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  1. Article: Asparagine synthetase genes (AsnS1 and AsnS2) in durum wheat: structural analysis and expression under nitrogen stress

    Curci, PasqualeL / Hélène Bergès / William Marande / Marco Maccaferri / Roberto Tuberosa / Gabriella Sonnante

    Euphytica. 2018 Feb., v. 214, no. 2

    2018  

    Abstract: Wheat is one of the most widely grown cereal crops based on the amount of calories it provides in the human diet. Durum wheat (Triticum turgidum ssp. durum) is largely used for production of pasta and other products. In order to use genetic knowledge to ... ...

    Abstract Wheat is one of the most widely grown cereal crops based on the amount of calories it provides in the human diet. Durum wheat (Triticum turgidum ssp. durum) is largely used for production of pasta and other products. In order to use genetic knowledge to improve the understanding of N-use efficiency, we carried out, for the first time in durum wheat, the isolation and the characterization of four members of the asparagine synthetase (AsnS) gene family. Phylogenetic inference clustered the Ttu-AsnS1 (1.1 and 1.2) and Ttu-AsnS2 (2.1 and 2.2) genes in AsnS gene class I, which is present in monocots and dicots. Class I genes underwent a subsequent duplication leading to the formation of two subgroups. Plants of Svevo cultivar were grown under N-stress conditions and expression of the four AsnS genes was investigated at three developmental stages (seedling, booting, and late milk development), crucial for N absorption, assimilation and remobilization. AsnS1 genes were down-regulated in N-stressed roots, stems and leaves during seedling growth and booting, but seemed to play a role in N remobilization in flag leaves during grain filling. AsnS2 genes were scarcely expressed in roots, stems, and leaves. In N-stressed spikes there was no differential expression in any of the genes. The genes were mapped in silico using a durum wheat SNP map, assigning Ttu-AsnS1 genes to chromosome 5 and Ttu-AsnS2 to chromosome 3. These findings provide a better understanding of the role of ASN genes in response to N stress in durum wheat.
    Keywords Magnoliopsida ; Triticum turgidum subsp. durum ; absorption ; aspartate-ammonia ligase ; chromosomes ; cultivars ; durum wheat ; filling period ; gene expression regulation ; genes ; grain crops ; leaves ; nitrogen ; nutrient use efficiency ; pasta ; phylogeny ; plant breeding ; roots ; seedling growth ; seedlings ; single nucleotide polymorphism ; stems
    Language English
    Dates of publication 2018-02
    Size p. 36.
    Publishing place Springer Netherlands
    Document type Article
    ZDB-ID 216568-5
    ISSN 1573-5060 ; 0014-2336
    ISSN (online) 1573-5060
    ISSN 0014-2336
    DOI 10.1007/s10681-017-2105-z
    Database NAL-Catalogue (AGRICOLA)

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  2. Article ; Online: A wheat cysteine-rich receptor-like kinase confers broad-spectrum resistance against Septoria tritici blotch

    Cyrille Saintenac / Florence Cambon / Lamia Aouini / Els Verstappen / Seyed Mahmoud Tabib Ghaffary / Théo Poucet / William Marande / Hélène Berges / Steven Xu / Maëlle Jaouannet / Bruno Favery / Julien Alassimone / Andrea Sánchez-Vallet / Justin Faris / Gert Kema / Oliver Robert / Thierry Langin

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 10

    Abstract: Septoria tritici blotch (STB) is a devastating foliar disease affecting worldwide wheat production. Here, the authors report a cysteine-rich receptor-like kinase that can confer resistance to Zymoseptoria tritici, the pathogen that causes STB, and slow ... ...

    Abstract Septoria tritici blotch (STB) is a devastating foliar disease affecting worldwide wheat production. Here, the authors report a cysteine-rich receptor-like kinase that can confer resistance to Zymoseptoria tritici, the pathogen that causes STB, and slow penetration and intercellular growth of the pathogen.
    Keywords Science ; Q
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Corrigendum

    Aurélien Blary / Adrián Gonzalo / Frédérique Eber / Aurélie Bérard / Hélène Bergès / Nadia Bessoltane / Delphine Charif / Catherine Charpentier / Laurence Cromer / Joelle Fourment / Camille Genevriez / Marie-Christine Le Paslier / Maryse Lodé / Marie-Odile Lucas / Nathalie Nesi / Andrew Lloyd / Anne-Marie Chèvre / Eric Jenczewski

    Frontiers in Plant Science, Vol

    FANCM Limits Meiotic Crossovers in Brassica Crops

    2020  Volume 11

    Keywords FANCM ; Translational biology ; Brassica ; meiotic crossover ; TILLING ; plant breeding ; Plant culture ; SB1-1110
    Language English
    Publishing date 2020-12-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article: The homoeologous genes encoding chalcone–flavanone isomerase in Triticum aestivum L.: Structural characterization and expression in different parts of wheat plant

    Shoeva, Olesya Y / Elena A. Salina / Elena K. Khlestkina / Helene Berges

    Gene. 2014 Apr. 01, v. 538

    2014  

    Abstract: Chalcone–flavanone isomerase (CHI; EC 5.5.1.6.) participates in the early step of flavonoid biosynthesis, related to plant adaptive and protective responses to environmental stress. The bread wheat genomic sequences encoding CHI were isolated, ... ...

