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Chromosome painting in cultivated banana and their wild relatives (Musa spp.) reveals differences in chromosome structure

Edible banana cultivars are diploid, triploid or tetraploid hybrids which originated by natural cross hybridization between subspecies of diploid Musa acuminata, or between M. acuminata and diploid M. balbisiana. Participation of two other wild diploid species M. schizocarpa and M. textilis was also indicated by molecular studies. Fusion of gametes with structurally different chromosome sets may give rise to progenies with structural chromosome heterozygosity and reduced fertility due to aberrant chromosome pairing and unbalanced chromosome segregation. Only a few translocations have been classified on the genomic level so far and a comprehensive molecular cytogenetic characterization of cultivars and species of the family Musaceae is still lacking. FISH with chromosome-arm specific oligo painting probes was used for comparative karyotype analysis in a set of wild Musa species and edible banana clones. The results revealed large differences in chromosome structure discriminating individual accessions. These results permitted identification of putative progenitors of cultivated clones and clarified genomic constitution and evolution of aneuploid banana clones, which seem to be common among the polyploid banana accessions. New insights into the chromosome organization and structural chromosome changes will be a valuable asset in breeding programs, particularly in selection of appropriate parents for cross hybridization. HighlightOligo painting FISH revealed chromosomal translocations in subspecies of Musa acuminata (A genome), their intra-specific hybrids as well as in M. balbisiana (B genome) and in interspecific hybrid clones originating from cross hybridization between M. acuminata and M. balbisiana

plant biology↗

The role of CLV1, CLV2 and HPAT homologs in nitrogen-regulation of root development

Plants use a variety of hormonal and peptide signals to control root development, including in adapting root development to cope with nutrient stress. Nitrogen (N) is a major limiting factor in plant growth and in response to N stress plants dramatically modulate root development, including in legumes influencing the formation of N-fixing nodules in response to external N supply. Recently, specific CLE peptides and/or receptors important for their perception, including CLV1 and CLV2, have been found to play important roles in root development in a limited number of species, including in some cases the response to N. In the legume Medicago truncatula, this response also appears to be influenced by RDN1, a member of the hydroxyproline O-arabinosyltransferase (HPAT) family which can modify specific CLE peptides. However, it not known if this signalling pathway plays a central role in root development across species, in particular root responses to N. In this study, we sought to systematically examine the role of homologues of these genes in root development of the legume pea (Pisum sativum. L) and non-legume tomato (Solanum lycopersicum) using a mutant based approach. This included a detailed examination of root development in response to N in these mutant series in tomato. We found no evidence for a role of these genes in pea seedling root development. Furthermore, the CLV1-like FAB gene did not influence tomato root development, including N response. In contrast, both CLV2 and the HPAT FIN appear to positively influence root size in tomato but do not mediate root responses to N. These suggest a relatively species-specific role for these genes in root development, including N regulation of root architecture.

plant biology↗

The Effect of Introgression of an R2R3 MYB Transcription Factor on Sulphur Metabolism in Brassica oleracea

BackgroundA diet rich in cruciferous vegetables is reported to have beneficial health effects, partially mediated by 4-methylsulfinylbutyl glucosinolate, or glucoraphanin, which is predominantly found within broccoli (Brassica oleracea var italica). We describe the downstream effects on transcription and metabolism in broccoli following the introgression of a genetic variant of MYB28 into broccoli from a wild Brassica relative which has previously been associated with enhancement of glucoraphanin. ResultsWhole genome sequencing, RNA expression and metabolite analyses were used to characterise the consequences of the introgression of either one or two copies of a genetic variant of the MYB28 transcription factor into a commercial broccoli genetic background. The introgression of the variant of MYB28 resulted in enhanced expression of genes involved in primary sulphate assimilation, sulphur metabolism and aliphatic glucosinolate biosynthesis, and enhanced accumulation of 4-methylsulphinyl butyl glucosinolate in florets. Other changes in transcription that may be related to non-targeted introgression events are reported. There were no consistent effects upon sulphur metabolites pools, apart from methionine-derived glucosinolates. ConclusionThis study illustrates the downstream effects on transcription and metabolism of the introgression of a genetic variant of MYB28 from a wild species into a commercial broccoli genotype.

