Biology subjects

Wells, R.

Publications and source records attributed to Wells, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Characterisation of gene expression markers and glucosinolates during discrete infection stages of Pyrenopeziza brassicae in Brassica napus

Light leaf spot (LLS), caused by subcuticular hemibiotrophic ascomycete fungus Pyrenopeziza brassicae, is a major constraint on oilseed rape (Brassica napus) production, yet the genetic and biochemical mechanisms of quantitative disease resistance (QDR) remain poorly defined. Here, disease phenotyping, pathogen quantification, microscopy, gene expression profiling and glucosinolate (GSL) analysis were integrated to dissect resistance mechanisms in B. napus. Disease assays of 19 diverse lines revealed clear contrasts between susceptible and resistant genotypes, with the commercial cultivar Ambassador showing a phenotype inconsistent with the UK Recommended List rating. Microscopy demonstrated that resistance within doubled haploid line Cubs Root does not inhibit spore germination or penetration but restricts hyphal branching and subcuticular colonisation from 4 to 8 days post-inoculation. Expression profiling of seven candidate gene expression markers (GEMs) and pathogenesis-related PR1 showed that cinnamate-4-hydroxylase, phospholipase C4, {beta}-adaptin, universal stress protein and the 40S ribosomal subunit protein S24 were strongly pathogen-induced in resistant lines, whereas a BAHD acyltransferase, a putative susceptibility factor, was induced only in susceptible cultivars. GSL profiling identified negative correlations between disease severity and total GSLs, particularly aliphatic and aromatic GSLs, with 2{square}phenylethyl and 7-methylsulfinyl heptyl GSLs showing the strongest associations with resistance. Together, these results highlight coordinated transcriptional and metabolic responses that limit pathogen proliferation and provide targets for breeding durable LLS resistance in B. napus.

plant biology↗

bioRxiv2026

The degree of subgenome expression bias in B. napus changes between cultivars, tissues and across time

Most extant plants show evidence of past polyploidization events in their genomes. Allopolyploids arise from hybridisation, resulting in the polyploid genome comprising subgenomes from different ancestors. Subsequent adaptation to their environment or selection pressure for specific traits has led to several allopolyploids exhibiting an unequal contribution from their subgenomes to their phenotype. Given the diversity of cultivars grown for different environments, it is possible that the associated regulatory changes may have given rise to different subgenome expression biases. Likewise, different tissues and developmental stages have distinct expression profiles that may correspond more strongly to one subgenome over the other(s). Here, we investigate different metrics for quantifying the contribution of each subgenome in space (tissue) and time (development) in cultivars of Brassica napus. Brassica napus has two subgenomes, A and C, from its ancestors Brassica rapa (A) and Brassica oleracea (C). We find that the C genome has higher overall expression than the A genome, whereas the average expression per gene is higher for the A genome. Direct comparison of homoeologous pairs reveals higher expression of genes on the C genome. We find that the degree of expression bias can change between cultivars, tissues and across time with bias quantification being strongly dependent on the metric. These findings help explain contradictory reports on expression bias and genome dominance. Significance statementWe demonstrate how different metrics of expression bias between subgenomes in polyploids can lead to conflicting inferences. We show that expression can be viewed as either A or C-biased, yet the differences are small, calling into question the relevance of subgenome dominance and expression bias in B. napus.

plant biology↗

bioRxiv2026

A Bayesian approach for identifying similar transcript dynamics using curve registration

Changes in gene expression over time can provide valuable insights into developmental processes and responses to the environment. Differences in expression may be indicative of potential differences in regulation. Comparing transcript dynamics may help identify correspondences between developmental stages within and between species, differences in the timing of key events during development, and transcriptional response to treatments or perturbations. A straightforward comparison between the dynamics is, however, hindered by measurements that were taken at different time points and over different timescales. To address this, we developed a statistical approach that seeks the optimal alignment between two time series as a function of a temporal shift and stretch. We validated our approach using simulated data and applied it to several transcriptome datasets, including comparisons between different plant species. Our development facilitates knowledge transfer from model systems to less studied species, the identification of modules of co-regulated genes, and the discovery of condition-specific, temporally differentially-expressed genes. The method is provided freely available as an R package.

