Biology subjects

Collins, B.

Publications and source records attributed to Collins, B..

At least 19 recordsLinked to original sources

bioRxiv2026

Copine-6 integrates calcium, phosphoinositide and Rab11 signals to coordinate glutamate receptor recycling

Endosomal trafficking is a major pathway that delivers cell-surface proteins, including glutamate receptors, to support neurotransmission and normal brain functions. Activity-dependent insertion of glutamate receptors is essential for synaptic plasticity, learning and memory. Copine-6 is a neuronal-specific calcium (Ca2+) binding protein that mediates activity-induced exocytosis of -amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA)-type glutamate receptors. The activation of N-methyl-D-aspartate (NMDA) receptors triggers Ca2+-dependent translocation of Copine-6 to intracellular endosomal compartments. However, the mechanisms underlying the activity-dependent accumulation of Copine-6 in endosomes remain unknown. Here, we show that Copine-6 exhibits Ca2+-dependent binding to phosphatidylinositol-3-phosphate (PI(3)P) through the C2B domain and displays enhanced interaction with active Rab11a in a Ca2+-independent manner via the vWA domain. Mutations in the C2B that inhibit binding to PI(3)P not only block the activity-induced translocation of Copine-6 to early endosomes, but it also causes an aberrant accumulation of Copine-6 in recycling endosomes. Consequently, loss of Copine-6 expression impairs the efficient coupling of early and recycling endosomes and blocks activity-dependent delivery of both AMPA and NMDA receptors onto the neuronal plasma membrane. These defects can be restored by re-expressing wild-type Copine-6, but not the C2B phospholipid-binding mutant. Together, our findings establish Copine-6 as a molecular bridge that enhances coupling between the early and recycling endosomal membranes, thereby facilitating the activity-dependent forward trafficking of glutamate receptors to the neuronal plasma membrane to maintain synaptic potentiation.

cell biology↗

bioRxiv2026

The GTPase activating protein Gyp6 binds Retromer and inactivates Rab7/Ypt7 to coordinate the formation of endosomal carriers

The Retromer coat is conserved in all eukaryotes and is crucial for the correct intracellular sorting of many transmembrane receptors and lysosomal hydrolases. Retromer is an effector of the late endosomal small GTPase RAB7 and is also implicated in its inactivation required for proper endosomal maturation. Here, we explore the role of controlled GTP hydrolysis by the RAB7 ortholog Ypt7 in the formation of Retromer-coated membrane carriers in yeast. Proximity labelling and genetic ablation identify the GTPase Activating Protein (GAP) Gyp6 as a critical regulator of Ypt7 activity in the context or Retromer. Structural studies show that Retromer recruits Gyp6 through its Vps29 subunit, which recognises a specific PL motif and a secondary binding site in the C-terminal domain of Gyp6. This interaction does not occur with other yeast GAPs. Ablation of the Gyp6-Retromer interface or the catalytic activity of Gyp6 leads to the accumulation of tubular structures on endo-lysosomal compartments and to increased association of Ypt7 with Retromer and its cargo Vps10. These results support a model in which Gyp6 controls the switch from Ypt7-dependent Retromer coat assembly and cargo collection to the departure of the carrier through membrane fission and uncoating.

cell biology↗

bioRxiv2025

An efficient eukaryotic cell-free expression and correlative cryo-electron tomography platform for structural biology of macromolecular complexes

Cell-free expression using Leishmania tarentolae lysates allows rapid expression of eukaryotic proteins directly from DNA templates. We develop a pipeline that combines cell-free expression system with cryogenic fluorescence microscopy that we term CC-FLEXCET (Correlative Cell-Free Leishmania EXpression and Cryo-Electron Tomography), to target and visualize expressed protein complexes by cryo-electron tomography at high resolution. We demonstrate the utility of this method by structurally characterising the filaments of the full-length apoptosis-associated speck like protein containing CARD (ASC) protein. Cell-free expression of ASC results in a polymeric structure characteristic of its cellular speck assembly. Sub-tomogram averaging allows us to resolve both the pyrin domain (PYD) to medium resolution, and show, for the first time, the arrangement of the flexibly linked caspase recruitment domain (CARD). Finally, we observed an interaction between the ASC filament and the L. tarentolae ribosome. Using template matching and quantitative approaches, we characterise this interaction and determine that there is a random structural association between the filament and the ribosome, with 57% of ribosomes oriented with the LSU toward the ASC polymer. CC-FLEXCET facilitates structural analysis of macromolecules and protein-lipid assemblies without need of purification, providing a pipeline from DNA template to protein expression to cryo-tilt series acquisition, within a single day.