plant biology↗

A constitutively monomeric UVR8 photoreceptor allele confers enhanced UV-B photomorphogenesis

The plant UV-B photoreceptor UVR8 plays an important role in UV-B acclimation and survival. UV-B absorption by homodimeric UVR8 induces its monomerization and interaction with the E3 ubiquitin ligase COP1, leading ultimately to gene expression changes. UVR8 is inactivated through redimerization, facilitated by RUP1 and RUP2. Here, we describe a novel semi-dominant, hyperactive allele, namely uvr8-17D, that harbors a glycine-101 to serine mutation. UVR8G101S-overexpression led to weak constitutive photomorphogenesis and extreme UV-B responsiveness. UVR8G101S was observed to be predominantly monomeric in vivo and, once activated by UV-B, was not efficiently inactivated. Analysis of a UVR8G101S crystal structure revealed the distortion of a loop region normally involved in stabilization of the UVR8 homodimer. Plants expressing a UVR8 variant combining G101S with the previously described W285A mutation exhibited robust constitutive photomorphogenesis. This work provides further insight into UVR8 activation and inactivation mechanisms, and describes a genetic tool for the manipulation of photomorphogenic responses.

plant biology↗

The XyloPhone: democratizing access to high-quality macroscopic imaging for wood and other substrates

One rate-limiting factor in the fight against illegal logging is the lack of powerful, affordable, scalable wood identification tools for field screening. Computer vision wood identification using smartphones fitted with customized imaging peripherals offer a potential solution but to date, such peripherals suffer from one or more weaknesses: low image quality, lack of lighting control, uncontrolled magnification, unknown distortion and spherical aberration, and/or no access to or publication of the system design. To address cost, optical concerns, and open access to designs and parameters, I present the XyloPhone, a 3D printed research quality macroscopic imaging attachment adaptable to any smartphone. It provides a fixed focal distance, exclusion of ambient light, selection of visible light or UV illumination, uses the lens from a commercially available loupe, is powered by a rechargeable external battery, is fully open-sourced, and at a price point of less than 110 USD is a highly affordable tool for the laboratory or the field, and can serve as the foundational hardware for a scalable field deployable computer vision wood identification system.

plant biology↗

Proteomic analysis of SUMO1-SUMOylome changes during defense elicitation in Arabidopsis

Rapid adaptation of plants to developmental or physiological cues is facilitated by specific receptors that transduce the signals mostly via post-translational modification (PTM) cascades of downstream partners. Reversible covalent attachment of SMALL UBIQUITIN-LIKE MODIFIER (SUMO), a process termed as SUMOylation, influence growth, development and adaptation of plants to various stresses. Strong regulatory mechanisms maintain the steady-state SUMOylome and mutants with SUMOylation disturbances display mis-primed immunity often with growth consequences. Identity of the SUMO-substrates undergoing SUMOylation changes during defences however remain largely unknown. Here we exploit either the auto-immune property of an Arabidopsis mutant or defense responses induced in wild-type plants against Pseudomonas syringae pv tomato (PstDC3000) to enrich and identify SUMO1-substrates. Our results demonstrate massive enhancement of SUMO1-conjugates due to increased SUMOylation efficiencies during defense responses. Of the 261 proteins we identify, 29 have been previously implicated in immune-associated processes. Role of others expand to diverse cellular roles indicating massive readjustments the SUMOylome alterations may cause during induction of immunity. Overall, our study highlights the complexities of a plant immune network and identifies multiple SUMO-substrates that may orchestrate the signalling.

plant biology↗

Spatially Restricted Immune Responses Allow for Root Meristematic Activity During Bacterial Colonisation

Plants circumscribe microbe-associated molecular pattern (MAMP)-triggered immune responses to weak points of the roots. This spatially restricted immunity was suggested to avoid constitutive responses to rhizosphere microbiota. To demonstrate its relevance, we combined cell-type specific expression of the plant flagellin receptor (FLS2) with fluorescent defence markers and mapped immune competency at cellular resolution. Our analysis distinguishes cell-autonomous and non-cell autonomous responses and reveals lignification to be tissue-independent, contrasting cell-type specific suberisation. Importantly, our analysis divides the non-responsive meristem into a central zone refractory to FLS2 expression, and a cortex that becomes highly sensitised by FLS2 expression, causing meristem collapse upon MAMP exposure. Meristematic epidermal expression generates super-competent lines that detect native bacterial flagellin and bypass the absence of response to commensals, providing a powerful tool for studying root immunity. Our precise manipulations and read-outs demonstrate incompatibility of meristematic activity and defence and the importance of cell-resolved studies of plant immunity.