bioinformatics↗

bioRxiv2026

Larval antibiosis to cabbage stem flea beetle (Psylliodes chrysocephala) is absent within oilseed rape (Brassica napus)

BACKGROUNDInsect pests present a global threat to crops, with plant resistance representing a key breeding goal. The cabbage stem flea beetle (Psylliodes chrysocephala; CSFB) is a key pest of oilseed rape (Brassica napus; OSR) within Europe; however, CSFB resistance is yet to be found within B. napus. To address this, we examine CSFB larval development over time, explore antibiosis across a genetically diverse B. napus panel, and test whether larvae can develop within model Brassicaceae species (Brassica rapa and Arabidopsis thaliana). RESULTSCSFB larvae completed development from four-weeks post-infestation, undergoing a 20-fold size increase, with larval recovery after two weeks allowing semi-high throughput resistance phenotyping. Applying this method to 98 Brassicaceae genotypes (97 B. napus and a single Sinapis alba), we found weak evidence for genotype effects on larval survival. However, phenotype validation with resistant and susceptible B. napus genotypes showed no differences in larval survival or adult emergence. Larval antibiosis was consistently observed in S. alba. Finally, we showed that model B. rapa and A. thaliana genotypes represent suitable hosts for CSFB, with larvae increasing 8-10x in size after two weeks. CONCLUSIONCSFB larval antibiosis appears absent within B. napus, possibly due to bottlenecks experienced during domestication. However, larval antibiosis is present within S. alba, and future work should study the basis of this resistance. Further, CSFB larval screening in Brassicaceae model species presents an opportunity to explore CSFB resistance genetics, informing breeding progress for insect resistance in B. napus.

plant biology↗

bioRxiv2025

Network analysis of flowering time genes suggests regulatory changes among SOC1 orthologues in response to cold in Brassica napus

Flowering plants respond to multiple environmental and endogenous cues to determine the timing of their transition from the vegetative to floral state. Most of our knowledge of the gene regulatory network (GRN) controlling flowering time has been derived from the model plant Arabidopsis thaliana. This knowledge needs to be translated to crop plants to support the development of varieties that can be grown in different and rapidly changing climatic conditions. However, due to increased genome complexity and limited prior knowledge, translation into crops is not always straightforward. Here, we present a study of the GRN controlling flowering time in Brassica napus (oilseed rape), an allotetraploid crop that is a close relative of Arabidopsis. Using a comparative transcriptomics approach, we show that the majority of the orthologous gene pairs have similar expression dynamics over development between Arabidopsis and Brassica napus. Some genes, however, have experienced regulatory changes, with flowering time genes in Brassica napus having higher than average differences in their expression profiles from their Arabidopsis orthologues. Despite these differences, the inferred GRN for flowering in Brassica napus exhibits a similar network topology to the network known in Arabidopsis. This is likely due to preferential retention of these genes in higher paralogue numbers, which allows subtle changes in the regulation of individual paralogues, while still conserving the overall regulatory structure through evolution. We discover and present a detailed analysis of one such example where orthologues of SUPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) have similar expression patterns under normal conditions, but different dynamics under cold temperature conditions, suggesting possible subfunctionalisation among paralogues in response to temperature change.

plant biology↗

bioRxiv2025

Associative transcriptomics in Brassica napus suggests a role for Arabidopsis Response Regulator orthologs in seedling vigour

