Publications of Hervé Vanderschuren
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See detailAsparagine accumulation in chicory storage roots is controlled by translocation and feedback regulation of asparagine biosynthesis in leaves.
Soares, Emanoella; Shumbe, Léonard ULiege; Dauchot, Nicolas et al

in New Phytologist (in press)

• The presence of acrylamide (AA), a potentially carcinogenic and neurotoxic compound, in food has become a major concern for public health. AA in plant-derived food mainly arises from the reaction of the ... [more ▼]

• The presence of acrylamide (AA), a potentially carcinogenic and neurotoxic compound, in food has become a major concern for public health. AA in plant-derived food mainly arises from the reaction of the amino acid asparagine (Asn) and reducing sugars during processing of foodstuffs at high temperature. • Using a selection of genotypes from the chicory (Cichorium intybus L.) germplasm we performed Asn measurements in storage roots and leaves to identify genotypes contrasting for Asn accumulation. We combined molecular analysis and grafting experiments to show that leaf to root translocation controls asparagine biosynthesis and accumulation in chicory storage roots. • We could demonstrate that Asn accumulation in storage roots depends on Asn biosynthesis and transport from the leaf, and that a negative feedback loop by Asn on CiASN1 expression impacts Asn biosynthesis in leaves. • Our results provide a new model for asparagine biosynthesis in root crop species and highlight the importance of characterizing and manipulating asparagine transport to reduce AA content in processed plant-based foodstuffs. [less ▲]

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See detailMorpho-physiological and molecular evaluation of drought tolerance in cassava (Manihot esculenta Crantz)
Orek, Charles; Gruissem, Wilhelm; Ferguson, Morag et al

in Field Crops Research (2020), 255

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See detailFull-length sequencing of extrachromosomal circular DNA using CIDER-Seq
Syed-Shan-e-Ali, Zaïdi ULiege; Mehta, Devang; Cornet, Luc et al

Scientific conference (2020, January 30)

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See detailVirus-Induced Gene Silencing (VIGS) in Cassava Using Geminivirus Agroclones.
Syed-Shan-e-Ali, Zaïdi ULiege; Vasudevan, Kumar ULiege; Lentz, Ezequiel Matias et al

in Methods in molecular biology (Clifton, N.J.) (2020), 2172

Virus-induced gene silencing (VIGS) is an efficient, low-cost, and rapid functional validation tool for candidate genes in planta. The VIGS approach is particularly suitable to perform reverse genetics ... [more ▼]

Virus-induced gene silencing (VIGS) is an efficient, low-cost, and rapid functional validation tool for candidate genes in planta. The VIGS approach is particularly suitable to perform reverse genetics studies in crop species. Here we present a detailed method to perform VIGS in cassava, from target gene fragment to agroinoculation and VIGS quantitation. [less ▲]

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See detailFull-length sequencing of circular DNA viruses and extrachromosomal circular DNA using CIDER-Seq.
Mehta, Devang; Cornet, Luc ULiege; Hirsch-Hoffmann, Matthias et al

in Nature Protocols (2020), 15(5), 1673-1689

Circular DNA is ubiquitous in nature in the form of plasmids, circular DNA viruses, and extrachromosomal circular DNA (eccDNA) in eukaryotes. Sequencing of such molecules is essential to profiling virus ... [more ▼]

Circular DNA is ubiquitous in nature in the form of plasmids, circular DNA viruses, and extrachromosomal circular DNA (eccDNA) in eukaryotes. Sequencing of such molecules is essential to profiling virus distributions, discovering new viruses and understanding the roles of eccDNAs in eukaryotic cells. Circular DNA enrichment sequencing (CIDER-Seq) is a technique to enrich and accurately sequence circular DNA without the need for polymerase chain reaction amplification, cloning, and computational sequence assembly. The approach is based on randomly primed circular DNA amplification, which is followed by several enzymatic DNA repair steps and then by long-read sequencing. CIDER-Seq includes a custom data analysis package (CIDER-Seq Data Analysis Software 2) that implements the DeConcat algorithm to deconcatenate the long sequencing products of random circular DNA amplification into the intact sequences of the input circular DNA. The CIDER-Seq data analysis package can generate full-length annotated virus genomes, as well as circular DNA sequences of novel viruses. Applications of CIDER-Seq also include profiling of eccDNA molecules such as transposable elements (TEs) from biological samples. The method takes ~2 weeks to complete, depending on the computational resources available. Owing to the present constraints of long-read single-molecule sequencing, the accuracy of circular virus and eccDNA sequences generated by the CIDER-Seq method scales with sequence length, and the greatest accuracy is obtained for molecules <10 kb long. [less ▲]

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See detailBringing the CRISPR revolution to the starch community
Vanderschuren, Hervé ULiege

