Biology subjects

Gruissem, W.

Publications and source records attributed to Gruissem, W..

11 recordsLinked to original sources

bioRxiv2026

Reducing transitory starch in cassava impairs photosynthesis and carbon export to storage roots

Optimizing source-sink relations is a central strategy for improving crop yield. In potato, reducing transitory leaf starch synthesis can redirect carbon to storage organs without impairing growth. To test whether this strategy is transferable to cassava, we suppressed the major small subunit of ADP-GLUCOSE PYROPHOSPHORYLASE, MeAPS1a. Transgenic plants were nearly devoid of transitory leaf starch and showed impaired photosynthetic carbon fixation. Under greenhouse conditions, shoots acclimated to the reduced carbon supply and exhibited only moderate biomass losses, and the data indicated reduced carbon supply to developing storage roots. This was reflected by lower leaf sucrose levels, reduced storage root biomass and starch accumulation, and downregulation of carbohydrate-responsive genes, including the major AGPase large subunit MeAPL3. Under field conditions, the absence of transitory starch was even more detrimental, causing severe growth inhibition and drastic reductions in both shoot and root biomass. We also found that MeAPS1a-derived small interfering RNAs moved systemically from leaves to roots, with lower root siRNA abundance in older, larger plants than in younger, smaller plants. Together, our results demonstrate that transitory starch is indispensable for sustaining carbon flux to cassava storage roots, highlighting species-specific constraints on engineering source-sink relations.

plant biology↗

bioRxiv2025

A non-rectifying potassium channel increases cassava drought tolerance and storage root yield

Cassava (Manihot esculenta) is an important crop for food security in the tropics, particularly for smallholder farmers in sub-Saharan Africa, where yields are often severely limited by pathogen pressure, nutrient deficiency, and water scarcity. We expressed a non-rectifying Arabidopsis thaliana potassium (K+) channel gene version, AKT2var, in the vascular tissue of cassava plants. The transgenic cassava plants had higher electron transport and CO2 assimilation rates, a higher bulk flow velocity, and increased source-sink carbohydrate transport, as demonstrated by comparative 11C-positron emission tomography and tissue-specific metabolite profiling. Cassava storage root yield was significantly increased in greenhouse experiments and in a multi-year field trial conducted under subtropical conditions. AKT2var plants were also more tolerant to drought stress and had higher storage root yield. Targeted alteration of K+ transport is therefore a promising strategy to improve cassava productivity without additional fertilizer input and in climate-adverse growing conditions.

plant biology↗

bioRxiv2022

Haplotype resolved DNA methylome of African cassava genome

Cytosine DNA methylation is involved in biological processes such as transposable element (TE) silencing, imprinting, and X chromosome inactivation. Plant methylation is mediated by MET1 (mammalian DNMT1), DRM2 (mammalian DNMT3), and two plant-specific DNA methyltransferases, CMT2 and CMT3 (Law and Jacobsen, 2010). De novo DNA methylation in plants is established by DRM2 via the plant specific RNA-directed DNA methylation (RdDM) pathway that depends on two DNA-dependent RNA polymerases, Pol IV and Pol V (Gallego-Bartolome et al., 2019; Law and Jacobsen, 2010; Stroud et al., 2013). The DNA methylome of cassava has been previously documented based on its haploid collapsed genome (Wang et al., 2015). Since the cassava genome is highly heterozygous, DNA methylome analysis of the haplotype-collapsed genome misses many features of the methylome. With the development of long read sequencing and chromosomal conformation capture techniques, haplotype resolved genomes are available for highly heterozygous genomes (Mansfeld et al., 2021; Qi et al., 2022; Zhou et al., 2020), which provides high-quality reference genomes facilitating studies of haplotype resolved DNA methylomes.

plant biology↗

bioRxiv2022

Mutations in DNA polymerase δ subunit 1 mediate CMD2-type resistance to Cassava Mosaic Geminiviruses

Cassava mosaic disease suppresses cassava yields across the tropics. The dominant CMD2 locus confers resistance to the cassava mosaic geminiviruses. It has been reported that CMD2-type landraces lose resistance after regeneration through de novo morphogenesis. As full genome bisulfite sequencing failed to uncover an epigenetic mechanism for loss of resistance, we performed whole genome sequencing and genetic variant analysis and fine-mapped the CMD2 locus to a 190 kilobase interval. Data suggest that CMD2-type resistance is caused by a nonsynonymous, single nucleotide polymorphism in DNA polymerase {delta} subunit 1 (MePOLD1) located within this region. Virus-induced gene silencing of MePOLD1 in a Cassava mosaic disease-susceptible cassava variety produced a recovery phenotype typical of CMD2-type resistance. Analysis of other CMD2-type cassava varieties identified additional resistance alleles within MePOLD1. MePOLD1 resistance alleles represent important genetic resources for resistance breeding or genome editing, and elucidating mechanisms of resistance to geminiviruses.

plant biology↗

bioRxiv2021

The haplotype-resolved chromosome pairs and transcriptome of a heterozygous diploid African cassava cultivar