Background and AimsOptimal seedling vigour determines successful crop establishment and its ability to overcome abiotic and biotic threats. Seedling vigour is regulated by several different factors, genetic, physiological, environmental, post-harvest storage, making it challenging to fully elucidate. The aim of this study was to dissect the genetic basis of post-germinative seedling traits and its implications in seedling establishment success in Brassica napus. MethodsA B. napus diversity set panel was used to phenotype seedling establishment traits in the soil including days to emergence, days to appearance of first and second true leaves, and days to reach 25% and 50% cotyledon expansion. An associative transcriptomics analysis was performed to identify the genetic factors regulating seedling establishment. Key ResultsThe study of different phenotypic traits highlighted the relevance of scoring more than one trait to determine good performers. Gene expression markers significantly associated with the studied traits were associated with the cytokinin signalling pathway and photomorphogenesis. Gene expression markers for orthologues of Arabidopsis thaliana RESPONSE REGULATOR 4 and 5 (ARR4, ARR5) were significantly associated with days to appearance of second leaf. SUPPRESSOR OF PHYA-105 1 (SPA1) orthologues were associated with cotyledon area, meanwhile ALTERED SEED GERMINATION 7 (ASG7) and PSEUDO-RESPONSE REGULATOR 7 (PRR7) orthologues were associated with days to emergence, suggesting a complex and interconnected regulatory pathway controlling several traits of seedling establishment. ConclusionsThese results uncovered promising genes that appear to work in a complex and interconnected manner controlling several post-germinative seedling traits affecting final seedling establishment speed.

plant biology↗

bioRxiv2025

First evidence for widespread sharing of stereotyped non-signature whistle types by wild dolphins

We have built a unique library of sounds produced by known individual common bottlenose dolphins (Tursiops truncatus), by recording them non-invasively with suction cup hydrophones during brief catch and release health assessments and with digital acoustic tags (DTAGs). We have catalogued the name-like signature whistles (SWs) of most animals in this resident community of 170 dolphins, which has enabled us to begin studying little known "non-signature whistles" (NSW). We have so far identified 22 shared NSW types, of which two, NSWA and NSWB, are known to have been produced by at least 25 and 35 different dolphins respectively. We are studying the functions of shared NSWs with playback experiments to free-swimming dolphins. We provide background on past playback studies and how they have informed our current research; in particular, received level (RL) of playbacks was found to significantly influence strength of response. Varied responses to playbacks reflect the complexity of dolphin communication, and highlight the need for larger sample sizes to be able to correctly interpret NSW functions. However, results so far have provided support for both the referential nature of SW and the affiliative nature of SW copies (SWCs), because a majority of control playbacks of a dolphins own signature whistle (self playbacks) elicited positive responses. NSWA elicited a majority of negative responses, suggesting an alarm-type function, and NSWB elicited varying responses, supporting our suggested function of this whistle type as a "query," produced when something unexpected or unfamiliar is heard. Given that SW and SWC are known to be learned and appear to be referential signals, it is likely that shared, stereotyped NSW are both learned and referential as well, an idea that is supported by the fact that dolphins are flexible, life-long vocal production learners, unlike most other non-human mammals. Our study provides the first evidence in dolphins for a wider repertoire of shared, context-specific signals, which could form the basis for a language-like communication system.

animal behavior and cognition↗

bioRxiv2024

Natural variation suggests new mechanisms for bract development in Arabidopsis, desynchronising bract suppression from the floral transition

Plant development may be viewed as a sequence of tightly orchestrated events in space and time. The coordination of developmental stages gives rise to various organs, such as leaves or flowers. For instance, in Arabidopsis thaliana, leaf/bract development ceases once the first flower emerges. Unravelling the mechanisms of this regulation is, therefore, key for understanding how developmental programs are coordinated during the floral transition. In this study, we take advantage of a previously overlooked natural variation that desynchronizes bract repression from the initiation of the first flowers. We found that prolonged bract formation after the floral transition depends on complex genetic interactions, involving at least four loci. Surprisingly, none of these loci contained the floral identity genes previously implicated in bract repression, suggesting that other genes are involved in the synchronisation of bract and flower programs. Furthermore, although ectopic bracts in inflorescences have been interpreted as a prolonged vegetative state, time-series transcriptomics and curve registration revealed a more complex scenario whereby many genes desynchronize in terms of expression between these developmental programs. As a consequence, transcriptional differences peak at the floral transition when bract development is prolonged, affecting a wide variety of biological processes not necessarily associated with vegetative state. A transient increase in transcriptome divergence has been proposed to account for morphological variation between species in animals and plants under the "inverse hourglass" model. Our results suggest that such a model could also explain the sensitivity of certain developmental transitions to phenotypic variation within species, as reported here for the floral transition.

