Sex and flowers: testing the resource-dependent selection hypothesis for flower sex allocation

Context: Monoecious plants can adjust their proportional investment in male and female flowers to maximise reproductive fitness. The female reproductive function (seeds) often has greater resource costs than the male (pollen). Larger plants are generally thought to have greater resource availability and should have a female biased sex ratio, referred to as the size-dependent selection hypothesis. However, empirical tests of this hypothesis have found mixed support. This may be because size alone is not always a reliable proximate value for resource availability, which can be influenced by other abiotic factors. Aims: Breynia oblongifolia (Phyllanthaceae) is a perennial monoecious plant with unisexual moth-pollinated flowers from eastern Australia. Fruit production in Breynia is heavily influenced by rainfall, which is highly variable. We hypothesised that where soil moisture limits female function, Breynia would produce more male flowers (i.e. resource-dependent selection). Methods: We used a multi-year observational dataset to look for evidence of resource-dependent flower sex ratios in a wild population and conducted a manipulative glasshouse experiment to test alternative hypotheses for flower sex selection. Key results: In both our manipulative glasshouse experiment and observed wild population, decreasing soil water content resulted in higher proportions of male flowers, supporting the resource-dependent sex selection hypothesis. Conclusions: Soil moisture influences flower sex ratios but plant size does not. Implications: Future studies should not assume that height equates to resource wealth, as this is often overly simplistic and ignores the potential for key resources, like soil moisture or light, to fluctuate

The roles of divergent and parallel molecular evolution contributing to thermal adaptive strategies in trees

Local adaptation is a driver of biological diversity, and species may develop analogous (parallel evolution) or alternative (divergent evolution) solutions to similar ecological challenges. We expect these adaptive solutions would culminate in both phenotypic and genotypic signals. Using two Eucalyptus species (Eucalyptus grandis and Eucalyptus tereticornis) with overlapping distributions grown under contrasting ‘local’ temperature conditions to investigate the independent contribution of adaptation and plasticity at molecular, physiological and morphological levels. The link between gene expression and traits markedly differed between species. Divergent evolution was the dominant pattern driving adaptation (91% of all significant genes); but overlapping gene (homologous) responses were dependent on the determining factor (plastic, adaptive or genotype by environment interaction). Ninety-eight percent of the plastic homologs were similarly regulated, while 50% of the adaptive homologs and 100% of the interaction homologs were antagonistical. Parallel evolution for the adaptive effect in homologous genes was greater than expected but not in favour of divergent evolution. Heat shock proteins for E. grandis were almost entirely driven by adaptation, and plasticity in E. tereticornis. These results suggest divergent molecular evolutionary solutions dominated the adaptive mechanisms among species, even in similar ecological circumstances. Suggesting that tree species with overlapping distributions are unlikely to equally persist in the future

Sugar sensing responses to low and high light in leaves of the C4 model grass Setaria viridis

Although sugar regulate photosynthesis, the signalling pathways underlying this process remain elusive, especially for C4 crops. To address this knowledge gap and identify potential candidate genes, we treated Setaria viridis (C4 model) plants acclimated to medium light intensity (ML, 500 µmol m-2 s-1) with low (LL, 50 µmol m-2 s-1) or high (HL, 1000 µmol m-2 s-1) light for 4 days and observed the consequences on carbon metabolism and the transcriptome of source leaves. LL impaired photosynthesis and reduced leaf content of signalling sugars (glucose, sucrose and trehalose-6-phosphate). Contrastingly, HL strongly induced sugar accumulation without repressing photosynthesis. LL more profoundly impacted leaf transcriptome, including photosynthetic genes. LL and HL contrastingly altered the expression of HXK and SnRK1 sugar sensors and trehalose pathway genes. The expression of key target genes of HXK and SnRK1 were affected by LL and sugar depletion, while surprisingly HL and strong sugar accumulation only slightly repressed the SnRK1 signalling pathway. In conclusion, we demonstrate that LL profoundly impacted photosynthesis and the transcriptome of S. viridis source leaves, while HL altered sugar levels more than LL. We also present the first evidence that sugar signalling pathways in C4 source leaves may respond to light intensity and sugar accumulation differently to C3 source leaves

