Biology subjects

Foo, E.

Publications and source records attributed to Foo, E..

9 recordsLinked to original sources

bioRxiv2026

Chromosome-level genome sequence of the C4 grass Themeda triandra reveals karyotype orthology with sorghum and genetic variation in accessions adapted to diverse environments

Themeda triandra (family Andropogoneae) is a pan-continental grass occurring throughout Australia. Recognising its remarkable adaptive capacity, we assembled the nuclear genome sequence of a diploid accession from eastern Australia, finding all ten chromosomes of the 755 Mb assembly highly syntenic with those of Sorghum bicolor. Genotyping and cytometry of range-wide accessions suggested several historical radiation events, with polyploids dominating in arid regions, apart from a notable diploid lineage from the arid north-west of Australia (PAN). A detailed comparison of PAN with two diploids from temperate south-eastern Australia through whole-genome resequencing revealed extensive copy number variation and polymorphism, with changes in genes for heat-shock proteins and flowering regulation reflecting their environmental origin. Exploration of the rich genetic diversity in T. triandra with respect to environmental adaptation is expected to benefit grassland management programs and enable introgression of novel genes into Andropogoneae crops for climate resilience.

genomics↗

bioRxiv2025

Linking drought strategy to climate of origin in a widespread C4 grass species: hydraulic traits, xylem anatomy and stomatal behaviour in Themeda triandra

O_LIHydraulic, stomatal and anatomical traits strongly influence drought survival and productivity, but the extent to which these trait-types are coordinated and relate to climate-of-origin in herbaceous species remains poorly understood. C_LIO_LIWe quantified hydraulic, stomatal and anatomical traits in eight populations of Themeda triandra selected from diverse temperature and precipitation regimes across Australia, grown under common conditions and exposed to drought. Trait - climate-of-origin relationships were quantified using multiple linear mixed models. C_LIO_LILeaf xylem embolism resistance (P50) was unrelated to climate-of-origin precipitation. Instead, plants from drier climates exhibited lower maximum stomatal conductance, earlier stomatal closure during drought and higher stomatal safety margins (the difference between water potential at stomatal closure and P50). Plants from warmer climates exhibited greater embolism resistance and higher hydraulic conductance, along with wider vessels and lower vein density, suggesting adaptation to high evaporative demand. C_LIO_LIOur findings highlight two primary hydraulic strategies related to climate-of-origin: 1) conservative water use and drought avoidance in drier climates, and 2) embolism resistance and hydraulic efficiency in warmer climates. These findings provide new insights into the intraspecific differences in traits and adaptive strategies used by C4 grasses to persist in contrasting climates. C_LI

ecology↗

bioRxiv2025

Parallel CLE peptide signaling pathways control nodulation in pea

Legume root nodulation with nitrogen-fixing bacteria requires precise control via root-shoot-root autoregulation of nodulation (AON). Post-translationally modified root-derived CLAVATA3/Embryo Surrounding Region-Related (CLE) peptides signal through shoot acting leucine-rich repeat receptors (CLAVATAs) to regulate nodule number and this pathway is a target to optimise nodulation. We characterise the AON system in the crop model pea (Pisum sativum L.) and address key gaps in our understanding of AON; the role of parallel signalling pathways, shoot receptor complexes and downstream targets. We use novel mutant combinations, overexpression, grafting, gene expression and careful analysis of infection and nodule organogenesis using GFP-labelled rhizobium. These studies provide evidence that in pea both PsCLE12 and PsCLE13 require arabinosylation via PsRDN1. Perception of PsCLE12 and PsCLE13 in the shoot to suppress the mature nodules in the root requires the pea CLAVATA1 orthologue PsNARK and PsCLV2. However, we found little evidence that PsCLE12 and PsCLE13 suppress infection thread development or that they act via PsTML1 and/or PsTML2, root acting suppressors of nodulation, indicating a role for additional CLE signals. Grafting and double mutant studies indicate that PsNARK can act together with PsCLV2, but also independently, to influences nodulation providing in planta evidence for shoot receptor complexes that control AON. HighlightWe characterise the specific CLE peptide signalling pathway that the model crop legume pea uses to control the number of nitrogen-fixing nodules formed on the root.