biochemistry↗

bioRxiv2025

Saving water to get 'more crop per drop' - A new phenotyping framework revealed wide plasticity in wheat

Improving transpiration efficiency (TE) offers a pathway to increase yield in drought-prone environments. This study examined genotypic variation in TE and its physiological determinants across diverse wheat lines. An initial experiment with six cultivars was expanded to 105 genetically-diverse genotypes evaluated under well-watered conditions and fluctuating vapour pressure deficit (VPD). Using a high-throughput lysimeter platform, transpiration rates were recorded every 10 minutes and normalised daily at low VPD to account for genotypic variations in canopy size. TE was strongly associated with reduced normalised transpiration rate at high VPD (TRnorm-highVPD), while no significant relationship was found with maximum photosynthetic capacity. High-TE lines achieved either greater biomass with similar water use or similar biomass with lower water use, reflecting a water-saving strategy under high evaporative demand. A complementary experiment under low VPD revealed limited genotypic variation in intrinsic TE, reinforcing the value of TRnorm-highVPD as a screening trait. Consistent correlations between TE and TRnorm-highVPD across experiments highlight the potential of TRnorm-highVPD as a robust phenotyping target. Several high-TE lines outperformed modern cultivars, offering promising sources of novel alleles. These findings provide a scalable framework to identify drought-resilient genotypes and support breeding strategies to improve water productivity and achieve more crop per drop. HIGHLIGHTWheat genotypes with reduced normalised transpiration rate under high evaporative demand achieved greater transpiration efficiency. A new automatised high-throughput phenotyping framework is proposed to assist drought-resilient breeding.

physiology↗

bioRxiv2025

Envirotyping Facilitates Understanding of Genotype x Environment Interactions and Highlights the Potential of Stay-green Traits in Wheat

Better understanding genotype by environment interaction (GxE) can help breeding for better adapted varieties. Envirotyping for environmental water status was applied to assist interpretation of GxE interactions for wheat yield in multi-environment trials conducted in drought-prone Australian environments. Genotypes from a multi-reference parent nested association mapping (MR-NAM) population were tested in 10 trials across the Australian wheatbelt. Genotype yield and phenology were measured in all trials, while traits associated with the stay-green phenotype were assessed for a subset of 5 trials. Envirotyping was conducted by characterizing water stress experienced by genotypes at each trial using crop modelling. Envirotyping facilitated the understanding of GxE interactions by explaining 75, 67, and 66% of the genotypic variance for yield in severe water-limited (ET3), mild terminal water-stress (ET2), and water-sufficient (ET1) environments, respectively. Yield and stay-green were negatively correlated with flowering time in most trials. However, when focusing on genotypes flowering at similar times within a trial, no significant correlation was found between yield and flowering. Importantly stay-green traits remained significantly correlated with yield. Stay-green traits such as delayed onset of senescence and slower senescence rate benefited yield by 0.2 to 1.1 t ha-1 across environments, highlighting the breeding potential for stay-green traits in both water-sufficient and water-limited environments. Hence, sustaining green leaf area during grain filling helped to enhance yield. Envirotyping to better understand GxE interactions for yield, coupled with screening for traits exhibiting superior adaptive mechanisms, are powerful assets in assisting plant breeders to select more effectively drought adapted genotypes. HighlightsGenotype x environment interaction for yield could be reduced with envirotyping. Envirotyping enabled a 75% gain in genotypic variance in severe drought conditions. Envirotyping clarified breeding potential of stay-green traits across environments. Stay-green has potential to enhance wheat yield across diverse environments.

physiology↗

bioRxiv2024

Mapping the endosomal proximity proteome reveals Retromer as a hub for RAB GTPase regulation.