Evidence for plant adaptation to a future high CO₂ world

Plant morphology and function are sensitive to rising atmospheric carbon dioxide (CO2) concentrations, but evidence that CO2 concentration can act as a selective pressure driving evolution is sparse. Plants originating from naturally high CO2 springs are subjected to elevated CO2 concentration over multiple generations, providing an opportunity to predict how adaptation to future atmospheres may occur, with important implications for future plant conservation and crop breeding strategies. Using Plantago lanceolata L. from such a site (the ‘spring’ site) and from an adjacent ambient CO2 site (‘control’ site), and growing the populations in ambient and elevated CO2 at 700 ?mol mol-1, I have characterised, for the first time, the functional and population genomics, alongside morphology and physiology, of plant adaptation to elevated CO2 concentrations. Growing plants in elevated CO2 caused relatively modest changes in gene expression, with fewer changes evident in the spring than control plants (33 vs 131 genes differentially expressed [DE], in spring and control plants respectively). In contrast, when comparisons were made between control and spring plants grown in either ambient or elevated CO2, there were a much larger number of loci showing DE (689 in the ambient and 853 in the elevated CO2 environment). Population genomic analysis revealed that genetic differentiation between the spring and control plants was close to zero with no fixed differences, suggesting that plants are adapted to their native CO2 environment at the level of gene expression. Growth at elevated CO2 led to an unusual phenotype, with an increase in stomatal density and index in the spring, but not in control plants. Focussing on previously characterised stomatal patterning genes revealed significant DE (FDR < 0.05) between spring and control plants for three loci (YODA, CDKB1;1, and SCRM2) and between ambient and elevated CO2 for four (ER, YODA, MYB88, and BCA1). We propose that the up-regulation in spring plants of two positive regulators of stomatal numbers (SCRM2 and CDKB1;1) act here as key controllers of stomatal adaptation to elevated CO2 on an evolutionary timescale. Significant transcriptome reprogramming of the photosynthetic pathway was identified, with an overall decrease in expression across the pathway in control plants, and an increase in spring plants, in response to elevated CO2. This was followed up by physiological measurements, where a significant increase (P < 0.05) in photosynthetic capacity and regeneration rate was exhibited in spring plants, compared to control plants, at both elevated and ambient CO2 concentrations. Through this comprehensive analysis, we have identified the basis of plant adaptation to elevated CO2 likely to occur in the future

The outlook for C4 crops in future climate scenarios

Several C4 crops dominate a large percentage of current agriculture due to the array of physiological benefits provided by C4 photosynthesis over the ancestral C3 photosynthesis, such as high productivity, resource use efficiency and stress tolerance. It is therefore imperative that we understand both how these crops will fare under future climate scenarios, and how we can further utilise C4 crops to help achieve future food security thresholds. The heightened water use efficiency of C4 plants suggests they may take a more prominent role in agriculture across the world to alleviate some of the future stress on fresh water supplies. However, as temperatures increase, they will begin to exceed the temperature optima of C4 crops such as Zea mays (maize) in key growing areas, which will shape the agricultural landscape of Z. mays and alternative C4 crops. Elevated CO2 has little direct effect on C4 plants due to the carbon concentrating mechanism, however, under water stressed conditions elevated CO2 does provide some drought tolerance to C4 plants due to decreased transpiration. However, the limited positive effects of elevated CO2 will likely not outweigh the stress of increased temperature and reduced water availability. Nevertheless, C4 crops are expected to play a major role in maintaining future food security due to their superior physiological attributes. Looking forward, two approaches to maintain or advance production of C4 crops seem feasible: (1) continued improvement of current crop lines via marker-assisted breeding, cutting-edge gene editing techniques and beneficial farming practices. This could allow current cropping practices to continue into the future without reduced yields. (2) Changes in the geographic distribution of C4 crops. As environments become more suitable, C4 crops will likely be introduced into those areas, while areas currently dominated by C4 crops may require alternative, more resilient species to maintain economic value

Genome-wide identification and characterisation of aquaporins in Nicotiana tabacum and their relationships with other Solanaceae species

BACKGROUND: Cellular membranes are dynamic structures, continuously adjusting their composition, allowing plants to respond to developmental signals, stresses, and changing environments. To facilitate transmembrane transport of substrates, plant membranes are embedded with both active and passive transporters. Aquaporins (AQPs) constitute a major family of membrane spanning channel proteins that selectively facilitate the passive bidirectional passage of substrates across biological membranes at an astonishing 108 molecules per second. AQPs are the most diversified in the plant kingdom, comprising of five major subfamilies that differ in temporal and spatial gene expression, subcellular protein localisation, substrate specificity, and post-translational regulatory mechanisms; collectively providing a dynamic transportation network spanning the entire plant. Plant AQPs can transport a range of solutes essential for numerous plant processes including, water relations, growth and development, stress responses, root nutrient uptake, and photosynthesis. The ability to manipulate AQPs towards improving plant productivity, is reliant on expanding our insight into the diversity and functional roles of AQPs. RESULTS: We characterised the AQP family from Nicotiana tabacum (NtAQPs; tobacco), a popular model system capable of scaling from the laboratory to the field. Tobacco is closely related to major economic crops (e.g. tomato, potato, eggplant and peppers) and itself has new commercial applications. Tobacco harbours 76 AQPs making it the second largest characterised AQP family. These fall into five distinct subfamilies, for which we characterised phylogenetic relationships, gene structures, protein sequences, selectivity filter compositions, sub-cellular localisation, and tissue-specific expression. We also identified the AQPs from tobacco's parental genomes (N. sylvestris and N. tomentosiformis), allowing us to characterise the evolutionary history of the NtAQP family. Assigning orthology to tomato and potato AQPs allowed for cross-species comparisons of conservation in protein structures, gene expression, and potential physiological roles. CONCLUSIONS: This study provides a comprehensive characterisation of the tobacco AQP family, and strengthens the current knowledge of AQP biology. The refined gene/protein models, tissue-specific expression analysis, and cross-species comparisons, provide valuable insight into the evolutionary history and likely physiological roles of NtAQPs and their Solanaceae orthologs. Collectively, these results will support future functional studies and help transfer basic research to applied agriculture