plant biology↗

bioRxiv2025

Drought, thermal response and climate-patterning in cuticular conductance of the widespread C4 grass, Themeda triandra

O_LIBackground and Aims: Grasslands underpin global biodiversity, carbon storage, and ecosystem resilience, yet are increasingly threatened by rising temperatures and water scarcity. Understanding how key physiological traits respond to drought and heat is essential for ensuring grassland function under future conditions. Here, we investigated intraspecific variation in leaf cuticular traits--specifically minimum cuticular conductance after stomatal closure (gmin) and its response to temperature--in six Australian accessions of Themeda triandra spanning a wide climatic gradient. We asked whether gmin and its response to drought reflect climate-of-origin and whether the cuticle shows a thermal threshold (Tp) beyond which conductance rises sharply. C_LIO_LIMethods: Plants from six accessions were grown under well-watered (control) glasshouse conditions and then exposed to drought. We measured gmin in both control and drought treatments and assessed the response of gmin to increasing temperature (30-55 {degrees}C) using fresh fully hydrated leaves (control). Climatic data for each site of origin were used to explore trait-environment relationships. C_LIO_LIKey results: Under well-watered conditions, gmin showed no link to climate-of-origin. Under drought, however, gmin displayed clearer climate-linked patterns: accessions from cooler, wetter regions had lower values, contrary to expectations. Drought responses varied strongly among accessions, ranging from marked reductions to significant increases in gmin. With increasing temperature, gmin declined gradually and no accession exhibited a distinct phase transition, indicating a thermally stable cuticle. C_LIO_LIConclusions: Themeda triandra shows considerable intraspecific diversity in gmin and its response to drought. The clearer alignment between climate of origin and gmin measured under drought conditions suggests drought stress is an important filter for gmin expression. These findings provide a physiological basis for identifying genotypes with enhanced resilience for use in grassland conservation and restoration under a warming, drying climate. C_LI

ecology↗

bioRxiv2025

COCHLEATA controls spatial regulation of cytokinin and auxin during nodule development

Root nodules develop in some legumes that host nitrogen-fixing bacteria and likely evolved through modifications of the ancestral lateral root program with plant hormones playing key regulatory roles. Members of the NOOT-BOP-COCH-LIKE transcriptional co-regulator family suppress root identity in legume nodules, including Pisum sativum coch1 that display root-nodule hybrids. However, how COCH/NOOT interacts with hormones to control nodule organogenesis is unclear. We show that PsCOCH (COCHLEATA) is required for spatial tight regulation of auxin and cytokinin during nodule organogenesis and identify key hormone and signalling genes regulated by COCH. COCH suppresses cytokinin levels and response during nodule formation, as cytokinin levels are elevated in Pscoch abnormal nodules and this is mirrored by ectopic cytokinin-responsive TCSn::GUS expression in Pscoch nodule apices, nodule vasculature and in root-like tissue. In contrast, PsCOCH promotes auxin accumulation and precise auxin response patterning in nodules, as Pscoch mutants show significantly reduced auxin levels and severely altered auxin-responsive DR5::GUS expression patterns. RNAseq analysis revealed that Pscoch developing nodules have gene expression profiles more similar to root primordia, with increased expression of defence and auxin response genes (IAA and ARF) and reduced expression of cytokinin biosynthesis genes (IPT3, CYP735A and LOG2) compared to wild type. We found gibberellin is unlikely to act downstream of PsCOCH, as Pscoch and gibberellin-deficient double mutants still form root-nodule hybrids. Ectopic constitutive expression of PsCOCH also produces root-nodule hybrids and we found intriguing links between autoregulation of nodulation pathway and COCH, suggesting that a complex feedback mechanism acts in COCH control of nodule identity.

plant biology↗

bioRxiv2023

Cell layer specific roles for hormones in root development: Gibberellins suppress infection thread progression, promote nodule and lateral root development in the endodermis and interact with auxin and cytokinin