plant biology↗

bioRxiv2024

Chloride intracellular channel 4 (CLIC4) is a global regulator of type 1 interferon signaling in Systemic Sclerosis (SSc) epithelial cells

ObjectivesSystemic sclerosis (SSc) is an autoimmune disease in which an immune-related injury induces fibrosis of the skin, progressing to affect the internal organs in the most serve cases. Type 1 interferon (IFN) signaling plays a major role in SSc disease progression. We have previously shown the chloride intracellular channel 4 (CLIC4) is upregulated in SSc skin fibroblasts and plays an important role in SSc fibrosis. In this study we investigated the role of CLIC4 in SSc keratinocyte biology. Methodshealthy (HC) and SSc skin biopsies were analysed by immunohistochemistry for the expression of CLIC4. The skin keratinocyte cell line Hacats was stimulated with a range of type 1 IFN signaling agonists (POLY I:C, POLY dA:Dt, ODN 2216 and IFN-). CLIC4 was inhibited with the chloride channel inhibitors NPPB and IAA-94 or siRNA. Conditioned media from HC or SSc fibroblasts was employed for indirect co-culture of Hacats and HUVECs. ResultsSSc skin biopsies showed high levels of CLIC4 in SSc skin fibroblasts, keratinocytes and endothelial cells compared to HC. Co-culture of Hacats and Huvecs with SSc fibroblast media induced CLIC4 expression. CLIC4 played an important role in type 1 IFN signalling in keratinocytes. Inhibition of CLIC4 blocked TLR3, TLR9 and cGAS mediated activation of the type 1 IFN signaling pathway. Additionally, inhibition of CLIC4 prevented SSc fibroblast media from inducing a type 1 IFN response in keratinocytes. ConclusionsThe data presented in this study suggests CLIC4 is a global regulator of type 1 IFN signalling in SSc epithelial cells. Key MessagesO_ST_ABSWhat is already knownC_ST_ABSSSc disease progression is driven in part by a Type 1 IFN signature and CLIC4 has previously been implicated in SSc fibroblast activation. What this study addsWe show for the first time CLIC4 is a regulator of type 1 interferon signalling in epithelial cells and plays an important role in the signalling found in SSc skin. How this study might affect researchTargeting CLIC4 in the context of SSc may disrupt the fibrosis and inflammation associated with SSc.

immunology↗

bioRxiv2024

Morphological Reprogramming of Primary Cilia Length Mitigates the Fibrotic Phenotype in fibroblasts across diverse fibrotic conditions

Fibrosis is a hallmark of systemic sclerosis (SSc) and many diverse and incurable diseases. Myofibroblast activation, a common cellular phenomenon shared across fibrotic diseases, is marked by actin polymerization known to affect primary cilia (PC) length. We discovered that fibroblasts from diverse fibrotic conditions display significantly reduced PC length ex vivo. Treatment of healthy fibroblasts with profibrotic TGF-{beta}1 induced PC shortening, while silencing ACTA2 in SSc skin fibroblasts caused PC elongation. Importantly, we found that PC length is negatively correlated with cellular expression of -SMA in TGF-{beta}1-stimulated healthy fibroblasts, or pharmacologically de-differentiated myofibroblasts. PC elongation by microtubule polymerization induction in SSc skin fibroblasts using LiCl or the HDAC6 inhibitor tubacin, reversed and mitigated fibrotic responses. Our results implicate a key role for microtubule polymerization in restraining fibrotic responses and suggest that modulation of PC dynamics may represent a potential therapeutic strategy for SSc and other treatment-resistant diseases associated with fibrosis. Teaser. PC length shortening is a hallmark of fibrosis.

cell biology↗

bioRxiv2024

Wild bird mass mortalities in eastern Canada associated with the Highly Pathogenic Avian Influenza A(H5N1) virus, 2022