Endosomal retrieval and recycling of integral cargo proteins is essential for cell, tissue and organism-level development and homeostasis and is orchestrated through a specialised retrieval sub-domain on the endosomal vacuole. However, although sub-domain dysfunction is associated with human disease our appreciation of the molecular details and functional components of the retrieval sub-domain(s) remains poorly described. Here, using comparative proximity proteomics of critical retrieval sub-domain components Retromer and Retriever, their cargo adaptors, and a component of the opposing ESCRT-degradative sub-domain, we provide a data-rich resource that identifies new molecular details of retrieval sub-domain composition and organization, including an unrecognised complexity in the interface of Retromer with RAB GTPases. Combining X-ray crystallography and in silico predictions with extensive biochemical and cellular analysis, we dissect the direct association of Retromer with RAB10 regulators DENND4A, DENND4C, TBC1D1, and TBC1D4, and the RAB35 regulator TBC1D13. Overall, we conclude that the Retromer retrieval sub-domain constitutes a major hub for the regulated switching of selected RAB GTPases and propose that this constitutes a major component of the role of Retromer in neuroprotection.

cell biology↗

bioRxiv2024

Unsaturated lipids as key control points for caveola formation and disassembly

Caveolae are specialized plasma membrane domains with a unique lipid composition. Recent work has implicated lipid peroxidation in triggering caveola disassembly, releasing caveolar proteins to regulate the cellular response to oxidative stress. Here we investigated the role of specific lipid species in caveola formation and response to oxidative stress. Systematic screening of lipid enzymes identified ACSL4, a critical enzyme in the synthesis of polyunsaturated fatty acid-containing lipids, and enzymes involved in the biosynthesis of pro-ferroptotic ether lipids, as key regulators of caveola formation. Omega-6 fatty acids promoted efficient caveola formation, while their oxidation or displacement by omega-3 or monounsaturated fatty acids disrupted this process. Moreover, we found that omega-6 fatty acid-containing membrane lipids were required for oxidative stress-induced caveola disassembly. These findings unveil a new model for caveola formation, highlighting specific unsaturated lipids as essential caveolar components and key control points for caveola disassembly in response to an oxidizing environment.

cell biology↗

bioRxiv2023

VAMP2/Munc18-1 domain 3a interaction controls the nanoscale reorganization underpinning vesicular priming

SNARE-mediated secretory vesicle (SV) exocytosis underpins neuronal communication. Munc18-1 orchestrates SNARE complex formation by controlling the opening of syntaxin-1A. How the SV-plasma membrane interface becomes fusion-competent at the nanoscale level is poorly understood. Here, we propose that the interaction of Munc18-1 with VAMP2 during vesicular docking triggers nanoscale re-organization which renders the SV-plasma membrane interface fusion-competent. We identified and mutated key residues in Munc18-1 domain 3a (A297 and T304) hypothesised to impair its interaction with VAMP2. Munc18-1A297H, and to a lesser extent Munc18-1T304H, constrained SVs on the plasma membrane and reduced stimulated secretion, under re-expression conditions in Munc18-1/2 double knockout neurosecretory cells. Moreover, the de-clustering of Munc18-1 in response to activity was lost for both mutants. The interaction of VAMP2 with the Munc18-1 domain 3a therefore controls the re-organization of the nanoscale environment of the docked SV-plasma membrane interface, fostering syntaxin-1A opening and Munc18-1 release to ensure that SNARE assembly only occurs within the confinement of docked vesicles.

neuroscience↗

bioRxiv2023

Pre- and post-flowering impacts of natural heat events on yield components in wheat

O_LICONTEXT Wheat crops are highly sensitive to elevated temperatures and experience significant yield losses when short periods of heat occur at sensitive developmental phases. C_LIO_LIOBJECTIVE This research aimed at quantifying wheat responses of grain yield and yield components to heat indicators in fluctuating field conditions. C_LIO_LIMETHODS The impacts of high temperature on yield and its components were assessed for 20-35 wheat lines in irrigated multi-environment trials over three years. Genotypes were cultivated using a novel photoperiod extension method adjacent to some conventional yield plots with different sowing dates. In the photoperiod-extension method, either single stems or plant quadrates were tagged at specific growth stages and hand-harvested at maturity, while conventional plots were mechanically harvested at maturity. The impact of heat was estimated for events occurring at different developmental stages and different temperature thresholds (26 to 35{circ}C). C_LIO_LIRESULTS The closest correlation between heat events and grain number was observed for a threshold temperature of 28{circ}C pre-flowering. For individual grain weight, the correlation was statiscally the closest for threshold temperatures above 32{degrees}C post-flowering. In the tested environments, grain number was most sensitive to heat between 300 and 200{circ}Cd before flowering. For each hot hour (T > 28{circ}C) during this period, wheat genotypes lost an extra 0.25 grains spike-1 or 90 grains m-2 on average. Post-flowering heat reduced individual grain weight by 0.26 mg (at spike harvest) and grain yield by 2.44 g m-2 (at plot harvest) for every hot hour (T > 32{circ}C) between 0 and 500{circ}Cd after flowering. Heat impacts were the clearest for plants with synchronised phenology. In addition, results suggest that heat impacts can be quantified more reliably using finer time units (i.e. hot hours rather than days). C_LIO_LIONCLUSIONS Natural heat events strongly impacted grain number and individual grain weight of wheat for temperatures above 28-30{degrees}C in well-watered conditions. Reduction in grain number and individual grain weight were strongly associated with accumulated hot hours that occurred during 200-300{degrees}Cd before and 0-500{degrees}Cd after flowering, respectively. C_LIO_LIIMPLICATIONS The findings from this study will assist improvement for crop modelling in response to heat, development of relevant phenotyping methods and selection of cultivars with better adaptation to warmer environments. C_LI