Conference (2019, November 01)

NA

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See detailThe PEBP family of genes in chicory and their role in flowering time and root development
Roumeliotis, Efstathios ULiege; Saintmard, Nicolas; Dauchot, Nicolas et al

Poster (2019, April 25)

The PHOSPHATIDYLETHANOLAMINE-BINDING PROTEIN (PEBP) gene family is present in all eukaryotic kingdoms. In plants, three separate subfamilies have been identified, all of which have diversified functions ... [more ▼]

The PHOSPHATIDYLETHANOLAMINE-BINDING PROTEIN (PEBP) gene family is present in all eukaryotic kingdoms. In plants, three separate subfamilies have been identified, all of which have diversified functions. In Arabidopsis thaliana, the PEBP family members have been assigned roles as promoting or repressing flowering, controlling inflorescence meristem determinacy and axillary bud growth. Members of the PEBP family have also been identified to play a role in tuber initiation in potato but not much is known about the role of PEBPs in root development, especially for species that form storage roots. Root chicory (Cichorium intybus var. sativum) is a biennial crop used for nutrition, animal feed and as coffee substitute and is one of the most important sources of inulin, a type of polysaccharides that is gaining great importance in the food and medical industry. Chicory root extracts have been found to have hepatoprotective, anti-bacterial, anti- inflammatory, anti-microbial, nematicidal and anti-cancer effects. With the use of bioinformatic tools, the sequences of chicory FLOWERING LOCUS T (CiFT) and TERMINAL FLOWER1 (CiTFL1-1 to 4) like genes were identified and the coding sequences were overexpressed in null A. thaliana mutants (ft-10 or tfl1). Independent transgenic lines for each gene were phenotyped for flowering time and root development. In addition, the expression pattern of these genes was analyzed in chicory in various tissues during early stages of plant development and initiation of root storage. Transformation of chicory is being performed using an Agrobacterium rhizogenes in vitro transformation protocol. The results of this project will help us elucidate the role for the PEBPs in flowering and root development in chicory. [less ▲]

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See detailLinking CRISPR-Cas9 interference in cassava to the evolution of editing-resistant geminiviruses.
Mehta, Devang; Sturchler, Alessandra; Anjanappa, Ravi B. et al

in Genome Biology (2019), 20(1), 80

BACKGROUND: Geminiviruses cause damaging diseases in several important crop species. However, limited progress has been made in developing crop varieties resistant to these highly diverse DNA viruses ... [more ▼]

BACKGROUND: Geminiviruses cause damaging diseases in several important crop species. However, limited progress has been made in developing crop varieties resistant to these highly diverse DNA viruses. Recently, the bacterial CRISPR/Cas9 system has been transferred to plants to target and confer immunity to geminiviruses. In this study, we use CRISPR-Cas9 interference 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 (Geminiviridae) of plant-pathogenic DNA viruses. RESULTS: Our results show that the CRISPR system fails to confer effective resistance to the virus during glasshouse inoculations. Further, we find that between 33 and 48% of edited virus genomes evolve a conserved single-nucleotide mutation that confers resistance to CRISPR-Cas9 cleavage. We also find that in the model plant Nicotiana benthamiana the replication of the novel, mutant virus is dependent on the presence of the wild-type virus. CONCLUSIONS: Our study highlights the risks associated with CRISPR-Cas9 virus immunity in eukaryotes given that the mutagenic nature of the system generates viral escapes in a short time period. Our in-depth analysis of virus populations also represents a template for future studies analyzing virus escape from anti-viral CRISPR transgenics. This is especially important for informing regulation of such actively mutagenic applications of CRISPR-Cas9 technology in agriculture. [less ▲]

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See detailA new full-length circular DNA sequencing method for viral-sized genomes reveals that RNAi transgenic plants provoke a shift in geminivirus populations in the field.
Mehta, Devang; Hirsch-Hoffmann, Matthias; Were, Mariam et al

in Nucleic Acids Research (2019), 47(2), 914

We present a new method, CIDER-Seq (Circular DNA Enrichment sequencing) for the unbiased enrichment and long-read sequencing of viral-sized circular DNA molecules. We used CIDER-Seq to produce single-read ... [more ▼]

We present a new method, CIDER-Seq (Circular DNA Enrichment sequencing) for the unbiased enrichment and long-read sequencing of viral-sized circular DNA molecules. We used CIDER-Seq to produce single-read full-length virus genomes for the first time. CIDER-Seq combines PCR-free virus enrichment with Single Molecule Real Time sequencing and a new sequence de-concatenation algorithm. We apply our technique to produce >1200 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 double-stranded RNA (dsRNA) in transgenic plants causes a consistent shift in virus populations towards species sharing low homology to the transgene derived dsRNA. Our method and its application in an economically important crop plant opens new possibilities in periodic virus sequence surveillance and accurate profiling of diverse circular DNA elements. [less ▲]