plant biology↗

Photosynthetic resistance and resilience under drought and rewatering in maize plants

Abnormally altered precipitation patterns induced by climate change have profound global effects on crop production. However, the plant functional responses to various precipitation regimes remain unclear. Here, greenhouse and field experiments were conducted to determine how maize plant functional traits respond to drought, flooding, and rewatering. Drought and flooding hampered photosynthetic capacity, particularly when severe and/or prolonged. Most photosynthetic traits recovered after rewatering, with few compensatory responses. Rewatering often elicited high photosynthetic resilience in plants exposed to severe drought at the end of plant development, with the response strongly depending on the drought severity/duration and plant growth stage. The associations of chlorophyll concentrations with photosynthetically functional activities were stronger during post-tasselling than pre-tasselling, implying an involvement of leaf age/senescence in responses to episodic drought and subsequent rewatering. Coordinated changes in chlorophyll content, gas exchange, fluorescence parameters (PSII quantum efficiency and photochemical/non-photochemical radiative energy dissipation) possibly contributed to the enhanced drought resistance and resilience and suggested a possible regulative trade-off. These findings provide fundamental insights into how plants regulate their functional traits to deal with sporadic alterations in precipitation. Breeding and management of plants with high resistance and resilience traits could help crop production under future climate change.

plant biology↗

The Arabidopsis thaliana NIP2;1 Lactic Acid Channel promotes Plant Survival Under Low Oxygen Stress

Under anaerobic stress Arabidopsis thaliana induces the expression of a collection of core hypoxia genes that encode proteins associated with an adaptive response. Included in these core hypoxia genes is NIP2;1, which encodes a member of the "Nodulin-like Intrinsic Protein" (NIP) subgroup of the aquaporin superfamily of membrane channel proteins. Under normal growth, NIP2;1 expression is limited to the "anoxia core" region of the root stele, but shows substantial induction in response to low oxygen stress (as high as 1000-fold by 2-4 hr of hypoxia challenge), and accumulates in all root tissues. During hypoxia, NIP2;1-GFP, accumulates on the cell surface by 2 hr and then is distributed between the cell surface and internal membranes during sustained hypoxia, and remains elevated in root tissues through 4 hrs of reoxygenation recovery. T-DNA insertional mutant nip2;1 plants show elevation of lactic acid within root tissues, and a reduced efflux of lactic acid and acidification of the external medium. Together with previous biochemical evidence demonstrating that NIP2;1 has lactic acid permease activity, the present work supports the hypothesis that the protein facilitates the release of cellular lactate to the rhizosphere to prevent lactic acid toxicity. In support of this, nip2;1 plants show poorer survival to argon-induced hypoxia stress. Nip2;1 mutant plants also show elevated expression of ethanolic fermentation transcripts, as well as reduced expression the lactate metabolic enzyme GOX3, suggesting that the altered efflux of lactate through NIP2;1 regulates other pyruvate and lactate metabolism pathways. One-sentence SummaryThe NIP2;1 lactic acid permease is necessary for an optimum response to low oxygen stress through the release of lactate from roots during hypoxia stress.

plant biology↗

Seed hemicelluloses tailor mucilage properties and salt tolerance

O_LIWhile Arabidopsis seed coat epidermal cells have become an excellent genetic system to study the biosynthesis and structural roles of various cell wall polymers, the physiological function of the secreted mucilaginous polysaccharides remains ambiguous. Seed mucilage is shaped by two distinct classes of highly substituted hemicelluloses along with cellulose and structural proteins, but their interplay has not been explored. C_LIO_LIWe deciphered the functions of four distinct classes of cell wall polymers by generating a series of double mutants with defects in heteromannan, xylan, cellulose, or the arabinogalactan protein SALT-OVERLY SENSITIVE 5 (SOS5), and evaluating their impact on mucilage architecture and on seed germination during salt stress. C_LIO_LIWe discovered that muci10 seeds, lacking heteromannan branches, had elevated tolerance to salt stress, while heteromannan elongation mutants exhibited reduced germination in CaCl2. In contrast, xylan made by MUCILAGE-RELATED21 (MUCI21) was found to be required for the adherence of mucilage pectin to microfibrils made by CELLULOSE SYNTHASE5 (CESA5) as well as to a SOS5-mediated network. C_LIO_LIOur results indicate that the substitution of xylan and glucomannan in seeds can fine-tune mucilage adherence and salt tolerance, respectively. The study of germinating seeds can thus provide insights into the synthesis, modification and function of complex glycans. C_LI