In 2022, a severe outbreak of clade 2.3.4.4b Highly Pathogenic Avian Influenza (HPAI) H5N1 virus resulted in unprecedented mortality among wild birds in eastern Canada. Tens of thousands of birds were reported sick or dead, prompting a comprehensive assessment of mortality spanning the breeding season between April 1 and September 30, 2022. Mortality reports were collated from federal, Indigenous, provincial, and municipal agencies, the Canadian Wildlife Health Cooperative, non-governmental organizations, universities, and citizen science platforms. A scenario analysis was conducted to refine mortality estimates, accounting for potential double counts from multiple sources under a range of spatial and temporal overlap. Correcting for double counting, an estimated 40,966 wild birds were reported sick or dead in eastern Canada during the spring and summer of 2022. Seabirds and sea ducks, long-lived species that are slow to recover from perturbations, accounted for 98.7% of reported mortalities. Mortalities were greatest among Northern Gannets (Morus bassanus; 26,193), Common Murres (Uria aalge; 8,133), and American Common Eiders (Somateria mollissima dresseri; 1,945), however, these figures underestimate total mortality as they exclude unreported deaths on land and at sea. In addition to presenting mortality estimates, we compare mortalities with known population sizes and trends and make an initial assessment of whether population-level impacts are possible for the Northern Gannet, a species that has suffered significant global mortality, and two harvested species, Common Murre and American Common Eider, to support management decisions. We hypothesize that population-level impacts in eastern Canada are possible for Northern Gannets and American Common Eiders but are unlikely for Common Murres. This study underscores the urgent need for further research to understand the broader ecological ramifications of the HPAI outbreak on wild bird populations.

zoology↗

bioRxiv2023

Pathogen lifestyle defines host genetic signature of quantitative disease resistance in oilseed rape (Brassica napus)

O_LICrops are affected by several pathogens, but these are rarely studied in parallel to identify common and unique genetic factors controlling diseases. Broad-spectrum quantitative disease resistance (QDR) is desirable for crop breeding as it confers resistance to several pathogen species. C_LIO_LIHere, we use associative transcriptomics (AT) to identify candidate gene loci associated with Brassica napus QDR to four contrasting fungal pathogens: Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae and Verticillium longisporum. C_LIO_LIWe did not identify any loci associated with broad-spectrum QDR to fungal pathogens with contrasting lifestyles. Instead, we observed QDR dependent on the lifestyle of the pathogen--hemibiotrophic and necrotrophic pathogens had distinct QDR responses and associated loci, including some loci associated with early immunity. Furthermore, we identify a genomic deletion associated with resistance to V. longisporum and potentially broad-spectrum QDR. C_LIO_LIThis is the first time AT has been used for several pathosystems simultaneously to identify host genetic loci involved in broad-spectrum QDR. C_LIO_LIWe highlight candidate loci for broad-spectrum QDR with no antagonistic effects on susceptibility to the other pathogens studies as candidates for crop breeding. C_LI

plant biology↗

bioRxiv2023

Recognition of Necrosis and Ethylene-inducing like peptides confers disease resistance in Brassica napus and is modulated by BSK1 in Arabidopsis

Brassicas are important crops susceptible to significant losses caused by disease: thus, breeding resistant lines can mitigate the effects of pathogens. MAMPs (microbe-associated molecular patterns) are conserved molecules of pathogens that elicit host defence responses known as pattern-triggered immunity (PTI). Necrosis & Ethylene-inducing peptide 1-like proteins (NLPs) are MAMPs found in a wide range of phytopathogens, including major disease-causing fungal species. We studied the response to the BcNEP2 from Botrytis cinerea as a representative NLP in Brassica napus to improve our understanding of recognition mechanisms that could enable the development of disease-resistant crops. To genetically map regions responsible for NLP recognition, we used an associative transcriptomics (AT) approach using diverse B. napus accessions and bulk segregant analysis (BSA) on DNA pools created from a bi-parental cross of NLP-responsive (Ningyou1) and non-responsive (Ningyou7) lines. In silico mapping with AT identified two peaks associated with NLP recognition on chromosomes A04 and C05 whereas the BSA narrowed it down to a main peak on A04. BSA delimited the region associated with NLP-responsiveness to 3 Mbp, containing [~]245 genes on the Darmor-bzh reference genome. Variants detected in the region were used for KASP marker design and four KASP markers were identified co-segregating with the phenotype. The same pipeline was performed with the ZS11 genome, and the highest associated region was confirmed on chromosome A04. Comparative BLAST analysis revealed there were unannotated clusters of RLP homologs on ZS11 chromosome A04. To reduce the number of candidate genes responsible for NLP recognition, RNA-Seq data was used to detect the unannotated expressed putative genes. Screening the BSA Ning1x7 population demonstrated a highly significant association between NLP-recognition and resistance to Botrytis cinerea. Also, the lines non-responsive to NLP had significantly greater response to the bacterial MAMP flg22. Additionally, BnaA01g02190D, a homologue of Arabidopsis AtBSK1 (At4g35230) BR-SIGNALLING KINASE1, was associated with a high BcNEP2-induced ROS response phenotype. We show that in Arabidopsis, Atbsk1 mutants had significantly lower response to BcNEP2 and increased susceptibility to B. cinerea (p-value=1.12e-14***). Overall, the results define the genomic location for NLP-recognition on the B. napus genome and demonstrate that NLP recognition has a positive contribution to disease resistance which can have practical application in crop improvement.