plant biology↗

bioRxiv2023

Molecular basis for the interaction of Mint proteins with Munc18-1 and interactome analyses with AlphaFold2

Munc18-interacting proteins (Mints) are multi-domain adaptors that regulate neuronal membrane trafficking, signalling and neurotransmission. Mint1 and Mint2 are highly expressed in the brain with overlapping roles in the regulation of synaptic vesicle fusion required for neurotransmitter release by interacting with the essential synaptic protein Munc18-1. Here, we have used AlphaFold2 to identify and then validate the mechanisms that underpin both the specific interactions of neuronal Mint proteins with Munc18-1 as well as their wider interactome. We find a short acidic -helical motif (AHM) within Mint1 and Mint2 is necessary and sufficient for specific binding to Munc18-1 and binds a conserved surface on Munc18-1 domain3b. In Munc18-1/2 double knockout neurosecretory cells mutation of the Mint-binding site reduces the ability of Munc18-1 to rescue exocytosis, and although Munc18-1 can interact with Mint and Sx1a proteins simultaneously in vitro we find they have mutually reduced affinities, suggesting an allosteric coupling between the proteins. Using AlphaFold2 to then examine the entire cellular network of putative Mint interactors provides a structural model for their assembly with a variety of known and novel regulatory and cargo proteins including ARF3/ARF4 small GTPases, and the AP3 clathrin adaptor complex. Validation of Mint1 interaction with a new predicted binder TJAP1 provides experimental support that AlphaFold2 can correctly predict interactions across such large-scale datasets. Overall, our data provides insights into the diversity of interactions mediated by the Mint family and shows that Mints may help facilitate a key trigger point in SNARE complex assembly and vesicle fusion.

biochemistry↗

bioRxiv2023

Structure of the Commander endosomal trafficking complex linked to X-linked intellectual disability/Ritscher-Schinzel syndrome

The Commander complex is required for endosomal recycling of diverse transmembrane cargos and is mutated in Ritscher-Schinzel syndrome. It comprises two subassemblies; Retriever composed of VPS35L, VPS26C and VPS29, and the CCC complex which contains ten subunits COMMD1-COMMD10 and two coiled-coil domain-containing (CCDC) proteins CCDC22 and CCDC93. Combining X-ray crystallography, electron cryomicroscopy and in silico predictions we have assembled a complete structural model of Commander. Retriever is distantly related to the endosomal Retromer complex but has unique features preventing the shared VPS29 subunit from interacting with Retromer-associated factors. The COMMD proteins form a distinctive hetero-decameric ring stabilised by extensive interactions with CCDC22 and CCDC93. These adopt a coiled-coil structure that connects the CCC and Retriever assemblies and recruits a sixteenth subunit, DENND10, to form the complete Commander complex. The structure allows mapping of disease-causing mutations and reveals the molecular features required for the function of this evolutionarily conserved trafficking machinery.

biochemistry↗

bioRxiv2022

A cross-scale analysis to understand and quantify effects of photosynthetic enhancement on crop growth and yield

Photosynthetic manipulation provides new opportunities for enhancing crop yield. However, understanding and quantifying effectively how the seasonal growth and yield dynamics of target crops might be affected over a wide range of environments is limited. Using a state-of-the-art cross-scale model we predicted crop-level impacts of a broad list of promising photosynthesis manipulation strategies for C3 wheat and C4 sorghum. The manipulation targets have varying effects on the enzyme-limited (Ac) and electron transport-limited (Aj) rates of photosynthesis. In the top decile of seasonal outcomes, yield gains with the list of manipulations were predicted to be modest, ranging between 0 and 8%, depending on the crop type and manipulation. To achieve the higher yield gains, large increases in both Ac and Aj are needed. This could likely be achieved by stacking Rubisco function and electron transport chain enhancements or installing a full CO2 concentrating system. However, photosynthetic enhancement influences the timing and severity of water and nitrogen stress on the crop, confounding yield outcomes. Strategies enhancing Ac alone offers more consistent but smaller yield gains across environments, Aj enhancement alone offers higher gains but is undesirable in less favourable environments. Understanding and quantifying complex cross-scale interactions between photosynthesis and crop yield will challenge and stimulate photosynthesis and crop research. Summary StatementLeaf-canopy-crop prediction using a state-of-the-art cross-scale model improves understanding of how photosynthetic manipulation alters wheat and sorghum growth and yield dynamics. This generates novel insights for quantifying impacts of photosynthetic enhancement on crop yield across environments.