plant biology↗

Plant carbohydrate depletion spreads via ectomycorrhizal networks impairing plant water relations

Carbon and water relations are fundamental to plant life and strongly interact. Under drought, the ability of plants to assimilate carbon is reduced, which increases their consumption of stored labile carbon in the form of non-structural carbohydrates (NSC). This process may impair plant water relations, but mechanisms are not clear, and we do not know if their effects are independent of water deficit. If so, carbon costs of fungal symbionts could also indirectly influence drought tolerance of plants through stored NSC depletion. We connected well-watered Pinus ponderosa seedling pairs via ectomycorrhizal (EM) networks where one seedling was shaded and the other experienced full light and compared responses to seedling pairs in the light. We measured plant water relations and traced carbon movements using 13CO2 to explore the mechanisms linking stored NSC to water relations, and to identify potential tradeoffs between drought tolerance and maintaining EM fungi under carbon-limiting conditions. We found that even in the absence of drought, mild NSC depletion decreased plant drought tolerance by indirectly impairing osmoregulation capacity and turgor maintenance. This demonstrates that NSC storage influences plant drought tolerance independently of plant water status. We also found that EM networks propagated NSC depletion and its negative effects on drought tolerance from carbon stressed hosts to non-stressed hosts. These results highlight carbon allocation tradeoffs between supporting fungal symbionts and retaining water via stored NSC and have implications for biotic interactions and forest drought responses. Significance StatementThe potential effects of future drought on global carbon cycles, vegetation-climate feedbacks, species distributions and their ecological impacts, urgently call for a clear understanding of factors influencing vegetation tolerance to drought. Key to this is the understanding of mechanisms and processes by which plants tolerate drought and how prevalent plant-fungal interactions may influence these processes. We demonstrate that even mild depletion of plant non-structural carbohydrate (NSC) storage readily decreases plant water retention capacity, therefore decreasing tolerance to drought. Because plant-fungal interactions depend on NSC exchange, plants face carbon-allocation tradeoffs between maintaining drought tolerance and feeding fungal symbionts. The impacts of these tradeoffs extend across plants connected via ectomycorrhizal networks as fungi propagate NSC depletion from NSC-limited plants to non-stressed individuals.

plant biology↗

Not out of the box: phylogeny of the broadly sampled Buxaceae

The Buxaceae constitute a morphologically diverse phylogenetic lineage of six genera, which includes about 140 species. The most well-known genera are Buxus, Sarcococca, and Pachysandra. Few species of woody Styloceras grow on mid-elevations in the Andes mountains region. Didymeles, with three species endemic to Madagascar, and the monotypic Haptanthus from Honduras, are the most unusual members of the group. The infra-familial classification of Buxaceae is controversial, and molecular data about many species, especially Old World, is still lacking. We used broad taxonomic sampling and molecular data from four chloroplast markers, and the nuclear ribosomal ITS to estimate their phylogeny. These data provide phylogenetic placements of 50 species and enabled better estimates of boundaries in Buxaceae. We described two subfamilies, two monotypic genera, two Buxus subgenera, and one new species of Didymeles from Madagascar.

plant biology↗

A semi-automated method for measuring xylem vessel length distribution

Knowledge about the length of xylem vessels is essential to understand water transport in plants because these multicellular units show a 100-fold variation, from less than a centimeter to many meters. However, the available methods to estimate vessel length distribution (VLD) are excessively time consuming and do not allow large and in-depth surveys. Here, we describe a semi-automated method to measure VLD using an automated Pneumatron device. Gas conductivity of a xylem tissue with a certain length is estimated in a straightforward and precise way with the Pneumatron in a way theoretically similar to the air-injection method. The method presented enables fast and easy measurements using multiple devices simultaneously (>50 samples day-1), which is a significant advantage. Here, the apparatus is described in detail as well as how measurements are taken. We also present the software and an R-script for data analysis. The method described represents an important contribution to studies on plant hydraulic architecture and can improve our understanding about the role of VLD in plant performance under varying water availability.