BackgroundCassava (Manihot esculenta) is an important clonally propagated food crop in tropical and sub-tropical regions worldwide. Genetic gain by molecular breeding is limited because cassava has a highly heterozygous, repetitive and difficult to assemble genome. FindingsHere we demonstrate that Pacific Biosciences high-fidelity (HiFi) sequencing reads, in combination with the assembler hifiasm, produced genome assemblies at near complete haplotype resolution with higher continuity and accuracy compared to conventional long sequencing reads. We present two chromosome scale haploid genomes phased with Hi-C technology for the diploid African cassava variety TME204. Genome comparisons revealed extensive chromosome re-arrangements and abundant intra-genomic and inter-genomic divergent sequences despite high gene synteny, with most large structural variations being LTR-retrotransposon related. Allele-specific expression analysis of different tissues based on the haplotype-resolved transcriptome identified both stable and inconsistent alleles with imbalanced expression patterns, while most alleles expressed coordinately. Among tissue-specific differentially expressed transcripts, coordinately and biasedly regulated transcripts were functionally enriched for different biological processes. We use the reference-quality assemblies to build a cassava pan-genome and demonstrate its importance in representing the genetic diversity of cassava for downstream reference-guided omics analysis and breeding. ConclusionsThe haplotype-resolved genome allows the first systematic view of the heterozygous diploid genome organization in cassava. The completely phased and annotated chromosome pairs will be a valuable resource for cassava breeding and research. Our study may also provide insights into developing cost-effective and efficient strategies for resolving complex genomes with high resolution, accuracy and continuity.

genomics↗

bioRxiv2020

Diurnal Dynamics of the Arabidopsis Rosette Proteome and Phosphoproteome

Plant growth depends on the diurnal regulation of cellular processes, but it is not well understood if and how transcriptional regulation controls diurnal fluctuations at the protein-level. Here we report a high-resolution Arabidopsis thaliana (Arabidopsis) leaf rosette proteome acquired over a 12 h light : 12 h dark diurnal cycle and the phosphoproteome immediately before and after the light-to-dark and dark-to-light transitions. We quantified nearly 5000 proteins and 800 phosphoproteins, of which 288 fluctuated in their abundance and 226 fluctuated in their phosphorylation status. Of the phosphoproteins, 60% were quantified for changes in protein abundance. This revealed six proteins involved in nitrogen and hormone metabolism that had concurrent changes in both protein abundance and phosphorylation status. The diurnal proteome and phosphoproteome changes involve proteins in key cellular processes, including protein translation, light perception, photosynthesis, metabolism and transport. The phosphoproteome at the light-dark transitions revealed the dynamics at phosphorylation sites in either anticipation of or response to a change in light regime. Phosphorylation site motif analyses implicate casein kinase II and calcium/calmodulin dependent kinases among the primary light-dark transition kinases. The comparative analysis of the diurnal proteome and diurnal and circadian transcriptome established how mRNA and protein accumulation intersect in leaves during the diurnal cycle of the plant. Summary StatementThe manuscript provides quantitative information of diurnal changes in the accumulation and phosphorylation of proteins in Arabidopsis thaliana rosettes grown in a 12 h photoperiod. The highly resolved time-scale of the datasets offer new proteome-level insights for future targeted studies.

plant biology↗

bioRxiv2019

A RETINOBLASTOMA-RELATED transcription factor network governs egg cell differentiation and stress response in Arabidopsis

The multicellular embryo, and ultimately the entire organism, is a derivative of the fertilized egg cell. Unlike in animals, transcription factor networks orchestrating faithful egg development are still largely unknown in plants. We have identified that egg cell differentiation in Arabidopsis require interplay between evolutionarily conserved onco-protein homologs RETINOBLASTOMA-RELATED (RBR) and redundant MYB proteins MYB64/MYB119. RBR physically interacts with the MYBs; and with plant-specific transcription factors belonging to the RWP-RK-domain (RKD) family and LEAFY COTYLEDON1 (LEC1), which participate in development of egg cells and inherent stress response. RBR binds to most of these egg cell-expressed loci at the DNA level, partially overlapping with sites of histone methylation H3K27me3. Since deregulation of RKDs phenocopies mutants of RBR and the MYBs in terms of cell proliferation in the egg cell spatial domain, all the corresponding proteins are likely required to restrict parthenogenetic cell divisions of the egg cells. Cross-talk among these transcription factors, and direct regulation by RBR, govern egg cell development and expression of egg-to-zygotic polarity factors of the WUSCHEL RELATED HOMEOBOX family. Together, a network of RBR-centric transcription factors underlies egg cell development and stress response, possibly, in combination with several other predicted nodes.\n\nAuthor summaryThe RETINOBLASTOMA protein is one of the core components of the Eukaryotic cell cycle, and corresponding evolutionary homologs have been implicated not only to repress cell division but also to control differentiation and development. How RETINOBLASTOMA RELATED (RBR) associate with other higher order regulators to control faithful egg cell development in sexual plants is pivotal for manipulation of successful reproduction in general, and engineering of parthenogenesis when asexual or apomictic seed progeny are desirable over sexual plants. Using a suite of molecular methods, we show that a RBR-associated transcription factor network operates to specify egg cells in Arabidopsis. Complex cross-regulation within these transcription factors seems to be necessary for successful maternal egg cell to zygotic transition and reproductive stress response. Detailed genetic analysis implicate that RBR and its interactive partners belonging to MYB and RWP-RK transcription factor families are possibly required to prevent parthenogenesis of the sexual egg cells. Novel RBR networks and stress nodes explained in this study might help to improve our understanding of sexual and asexual reproduction.