plant biology↗

bioRxiv2022

Proteostatic regulation of caveolins avoids premature oligomerisation and preserves ER homeostasis

Caveolin-1 (CAV1) and CAV3 are membrane sculpting proteins driving formation of plasma membrane caveolae. Caveola formation is unique as it requires oligomerisation of newly synthesised caveolins through the biosynthetic-secretory pathway. Here, we combine structural, biochemical, and microscopy analyses to examine the early proteostasis of caveolin family members and mutants. We describe striking trafficking differences between newly synthesised caveolins, with CAV1 rapidly exported to the Golgi but CAV3 showing ER retention and targeting to lipid droplets. Only monomeric/low oligomeric caveolins are efficiently exported from the ER, with oligomers assembling beyond the cis-Golgi and disease-causing mutations leading to detrimental non-functional complexes. Caveolins in the ER are maintained at low levels by active proteasomal degradation, avoiding premature oligomerisation and ER stress. Increasing lipid availability, cholesterol for CAV1 and fatty acids for CAV3, enhances trafficking and reduces proteasomal degradation. In conclusion, we identify proteostatic mechanisms that modulate stability and trafficking of newly synthesised caveolins, protecting cells against ER stress but perturbed in caveolin-related disease. SummaryUnderstanding the unique proteostasis of caveolins has important implications for cell biology and physiopathology. Combining structural, microscopy, and biochemical analyses, we uncover new insights into the mechanisms that differentiate the early biosynthetic steps of caveolin family members, isoforms, and pathogenic mutants.

cell biology↗

bioRxiv2021

Experimental and in silico Alphafold2 derived structures of the SNX-RGS proteins suggest a new class of lipid transfer protein

Recent advances in protein structure prediction using machine learning such as AlphaFold2 and RosettaFold presage a revolution in structural biology. Genome-wide predictions of protein structures are providing unprecedented insights into their architecture and intradomain interactions, and applications have already progressed towards assessing protein complex formation. Here we present detailed analyses of the sorting nexin proteins that contain regulator of G-protein signalling domains (SNX-RGS proteins), providing a key example of the ability of AlphaFold2 to reveal novel structures with previously unsuspected biological functions. These large proteins are conserved in most eukaryotes and are known to associate with lipid droplets (LDs) and sites of LD-membrane contacts, with key roles in regulating lipid metabolism. They possess five domains, including an N-terminal transmembrane domain that anchors them to the endoplasmic reticulum, an RGS domain, a lipid interacting phox homology (PX) domain and two additional domains named the PXA and PXC domains of unknown structure and function. Here we report the crystal structure of the RGS domain of sorting nexin 25 (SNX25) and show that the AlphaFold2 prediction closely matches the experimental structure. Analysing the full-length SNX-RGS proteins across multiple homologues and species we find that the distant PXA and PXC domains in fact fold into a single unique structure that notably features a large and conserved hydrophobic pocket. The nature of this pocket strongly suggests a role in lipid or fatty acid binding, and we propose that these molecules represent a new class of conserved lipid transfer proteins.

biochemistry↗

bioRxiv2021

Proteomic identification and structural basis for the interaction between sorting nexin SNX17 and PDLIM family proteins