plant biology↗

A Failure Mode and Effect Analysis of plant metabolism reveals why cytosolic fumarase is required for temperature acclimation in Arabidopsis

Plants acclimate their photosynthetic capacity in response to changing environmental conditions. In Arabidopsis thaliana, photosynthetic acclimation to cold requires the accumulation of the organic acid fumarate, catalysed by a cytosolic fumarase FUM2, however the role of this is currently unclear. In this study, we use an integrated experimental and modelling approach to examine the role of FUM2 and fumarate across the physiological temperature range. Using physiological and biochemical analyses, we demonstrate that FUM2 is necessary for high as well as low temperature acclimation. To understand the role of FUM2 activity, we have adapted a reliability engineering technique, Failure Mode and Effect Analysis (FMEA), to formalize a rigorous approach for ranking metabolites according to the potential risk that they pose to the metabolic system. FMEA identifies fumarate as a low-risk metabolite. Its precursor, malate, is shown to be high-risk and liable to cause system instability. We conclude that the role of cytosolic fumarase, FUM2, is to provide a fail-safe, maintaining system stability under changing environmental conditions. We argue that FMEA is a technique which is not only useful in understanding plant metabolism, it can also be used to study reliability in other systems and aid the design of synthetic pathways.

plant biology↗

Salicylic acid mediated immune response of Citrus Sinensis to varying frequencies of herbivory and pathogen inoculation

Plant immunity against pathogens and pests is comprised of complex mechanisms orchestrated by signaling pathways regulated by plant hormones [Salicylic acid (SA) and Jasmonic acid (JA)]. Investigations of plant immune response to phytopathogens and phloem-feeders have revealed that SA plays a critical role in reprogramming of the activity and/or localization of transcriptional regulators via post-translational modifications. We explored the contributing effects of herbivory by a phytopathogen vector [Asian citrus psyllid, Diaphorina citri] and pathogen [Candidatus Liberibacter asiaticus (CLas)] infection on response of sweet orange [Citrus sinensis (L.) Osbeck] using manipulative treatments designed to mimic the types of infestations/infections that citrus growers experience when cultivating citrus in the face of Huanglongbing (HLB) disease. A one-time (7 d) inoculation access period with CLas-infected vectors caused SA-associated upregulation of PR-1, stimulating defense response after a long period of infection without herbivory (270 and 330 days). In contrast, while repeated (monthly) pulses of 7 d psyllid feeding injury stimulated immunity in CLas-infected citrus by increasing [SA] in leaves initially (up to 120 d), long-term (270 and 330 days) repeated herbivory caused [SA] to decrease coincident with upregulation of genes associated with SA metabolism (BMST and DMR6). Similarly, transcriptional responses and metabolite (SA and its analytes) accumulation in citrus exposed to a continuously reproducing population of D. citri exhibited a transitory upregulation of genes associated with SA signaling at 120 days and a posterior downregulation after long-term psyllid (adults and nymphs) feeding (270 and 330 days). Herbivory played an important role in regulation of SA accumulation in mature leaves of C. sinensis, whether or not those trees were coincidentally infected with CLas. Our results indicate that prevention of feeding injury inflicted by D. citri from the tritrophic interaction may allow citrus plants to better cope with the consequences of CLas infection, highlighting the importance of vector suppression as a component of managing this cosmopolitan disease. Author SummaryWe explored tritrophic interactions among an insect vector (Diaphorina citri) - phytopathogen (Candidatus Liberibacter asiaticus) - and cultivated fruit crop [sweet orange, Citrus sinensis (L) Osbeck]. Transcriptional and metabolic responses of plants were analyzed over an extended time-course of disease progression after various frequencies of herbivore feeding and durations of pathogen infection using manipulative treatments designed to mimic the types of infestations/infections that citrus growers experience when cultivating citrus in the presence of the devastating citrus disease, huanglongbing. We found that in the absence of coincident psyllid feeding damage, citrus trees could mount a defense response against the pathogen by activating the salicylic acid (SA) pathway. Repeated, monthly pulses of herbivory led to pronounced stimulation of SA transcription that was coincident with diminished pathogen titers in plants. Although insect injury initially activated SA-dependent defense responses, continuous and/or long-term ([≥] 270 d) herbivory shut down PR-1-dependent defense responses against the pathogen. Our results provide a mechanism explaining how vector suppression contributes to maintaining health of cultivated citrus in areas where huanglongbing is endemic. Our results also point to specific gene targets that may yield novel genotypes expressing tolerance against CLas after appropriate manipulations.