genetics↗

bioRxiv2018

CRISPR-Cas9 interference in cassava linked to the evolution of editing-resistant geminiviruses

We used CRISPR-Cas9 in the staple food crop cassava with the aim of engineering resistance to African cassava mosaic virus, a member of a widespread and important family of plant-pathogenic DNA viruses. We found that between 33 and 48% of edited virus genomes evolved a conserved single-nucleotide mutation that confers resistance to CRISPR-Cas9 cleavage. Our study highlights the potential for virus escape from this technology. Care should be taken to design CRISPR-Cas9 experiments that minimize the risk of virus escape.

plant biology↗

bioRxiv2017

Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism

Plants respond to seasonal cues, such as the photoperiod, to adapt to current conditions and to prepare for environmental changes in the season to come. To assess photoperiodic responses at the protein level, we quantified the proteome of the model plant Arabidopsis thaliana by mass spectrometry across four photoperiods. This revealed coordinated changes of abundance in proteins of photosynthesis, primary and secondary metabolism, including pigment biosynthesis, consistent with higher metabolic activity in long photoperiods. Higher translation rates in the daytime than the night likely contribute to these changes via rhythmic changes in RNA abundance. Photoperiodic control of protein levels might be greatest only if high translation rates coincide with high transcript levels in some photoperiods. We term this proposed mechanism {acute}translational coincidence{acute}, mathematically model its components, and demonstrate its effect on the Arabidopsis proteome. Datasets from a green alga and a cyanobacterium suggest that translational coincidence contributes to seasonal control of the proteome in many phototrophic organisms. This may explain why many transcripts but not their cognate proteins exhibit diurnal rhythms.

plant biology↗

bioRxiv2017

CIDER-Seq: unbiased virus enrichment and single-read, full length genome sequencing

Deep-sequencing of virus isolates using short-read sequencing technologies is problematic since viruses are often present in complexes sharing a high-degree of sequence identity. The full-length genomes of such highly-similar viruses cannot be assembled accurately from short sequencing reads. We present a new method, CIDER-Seq (Circular DNA Enrichment Sequencing) which successfully generates accurate full-length virus genomes from individual sequencing reads with no sequence assembly required. CIDER-Seq operates by combining a PCR-free, circular DNA enrichment protocol with Single Molecule Real Time sequencing and a new sequence deconcatenation algorithm. We apply our technique to produce more than 1,200 full-length, highly accurate geminivirus genomes from RNAi-transgenic and control plants in a field trial in Kenya. Using CIDER-Seq we can demonstrate for the first time that the expression of antiviral doublestranded RNA (dsRNA) in transgenic plants causes a consistent shift in virus populations towards species sharing low homology to the transgene derived dsRNA. Our results show that CIDER-seq is a powerful, cost-effective tool for accurately sequencing circular DNA viruses, with future applications in deep-sequencing other forms of circular DNA such as transposons and plasmids.

genomics↗

bioRxiv2017

Early transcriptome response to brown streak virus infection in susceptible and resistant cassava varieties

Cassava brown streak viruses (CBSVs) are responsible for significant cassava yield losses in eastern sub-Saharan Africa. In the present work, we inoculated CBSV-susceptible and -resistant cassava varieties with a mixed infection of CBSVs using top-cleft grafting. Virus titres in grafted scions were monitored in a time course experiment in both varieties. We performed RNA-seq of the two cassava varieties at the earliest time-point of full infection in the susceptible scions. Genes encoding proteins in RNA silencing and salicylic acid pathways were regulated in the susceptible cassava variety but transcriptional changes were limited in the resistant variety. After infection, genes related to callose deposition at plasmodesmata were regulated and callose deposition was significantly reduced in the susceptible cassava variety. We also show that {beta}-1,3-glucanase enzymatic activity is differentially regulated in the susceptible and resistant varieties. The differences in transcriptional responses to CBSV infection indicate that resistance involves callose deposition at plasmodesmata but does not trigger typical anti-viral defence responses. A meta-analysis of the current RNA-seq dataset and selected, previously reported, host-potyvirus and virus-cassava RNA-seq datasets revealed comparable host responses across pathosystems only at similar time points after infection or infection of a common host.\n\nHIGHLIGHTOur results suggest that resistance to CBSV in cassava involves callose deposition at the plasmodesmata and our meta-analysis of multiple virus-crop RNA-seq studies suggests that conserved responses across different host-virus systems are limited and depend greatly on time after infection.

plant biology↗