Gene expression profile of the developing endosperm in durum wheat provides insight into starch biosynthesis

Background: Durum wheat (Triticum turgidum subsp. durum) is widely grown for pasta production, and more recently, is gaining additional interest due to its resilience to warm, dry climates and its use as an experimental model for wheat research. Like in bread wheat, the starch and protein accumulated in the endosperm during grain development are the primary contributors to the calorific value of durum grains. Results: To enable further research into endosperm development and storage reserve synthesis, we generated a high-quality transcriptomics dataset from developing endosperms of variety Kronos, to complement the extensive mutant resources available for this variety. Endosperms were dissected from grains harvested at eight timepoints during grain development (6 to 30 days post anthesis (dpa)), then RNA sequencing was used to profile the transcriptome at each stage. The largest changes in gene expression profile were observed between the earlier timepoints, prior to 15 dpa. We detected a total of 29,925 genes that were significantly differentially expressed between at least two timepoints, and clustering analysis revealed nine distinct expression patterns. We demonstrate the potential of our dataset to provide new insights into key processes that occur during endosperm development, using starch metabolism as an example. Conclusion: We provide a valuable resource for studying endosperm development in this increasingly important crop species

Investigating the NAD-ME biochemical pathway within C4 grasses using transcript and amino acid variation in C4 photosynthetic genes

Expanding knowledge of the C4 photosynthetic pathway can provide key information to aid biological improvements to crop photosynthesis and yield. While the C4 NADP-ME pathway is well characterised, there is increasing agricultural and bioengineering interest in the comparably understudied NAD-ME and PEPCK pathways. Within this study, a systematic identification of key differences across species has allowed us to investigate the evolution of C4-recruited genes in one C3 and eleven C4 grasses (Poaceae) spanning two independent origins of C4 photosynthesis. We present evidence for C4-specific paralogs of NAD-malic enzyme 2, MPC1 and MPC2 (mitochondrial pyruvate carriers) via increased transcript abundance and associated rates of evolution, implicating them as genes recruited to perform C4 photosynthesis within NAD-ME and PEPCK subtypes. We then investigate the localisation of AspAT across subtypes, using novel and published evidence to place AspAT3 in both the cytosol and peroxisome. Finally, these findings are integrated with transcript abundance of previously identified C4 genes to provide an updated model for C4 grass NAD-ME and PEPCK photosynthesis. This updated model allows us to develop on the current understanding of NAD-ME and PEPCK photosynthesis in grasses, bolstering our efforts to understand the evolutionary ‘path to C4’ and improve C4 photosynthesis

The transcriptomic responses of C4 grasses to subambient CO2 and low light are largely species specific and only refined by photosynthetic subtype

Three subtypes of C4 photosynthesis exist (NADP-ME, NAD-ME and PEPCK), each known to be beneficial under specific environmental conditions. However, the influence of photosynthetic subtype on transcriptomic plasticity, as well as the genes underpinning this variability, remain largely unknown. Here, we comprehensively investigate the responses of six C4 grass species, spanning all three C4 subtypes, to two controlled environmental stresses: low light (200 µmol m−2 sec−1) and glacial CO2 (subambient; 180 ppm). We identify a susceptibility within NADP-ME species to glacial CO2. Notably, although glacial CO2 phenotypes could be tied to C4 subtype, biochemical and transcriptomic responses to glacial CO2 were largely species specific. Nevertheless, we were able to identify subtype specific subsets of significantly differentially expressed transcripts which link resource acquisition and allocation to NADP-ME species susceptibility to glacial CO2. Here, low light phenotypes were comparable across species with no clear subtype response, while again, transcriptomic responses to low light were largely species specific. However, numerous functional similarities were noted within the transcriptomic responses to low light, suggesting these responses are functionally relatively conserved. Additionally, PEPCK species exhibited heightened regulation of transcripts related to metabolism in response to both stresses, likely tied to their C4 metabolic pathway. These results highlight the influence that both species and subtype can have on plant responses to abiotic stress, building on our mechanistic understanding of acclimation within C4 grasses and highlighting avenues for future crop improvements

Additional file 5 of Gene expression profile of the developing endosperm in durum wheat provides insight into starch biosynthesis

Supplementary File