The sorting nexin SNX17 controls endosome-to-cell surface recycling of diverse transmembrane cargo proteins including integrins, the amyloid precursor protein and lipoprotein receptors. This requires association with the multi-subunit Commander trafficking complex, which depends on the C-terminus of SNX17 through unknown mechanisms. Using affinity enrichment proteomics, we find that a C-terminal peptide of SNX17 is not only sufficient for Commander interaction but also associates with members of the actin-associated PDZ and LIM domain (PDLIM) family. We show that SNX17 contains a type III PSD95/Dlg/Zo1 (PDZ) binding motif (PDZbm) that binds specifically to the PDZ domains of PDLIM family proteins but not to other PDZ domains tested. The structure of the PDLIM7 PDZ domain bound to the SNX17 C-terminus was determined by NMR spectroscopy and reveals an unconventional perpendicular peptide interaction. Mutagenesis confirms the interaction is mediated by specific electrostatic contacts and a uniquely conserved proline-containing loop sequence in the PDLIM protein family. Our results define the mechanism of SNX17-PDLIM interaction and suggest that the PDLIM proteins may play a role in regulating the activity of SNX17 in conjunction with Commander and actin-rich endosomal trafficking domains.

biochemistry↗

bioRxiv2021

Sex-Specific Function and Morphology of the Anterior Cruciate Ligament During Skeletal Growth in a Porcine Model

Pediatric anterior cruciate ligament (ACL) injuries are on the rise, and females experience higher ACL injury risk than males during adolescence. Studies in skeletally immature patients indicate differences in ACL size and joint laxity between males and females after the onset of adolescence. However, functional data regarding the ACL and its anteromedial and posterolateral bundles in the pediatric population remain rare. Therefore, this study uses a porcine model to investigate the sex-specific morphology and function of the ACL and its bundles throughout skeletal growth. Hind limbs from male and female Yorkshire pigs aged early youth to late adolescence were imaged using magnetic resonance imaging to measure the size and orientation of the ACL and its bundles, then biomechanically tested under anterior-posterior drawer using a robotic testing system. Joint laxity decreased (p<0.001) while joint stiffness increased (p<0.001) throughout skeletal growth in both sexes. The ACL was the primary stabilizer against anterior tibial loading in all specimens, while the functional role of the anteromedial bundle increased with age (p<0.001), with an earlier shift in males. ACL and posterolateral bundle cross-sectional area and ACL and anteromedial bundle length were larger in males than females during adolescence (p<0.01 for all), while ACL and bundle sagittal angle remained similar between sexes. Additionally, in situ ACL stiffness correlated with cross-sectional area across skeletal growth (r2=0.75, p<0.001 in males and r2=0.64, p<0.001 in females), but not within age groups. This study has implications for age and sex-specific surgical intervention strategies and suggests the need for human studies.

bioengineering↗

bioRxiv2021

ChromeBat: A Bio-Inspired Approach to 3D Genome Reconstruction

BackgroundWith the advent of Next Generation Sequencing and the Hi-C experiment, high quality genome-wide contact data is becoming increasingly available. This data represents an empirical measure of how a genome interacts inside the nucleus. Genome conformation is of particular interest as it has been experimentally shown to be a driving force for many genomic functions from regulation to transcription. Thus, the Three Dimensional Genome Reconstruction Problem seeks to take Hi-C data and produce the complete physical genome structure as it appears in the nucleus for genomic analysis. ResultsWe propose and develop a novel method to solve the Chromosome and Genome Reconstruction problem based on the Bat Algorithm which we called ChromeBat. We demonstrate on real Hi-C data that ChromeBat is capable of state of the art performance. Additionally, the domain of Genome Reconstruction has been criticized for lacking algorithmic diversity, and the bio-inspired nature of ChromeBat contributes algorithmic diversity to the problem domain. ConclusionsChromeBat is an effective approach at solving the Genome Reconstruction Problem. The source code and usage guide can be found here: https://github.com/OluwadareLab/ChromeBat.

bioinformatics↗

bioRxiv2021

Contribution of climate models and APSIM phenological parameters to uncertainties in spring wheat simulations: application of SUFI-2 algorithm in northeast Australia

We used SUFI-2 for the first time to calibrate the phenology module of the APSIM-wheat model for 10 spring wheat cultivars cultivated in northeast Australia (south-eastern Queensland). Calibration resulted in an average RMSE of 5.5 d for developmental stages from stem elongation up to flowering. Projections from 33 climate models under the representative concentration pathway 8.5 were used for simulations at 17 sites. Using adapted sowing times, we simulated significantly shorter crop cycles and grain yield improvements for the period 2036-2065 relative to 1990-2019 for three selected cultivars (Hartog, Scout and Gregory). Photoperiod and vernalisation sensitivities were shown to be the largest and smallest contributors to total uncertainties in the simulated flowering day and grain yield. Uncertainties in climate models had a relatively minor contribution to the total uncertainties in the simulated values of target traits. This contribution significantly increased when climate change impact on the target traits was estimated.

plant biology↗