plant biology↗

Differential expression of starch and sucrose metabolic genes linked to varying biomass yield in Miscanthus hybrids

Miscanthus is a commercial lignocellulosic biomass crop owing to its high biomass productivity and low chemical input requirements. Interspecific Miscanthus hybrids with high biomass yield were shown to have low concentrations of starch and sucrose but high concentrations of fructose. We performed a transcriptional RNA-seq analysis between selected Miscanthus hybrids with contrasting values for these phenotypes to clarify how these phenotypes are genetically controlled. We observed that genes directly involved in the synthesis and degradation of starch and sucrose were down-regulated in high yielding Miscanthus hybrids. At the same time, glycolysis and export of triose phosphates were up-regulated in high yielding Miscanthus hybrids. Our results evidence a direct relationship between high expression of essential enzymatic genes in the starch and sucrose pathways, high starch concentrations, and lower biomass production. The strong interconnectivity between genotype, chemotype and agronomic traits opens the door to use the expression of well-characterised genes in the starch and sucrose pathway for the early selection of high biomass yielding genotypes from large Miscanthus populations.

plant biology↗

An improved Nicotiana benthamiana strain for aphid and whitefly research

Nicotiana benthamiana is used extensively as a platform for transient gene expression and as a model system for studying plant-virus interactions. However, many tobacco-feeding generalist herbivores, including Myzus persicae (green peach aphid), Bemisia tabaci (whitefly), Macrosiphum euphorbiae (potato aphid), Heliothis virescens (tobacco budworm), Trichoplusia ni (cabbage looper), and Helicoverpa zea (corn earworm), grow poorly on N. benthamiana, limiting its utility for research on plant-insect interactions. Using CRISPR/Cas9, we generated knockout mutations in two N. benthamiana acylsugar acyltransferases, ASAT1 and ASAT2, which contribute to the biosynthesis of insect-deterrent acylsucroses. Whereas asat1 mutations reduced the abundance of two predominant acylsucroses, asat2 mutations caused almost complete depletion of foliar acylsucroses. The tested hemipteran and lepidopteran species survived, gained weight, and/or reproduced significantly better on asat2 mutant plants than on wildtype N. benthamiana. Furthermore, both asat1 and asat2 mutations reduced the water content and increased the temperature of leaves, indicating that foliar acylsucroses can protect against desiccation. Two experiments demonstrated the utility of the N. benthamiana asat2 mutant line for insect bioassays. Transmission of turnip mosaic virus by M. persicae was significantly improved by an asat2 mutation. Tobacco rattle virus constructs were used for virus-induced gene silencing of acetylcholinesterase, squalene synthase, toll-like receptor 7, and tubulin-specific chaperon D genes in B. tabaci, an experiment that would have been difficult with wild-type N. benthamiana due to high insect mortality. Additionally, the absence of acylsugars in asat2 mutant lines will simplify transient expression assays for the functional analysis of acylsugar biosynthesis genes from other Solanaceae.

plant biology↗

Does plant root architecture respond to potassium nutrition under water stress? A case from rice seedling root system architectural and growth responses.

The root is the sensing organ for potassium (K) and water availability. We evaluated whether K availability influences root architecture and contributes to drought tolerance under moisture stress. Rice seedling growth was severely affected by low K availability under water stress, and the substantial reductions in root projected area, maximum width, and width to depth ratio were observed. High K availability helps maintain root top and bottom angles and reduces root steepness under mild water stress, but over K nutrition does not ensure higher seedling growth. Under severe water stress, the steepness was more regulated by water than K availability.

plant biology↗