plant biology↗

bioRxiv2023

Integrated Phenomics and Genomics reveals genetic loci associated with inflorescence growth in Brassica napus

A fundamental challenge to the production of climate-resilient crops is how to measure dynamic yield-relevant responses to the environment, such as growth rate, at a scale which informs mechanistic understanding and accelerates breeding. The timing, duration and architectural characteristics of inflorescence growth are crucial for optimising crop productivity and have been targets of selection during domestication. We report a robust and versatile procedure for computationally assessing environmentally-responsive flowering dynamics. In the oilseed crop, Brassica napus, there is wide variation in flowering response to winter cold (vernalization). We subjected a diverse set of B. napus accessions to different vernalization temperatures and monitored shoot responses using automated image acquisition. We developed methods to computationally infer multiple aspects of flowering from this dynamic data, enabling characterisation of speed, duration and peaks of inflorescence development across different crop types. We input these multiple traits to genome- and transcriptome-wide association studies, and identified potentially causative variation in a priori phenology genes (including EARLY FLOWERING3) for known traits and in uncharacterised genes for computed traits. These results could be used in marker assisted breeding to design new ideotypes for improved yield and better adaptation to changing climatic conditions.

plant biology↗

bioRxiv2020

Validation of a novel associative transcriptomics pipeline in Brassica oleracea: Identifying candidates for vernalisation response

Associative transcriptomics has been used extensively in Brassica napus to enable the rapid identification of markers correlated with traits of interest. However, within the important vegetable crop species, Brassica oleracea, the use of associative transcriptomics has been limited due to a lack of fixed genetic resources and the difficulties in generating material due to self-incompatibility. Within Brassica vegetables, the harvestable product can be vegetative or floral tissues and therefore synchronisation of the floral transition is an important goal for growers and breeders. Vernalisation is known to be a key determinant of the floral transition, yet how different vernalisation treatments influence flowering in B. oleracea is not well understood. Here, we present results from phenotyping a diverse set of 69 B. oleracea accessions for heading and flowering traits under different environmental conditions. We developed a new associative transcriptomics pipeline, and inferred and validated a population structure, for the phenotyped accessions. A genome-wide association study identified miR172D as a candidate for the vernalisation response. Gene expression marker association identified variation in expression of BoFLC.C2 as a further candidate for vernalisation response. This study provides insights into the genetic basis of vernalisation response in B. oleracea through associative transcriptomics and confirms its characterisation as a complex G x E trait. Candidate leads were identified in miR172D and BoFLC.C2. These results could facilitate marker-based breeding efforts to produce B. oleracea lines with more synchronous heading dates, potentially leading to improved yields.

plant biology↗

bioRxiv2020

Comparative transcriptomics identifies differences in the regulation of the floral transition between Arabidopsis and Brassica rapa cultivars

