the existence of different leaf shapes and sizes on the same plant, has been observed in many flowering plant species. Yet, the genetic characteristics and genetic basis of heterophylly in soybean remain unknown. Here, two populations of recombinant inbred lines (RILs) with distinctly different leaf shapes were used to identify loci controlling heterophylly in two environments. The ratio of apical leaf shape (LSUP) to basal leaf shape (LSDOWN) at the reproductive growth stage (RLS) was used as a parameter for classifying heterophylly. A total of eight QTL were detected for RLS between the two populations and four of them were stably identified in both environments. Among them, qRLS20 had the largest effect in the JS population, with a maximum LOD value of 46.9 explaining up to 47.2% of phenotypic variance. This locus was located in the same genomic region as the basal leaf shape QTL qLSDOWN20 on chromosome 20. The locus qRLS19 had the largest effect in the JJ population, with a maximum LOD value of 15.2 explaining up to 27.0% of phenotypic variance. This locus was located in the same genomic region as the apical leaf shape QTL qLSUP19 on chromosome 19. Four candidate genes for heterophylly were identified based on sequence differences among the three parents of the two mapping populations, RT-qPCR analysis, and gene functional annotation analysis. The QTL and candidate genes detected in this study lay a foundation for further understanding the genetic mechanism of heterophylly and are invaluable in marker-assisted breeding.

Comparative analysis of differential gene expression indicates divergence in ontogenetic strategies of leaves in two conifer genera

In land plants, heteroblasty broadly refers to a drastic change in morphology during growth through ontogeny. Juniperus flaccida and Pinus cembroides are conifers of independent lineages known to exhibit leaf heteroblasty between the juvenile and adult life stage of development. Juvenile leaves of P. cembroides develop spirally on the main stem and appear decurrent, flattened, and needle-like; whereas adult photosynthetic leaves are triangular or semi-circular needle-like, and grow in whorls on secondary or tertiary compact dwarf shoots. By comparison, J. flaccida juvenile leaves are decurrent and needle-like, and adult leaves are compact, short, and scale-like. Comparative analyses were performed to evaluate differences in anatomy and gene expression patterns between developmental phases in both species. RNA from 12 samples was sequenced and analyzed with available software. They were assembled de novo from the RNA-Seq reads. Following assembly, 63,741 high-quality transcripts were functionally annotated in P. cembroides and 69,448 in J. flaccida. Evaluation of the orthologous groups yielded 4140 shared gene families among the four references (adult and juvenile from each species). Activities related to cell division and development were more abundant in juveniles than adults in P. cembroides, and more abundant in adults than juveniles in J. flaccida. Overall, there were 509 up-regulated and 81 down-regulated genes in the juvenile condition of P. cembroides and 14 up-regulated and 22 down-regulated genes in J. flaccida. Gene interaction network analysis showed evidence of co-expression and co-localization of up-regulated genes involved in cell wall and cuticle formation, development, and phenylpropanoid pathway, in juvenile P. cembroides leaves. Whereas in J. flaccida, differential expression and gene interaction patterns were detected in genes involved in photosynthesis and chloroplast biogenesis. Although J. flaccida and P. cembroides both exhibit leaf heteroblastic development, little overlap was detected, and unique genes and pathways were highlighted in this study.

MicroRNA156-mediated changes in leaf composition lead to altered photosynthetic traits during vegetative phase change

Plant morphology and physiology change with growth and development. Some of these changes are due to change in plant size and some are the result of genetically programmed developmental transitions. In this study we investigate the role of the developmental transition, vegetative phase change (VPC), on morphological and photosynthetic changes. We used overexpression of microRNA156, the master regulator of VPC, to modulate the timing of VPC in Populus tremula × alba, Zea mays, and Arabidopsis thaliana to determine its role in trait variation independent of changes in size and overall age. Here, we find that juvenile and adult leaves in all three species photosynthesize at different rates and that these differences are due to phase-dependent changes in specific leaf area (SLA) and leaf N but not photosynthetic biochemistry. Further, we found juvenile leaves with high SLA were associated with better photosynthetic performance at low light levels. This study establishes a role for VPC in leaf composition and photosynthetic performance across diverse species and environments. Variation in leaf traits due to VPC are likely to provide distinct benefits under specific environments; as a result, selection on the timing of this transition could be a mechanism for environmental adaptation.

Leaf development stages and ontogenetic changes in passionfruit (Passiflora edulis Sims.) are detected by narrowband spectral signal

During shoot development, leaves undergo various ontogenetic changes, including variation in size, shape, and geometry. Passiflora edulis (passionfruit) is a heteroblastic species, which means that it experiences conspicuous changes throughout development, enabling a morphological distinction between the juvenile and adult vegetative phases. Quantification of heteroblasty requires a practical, inexpensive, reliable, and non-destructive method, such as remote sensing. Moreover, relationships among ontogenetic changes and spectral signal at leaf level can be scaled up to support precision agriculture in passion fruit crops. In the present study, we used laboratory spectroscopic measurements (400-2500 nm) and narrowband vegetation indexes (or hyperspectral vegetation indexes - HVIs) to evaluate ontogenetic changes related to development and aging in P. edulis leaves. We also assessed leaf pigment concentration to further support the application of biochemical-related narrowband indexes. We report that 30-d-old leaves can be discriminated into developmental stages through their spectral signals. MSI (Moisture Stress Index) and NDVI₇₅₀ (Normalized Difference Vegetation Index ρ750) contribute most to the variation of age (15 to 30-d-old leaves) and developmental stage (phytomer positions along the plant axis) in passionfruit leaves. PRI (Photochemical Reflectance Index) played an important role in detecting age and development alterations, including heteroblasty. A biochemical and spectral comparison of pigments revealed that spectroscopy offered potential for diagnosing phenology in P. edulis, as some narrowband indexes correlated strongly with chlorophylls and carotenoids content. Narrowband vegetation indexes are found to be a suitable tool for monitoring passionfruit crops.