O_LIGibberellins have a profound influence on the formation of lateral root organs. However, the precise role this hormone plays in the cell-specific events during lateral root formation, rhizobial infection and nodule organogenesis, including interactions with auxin and cytokinin, is not clear. C_LIO_LIWe performed epidermal- and endodermal-specific complementation of the severely gibberellin-deficient na pea (Pisum sativum) mutant with Agrobacterium rhizogenes. Gibberellin mutants were used to examine the spatial expression pattern of cytokinin (TCSn) and auxin (DR5) responsive promoters and hormone levels. C_LIO_LIWe found that gibberellins produced in the endodermis promote lateral root and nodule organogenesis and can induce a mobile signal(s) that suppresses rhizobial infection. In contrast, epidermal-derived gibberellins suppress infection but have little influence on root or nodule development. Gibberellins suppress the cytokinin-responsive TCSn promoter in the cortex and are required for normal auxin activation during nodule primordia formation. C_LIO_LIOur findings indicate that gibberellins regulate the checkpoints between infection thread penetration of the cortex and invasion of nodule primordial cells and promotes the subsequent progression of nodule development. It appears that gibberellins limit the progression and branching of infection threads in the cortex by restricting cytokinin response and activate auxin response to promote nodule primordia development. C_LI

plant biology↗

bioRxiv2023

CLE11 and CLE10 Suppress Mycorrhizal Colonisation in Tomato

Symbioses with beneficial microbes are widespread in plants, but these relationships must balance the energy invested by the plants with the nutrients acquired. Symbiosis with arbuscular mycorrhizal (AM) fungi occurs throughout land plants but our understanding of the genes and signals that regulate colonisation levels is limited. Here, we demonstrate that in tomato two CLV3/EMBRYO-SURROUNDING REGION (CLE) peptides, SlCLE10 and SlCLE11, act to suppress AM colonisation of roots. Mutant studies and overexpression via hairy transformation indicate SlCLE11 acts locally in the root to limit AM colonisation. Indeed, SlCLE11 expression is strongly induced in AM colonised roots but SlCLE11 is not required for phosphate suppression of AM colonisation. SlCLE11 may act through as yet uncharacterised signalling pathways, as SlCLE11 does not suppress AM colonisation by acting through two previously characterised receptors with roles in regulating AM colonisation, SlFAB (CLAVATA1 orthologue) or SlCLV2. SlCLE10 appears to play a more minor or redundant role, as cle10 mutants did not influence AM, although the fact that ectopic overexpression of SlCLE10 did suppress colonisation suggests SlCLE10 may play a role in regulating AM colonisation. Our findings show that CLE peptides regulate AM colonisation in the non-legume species tomato.

plant biology↗

bioRxiv2020

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↗

bioRxiv2020

The role of CLV signalling in the negative regulation of mycorrhizal colonisation and nitrogen response of tomato

Plants form mutualistic nutrient acquiring symbioses with microbes, including arbuscular mycorrhizal fungi. The formation of these symbioses is costly and plants employ a negative feedback loop termed autoregulation of mycorrhizae (AOM) to limit arbuscular mycorrhizae (AM) formation. We provide evidence for the role of one leucine-rich-repeat receptor like kinase (FAB), a hydroxyproline O-arabinosyltransferase enzyme (FIN) and additional evidence for one receptor like protein (SlCLV2) in the negative regulation of AM formation in tomato. Reciprocal grafting experiments suggest that the FAB gene acts locally in the root, while the SlCLV2 gene may act in both the root and the shoot. External nutrients including phosphate and nitrate can also strongly suppress AM formation. We found that FAB and FIN are required for nitrate suppression of AM but are not required for the powerful suppression of AM colonisation by phosphate. This parallels some of the roles of legume homologs in the autoregulation of the more recently evolved symbioses with nitrogen-fixing bacteria leading to nodulation. This deep homology in the symbiotic role of these genes suggests that in addition to the early signalling events that lead to the establishment of AM and nodulation, the autoregulation pathway might also be considered part of the common symbiotic toolkit that enabled plants to form beneficial symbioses. HighlightWe describe the role of CLV signalling elements in the negative regulation of arbuscular mycorrhizal symbioses of tomato, including influencing nitrate but not phosphate suppression of mycorrhizal colonisation.

plant biology↗