The timing of the floral transition affects reproduction and yield, however its regulation in crops remains poorly understood. Here, we use RNA-Seq to determine and compare gene expression dynamics through the floral transition in the model species Arabidopsis thaliana and the closely related crop Brassica rapa. A direct comparison of gene expression over time between species shows little similarity, which could lead to the inference that different gene regulatory networks are at play. However, these differences can be largely resolved by synchronisation, through curve registration, of gene expression profiles. We find that different registration functions are required for different genes, indicating that there is no common developmental time to which Arabidopsis and B. rapa can be mapped through gene expression. Instead, the expression patterns of different genes progress at different rates. We find that co-regulated genes show similar changes in synchronisation between species, suggesting that similar gene regulatory sub-network structures may be active with different wiring between them. A detailed comparison of the regulation of the floral transition between Arabidopsis and B. rapa, and between two B. rapa accessions reveals different modes of regulation of the key floral integrator SOC1, and that the floral transition in the B. rapa accessions is triggered by different pathways, even when grown under the same environmental conditions. Our study adds to the mechanistic understanding of the regulatory network of flowering time in rapid cycling B. rapa under long days and highlights the importance of registration methods for the comparison of developmental gene expression data.

plant biology↗

bioRxiv2019

The power of model-to-crop translation illustrated by reducing seed loss from pod shatter in oilseed rape

In the 1980s, plant scientists descended on a small weed Arabidopsis thaliana (thale cress) and developed it into a powerful model system to study plant biology. The massive advances in genetics and genomics since then has allowed us to obtain incredibly detailed knowledge on specific biological processes of Arabidopsis growth and development, its genome sequence and the function of many of the individual genes. This wealth of information provides immense potential for translation into crops to improve their performance and address issues of global importance such as food security. Here we describe how fundamental insight into the genetic mechanism by which seed dispersal occurs in members of the Brassicaceae family can be exploited to reduce seed loss in oilseed rape (Brassica napus). We demonstrate that by exploiting data on gene function in model species, it is possible to adjust the pod-opening process in oilseed rape thereby significantly increasing yield. Specifically, we identified mutations in multiple paralogues of the INDEHISCENT and GA4 genes in B. napus and have overcome genetic redundancy by combining mutant alleles. Finally, we present novel software for the analysis of pod shatter data that is applicable to any crop for which seed dispersal is a serious problem. These findings highlight the tremendous potential of fundamental research in guiding strategies for crop improvement.\n\nKeymessageElucidation of key regulators in Arabidopsis fruit patterning has facilitated knowledge-translation into crop species to address yield loss caused by premature seed dispersal (pod shatter).

plant biology↗

bioRxiv2019

A high-throughput delayed fluorescence method reveals underling differences in the control of circadian rhythms in Triticum aestivum and Brassica napus

BackgroundA robust circadian clock has been implicated in plant resilience, resource-use efficiency, competitive growth and yield. A huge number of physiological processes are under circadian control in plants including: responses to biotic and abiotic stresses; flowering time; plant metabolism; and mineral uptake. Understanding how the clock functions in crops such as Triticum aestivum (bread wheat) and Brassica napus (oilseed rape) therefore has great agricultural potential. Delayed fluorescence (DF) imaging has been shown to be applicable to a wide range of plant species and requires no genetic transformation. Although DF has been used to measure period length of both mutants and wild ecotypes of Arabidopsis, this assay has never been systematically optimised for crop plants. The physical size of both B. napus and T. aestivum led us to develop a representative sampling strategy which enables high-throughput imaging of these crops.\n\nResultsIn this study, we describe the plant-specific optimisation of DF imaging to obtain reliable circadian phenotypes with the robustness and reproducibility to detect diverging periods between cultivars of the same species. We find that the age of plant material, light regime and temperature conditions all significantly effect DF rhythms and describe the optimal conditions for measuring robust rhythms in each species. We also show that sections of leaf can be used to obtain period estimates with improved throughput for larger sample size experiments.\n\nConclusionsWe present an optimized protocol for high-throughput phenotyping of circadian period specific to two economically valuable crop plants. Application of this method revealed significant differences between the periods of several widely grown elite cultivars. This method also identified intriguing differential responses of circadian rhythms in T. aestivum compared to B. napus; specifically the dramatic change to rhythm robustness when plants were imaged under constant light versus constant darkness. This points towards diverging networks underling circadian control in these two species.

plant biology↗