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See detailNew plant breeding technologies for food security
Shan-e-Ali Zaidi, S.; Vanderschuren, Hervé ULiege; Qaim, M. et al

in Science (2019), 363(6434), 1390-1391

[No abstract available]

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See detailEnhancement of vitamin B6 levels in rice expressing Arabidopsis vitamin B6 biosynthesis de novo genes.
Mangel, Nathalie; Fudge, Jared B.; Li, Kuan-Te et al

in The Plant journal : for cell and molecular biology (2019)

Vitamin B6 (pyridoxine) is vital for key metabolic reactions and reported to have antioxidant properties in planta. Thus, enhancement of vitamin B6 content has been hypothesized to be a route to improve ... [more ▼]

Vitamin B6 (pyridoxine) is vital for key metabolic reactions and reported to have antioxidant properties in planta. Thus, enhancement of vitamin B6 content has been hypothesized to be a route to improve resistance to biotic and abiotic stresses. Most of the current studies on vitamin B6 in plants are on eudicot species, with monocots remaining largely unexplored. In this study, we investigated vitamin B6 biosynthesis in rice, with a view to examining the feasibility and impact of enhancing vitamin B6 levels. Constitutive expression in rice of two Arabidopsis thaliana genes from the vitamin B6 biosynthesis de novo pathway, AtPDX1.1 and AtPDX2, resulted in a considerable increase in vitamin B6 in leaves (up to 28.3-fold) and roots (up to 12-fold), with minimal impact on general growth. Rice lines accumulating high levels of vitamin B6 did not display enhanced tolerance to abiotic stress (salt) or biotic stress (resistance to Xanthomonas oryzae infection). While a significant increase in vitamin B6 content could also be achieved in rice seeds (up to 3.1-fold), the increase was largely due to its accumulation in seed coat and embryo tissues, with little enhancement observed in the endosperm. However, seed yield was affected in some vitamin B6 -enhanced lines. Notably, expression of the transgenes did not affect the expression of the endogenous rice PDX genes. Intriguingly, despite transgene expression in leaves and seeds, the corresponding proteins were only detectable in leaves and could not be observed in seeds, possibly pointing to a mode of regulation in this organ. This article is protected by copyright. All rights reserved. [less ▲]

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See detailHaplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars.
Kuon, Joel-E.; Qi, Weihong; Schläpfer, Pascal et al

in BMC Biology (2019), 17(1), 75

BACKGROUND: Cassava is an important food crop in tropical and sub-tropical regions worldwide. In Africa, cassava production is widely affected by cassava mosaic disease (CMD), which is caused by the ... [more ▼]

BACKGROUND: Cassava is an important food crop in tropical and sub-tropical regions worldwide. In Africa, cassava production is widely affected by cassava mosaic disease (CMD), which is caused by the African cassava mosaic geminivirus that is transmitted by whiteflies. Cassava breeders often use a single locus, CMD2, for introducing CMD resistance into susceptible cultivars. The CMD2 locus has been genetically mapped to a 10-Mbp region, but its organization and genes as well as their functions are unknown. RESULTS: We report haplotype-resolved de novo assemblies and annotations of the genomes for the African cassava cultivar TME (tropical Manihot esculenta), which is the origin of CMD2, and the CMD-susceptible cultivar 60444. The assemblies provide phased haplotype information for over 80% of the genomes. Haplotype comparison identified novel features previously hidden in collapsed and fragmented cassava genomes, including thousands of allelic variants, inter-haplotype diversity in coding regions, and patterns of diversification through allele-specific expression. Reconstruction of the CMD2 locus revealed a highly complex region with nearly identical gene sets but limited microsynteny between the two cultivars. CONCLUSIONS: The genome maps of the CMD2 locus in both 60444 and TME3, together with the newly annotated genes, will help the identification of the causal genetic basis of CMD2 resistance to geminiviruses. Our de novo cassava genome assemblies will also facilitate genetic mapping approaches to narrow the large CMD2 region to a few candidate genes for better informed strategies to develop robust geminivirus resistance in susceptible cassava cultivars. [less ▲]

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See detailA Novel Method of Capturing and Sequencing Rolling Circle-Replicating Helitron Transposons
Syed-Shan-e-Ali, Zaïdi ULiege; Cornet, Luc ULiege; Mehta, Devang et al

Scientific conference (2018, October 28)

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See detailCombining BAC and PacBio sequencing to resolve cassava mosaic disease resistance locus CMD2
Syed-Shan-e-Ali, Zaïdi ULiege; Cornet, Luc ULiege; Comadira, Gloria et al

Scientific conference (2018, October 16)

Cassava provides staple food to an estimated 800 million people worldwide and is the most important source of food in developing countries after maize, rice, and wheat. However, cassava production is ... [more ▼]

Cassava provides staple food to an estimated 800 million people worldwide and is the most important source of food in developing countries after maize, rice, and wheat. However, cassava production is severely affected by virus-borne cassava mosaic disease (CMD) in Africa and the Indian subcontinent. Annual yield losses due to CMD are estimated to be 55 million tones. A milestone in molecular breeding to for CMD was the identification of single dominant disease resistance locus CMD2. But recent studies have shown that CMD2 cultivars lost resistance during early stages of somatic embryogenesis in tissue culture. It is therefore necessary to understand the mechanism of CMD2-mediated resistance for its efficient utilization in the cassava improvement. My research aims at combining BAC sequencing, whole genome PacBio sequencing and mapping population of CMD resistant (TME3) and susceptible (60444) accessions to fully sequence, assemble and compare the CMD2 locus. We have generated BAC libraries for both cassava genotypes and screened these libraries to identify CMD2-associatted BACs. We have used the information available from classical marker-assisted breeding studies to develop high quality probes for BAC hybridization. Using this pipeline, we have selected and sequenced 33 BACs on PacBio platform, that cover ~3MB of estimated 8MB CMD2 locus. Further, we have used the latest whole genome assemblies of TME3 and 60444 (accessible from ETH Zurich), to perform comparative analysis. In summary, our results have shown that BAC sequencing is an efficient approach for resolving CMD2, specially in the highly repetitive regions. These results have important implications in understanding CMD and developing a long term strategy to control CMD in farmer fields. [less ▲]

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See detailAccelerated ex situ breeding of GBSS- and PTST1-edited cassava for modified starch
Bull, Simon; Seung, David; Chanez, Christelle et al

in Science Advances (2018), 4

Crop diversification required to meet demands for food security and industrial use is often challenged by breeding time and amenability of varieties to genome modification. Cassava is one such crop. Grown ... [more ▼]

Crop diversification required to meet demands for food security and industrial use is often challenged by breeding time and amenability of varieties to genome modification. Cassava is one such crop. Grown for its large starch-rich storage roots, it serves as a staple food and a commodity in the multibillion-dollar starch industry. Starch is composed of the glucose polymers amylopectin and amylose, with the latter strongly influencing the physicochemical properties of starch during cooking and processing. We demonstrate that CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9)–mediated targeted mutagenesis of two genes involved in amylose biosynthesis, PROTEIN TARGETING TO STARCH (PTST1) or GRANULE BOUND STARCH SYNTHASE (GBSS), can reduce or eliminate amylose content in root starch. Integration of the Arabidopsis FLOWERING LOCUS T gene in the genome-editing cassette allowed us to accelerate flowering—an event seldom seen under glasshouse conditions. Germinated seeds yielded S1, a transgene-free progeny that inherited edited genes. This attractive new plant breeding technique for modified cassava could be extended to other crops to provide a suite of novel varieties with useful traits for food and industrial applications. [less ▲]

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See detailStories from the lab, stories from the field: advancing tropical crop biotechnology
Vanderschuren, Hervé ULiege

Conference (2018, August 31)

The use of crop biotechnology is steadily increasing in the agrosystems of industrialized countries. Recent advances in genome editing are anticipated to further accentuate this trend. Given its potential ... [more ▼]

The use of crop biotechnology is steadily increasing in the agrosystems of industrialized countries. Recent advances in genome editing are anticipated to further accentuate this trend. Given its potential for low input agriculture, there is a need to bring the benefits of crop biotechnology to developing and emerging countries. The challenge goes beyond the mere generation of transgenic crops because development and deployment of genetically engineered crops require local capacities and support from the authorities. In the recent years, we have used biotechnological approaches to improve cassava, the most important root crop in the tropics. Cassava production and processing suffer from several constraints, including viral diseases, drought and post-harvest deterioration. A better understanding of crop responses to biotic and abiotic stresses combined with genetic engineering approaches can be particularly instrumental to generate plants with improved traits. We have used Omics approaches to characterize cassava response to stresses and to subsequently implement biotechnological approaches for trait improvement. Smallholders and industries in cassava growing regions need traits such as resistance against cassava mosaic and brown streak diseases, prolonged shelf-life, drought tolerance, modified starch and improved nutritional content. Importantly those technologies should be implemented in local germplasm to secure impact for the local value chains. We actively collaborate with local institutions for technology transfer and assessment of cassava technologies in the field. [less ▲]

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See detailAfter the data deluge: biological characterization of the new variants and viral species identified by HTS
Massart, Sébastien ULiege; Candresse, Thierry; Gil, José et al

Conference (2018, August 03)

Detailed reference viewed: 48 (3 ULiège)