    Abstract Chalcone–flavanone isomerase (CHI; EC 5.5.1.6.) participates in the early step of flavonoid biosynthesis, related to plant adaptive and protective responses to environmental stress. The bread wheat genomic sequences encoding CHI were isolated, sequenced and mapped to the terminal segment of the long arms of chromosomes 5A, 5B and 5D. The loss of the final Chi intron and junction of the two last exons was found in the wheat A, B and D genomes compared to the Chi sequences of most other plant species. Each of the three diploid genomes of hexaploid wheat encodes functional CHI; however, transcription of the three homoeologous genes is not always co-regulated. In particular, the three genes demonstrated different response to salinity in roots: Chi-D1 was up-regulated, Chi-A1 responds medially, whereas Chi-B1 was not activated at all. The observed variation in transcriptional activity between the Chi homoeologs is in a good agreement with structural diversification of their promoter sequences. In addition, the correlation between Chi transcription and anthocyanin pigmentation in different parts of wheat plant has been studied. The regulatory genes controlling anthocyanin pigmentation of culm and pericarp modulated transcription of the Chi genes. However, in other organs, there was no strong relation between tissue pigmentation and the transcription of the Chi genes, suggesting complex regulation of the Chi expression in most parts of wheat plant.
    Keywords anthocyanins ; biosynthesis ; chalcone isomerase ; chromosomes ; culms ; diploidy ; exons ; gene expression regulation ; hexaploidy ; introns ; pericarp ; pigmentation ; promoter regions ; regulator genes ; roots ; salinity ; transcription (genetics) ; Triticum aestivum ; wheat
    Language English
    Dates of publication 2014-0401
    Size p. 334-341.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2014.01.008
    Database NAL-Catalogue (AGRICOLA)

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  5. Article: Map-based cloning of the fertility restoration locus Rfm1 in cultivated barley (Hordeum vulgare)

    Rizzolatti, Carine / Paul Bury / Edouard Tatara / Pierre A. Pin / Nathalie Rodde / Hélène Bergès / Françoise Budar / Hakim Mireau / Jan J. L. Gielen

    Euphytica. 2017 Dec., v. 213, no. 12

    2017  

    Abstract: Hybridization technology has proven valuable in enhancing yields in many crops, but was only recently adopted in the small grain cereals. Hybrid varieties in barley (Hordeum vulgare) rely on the cytoplasmic male sterility (CMS) system msm1 derived from ... ...

    Abstract Hybridization technology has proven valuable in enhancing yields in many crops, but was only recently adopted in the small grain cereals. Hybrid varieties in barley (Hordeum vulgare) rely on the cytoplasmic male sterility (CMS) system msm1 derived from Hordeum vulgare ssp. spontaneum. The major restorer gene described for the msm1 system is known as Rfm1 and maps to the top of chromosome 6H. To gain further insight into mechanisms underlying male fertility restoration in barley, we used a map-based cloning approach to identify the nuclear gene involved in the restoration mechanism of this hybridization system. Taking advantage of the available genomic resources in barley in combination with a custom-made non-gridded BAC library developed from a restorer line, we cloned and sequenced the Rfm1 restorer locus. The characterization and annotation of the nucleotide sequence for the Rfm1 restorer allele allowed for the identification of the candidate gene for Rfm1. The Rfm1 locus carries a tandem repeat of a gene encoding a pentatricopeptide repeat (PPR) protein. Surprisingly, Rfm1 belongs to the PLS-DYW subfamily of PPR genes known for their involvement in RNA editing in plants organelles, but that to date have not been identified as restorer genes.
    Keywords Hordeum vulgare ; RNA editing ; alleles ; bacterial artificial chromosomes ; barley ; crops ; cultivars ; cytoplasmic male sterility ; genomics ; hybridization ; hybrids ; loci ; molecular cloning ; nucleotide sequences ; organelles ; plant breeding ; sequence analysis
    Language English
    Dates of publication 2017-12
    Size p. 276.
    Publishing place Springer Netherlands
    Document type Article
    ZDB-ID 216568-5
    ISSN 1573-5060 ; 0014-2336
    ISSN (online) 1573-5060
    ISSN 0014-2336
    DOI 10.1007/s10681-017-2056-4
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication

    Hélène Badouin / Amandine Velt / François Gindraud / Timothée Flutre / Vincent Dumas / Sonia Vautrin / William Marande / Jonathan Corbi / Erika Sallet / Jérémy Ganofsky / Sylvain Santoni / Dominique Guyot / Eugenia Ricciardelli / Kristen Jepsen / Jos Käfer / Hélène Berges / Eric Duchêne / Franck Picard / Philippe Hugueney /
    Raquel Tavares / Roberto Bacilieri / Camille Rustenholz / Gabriel A. B. Marais

    Genome Biology, Vol 21, Iss 1, Pp 1-

    2020  Volume 24

    Abstract: Abstract Background A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known ...

    Abstract Abstract Background A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known that V. sylvestris has an XY system and V. vinifera a modified Y haplotype (Yh) and that the sex locus is small, but it has not previously been precisely characterized. Results We generate a high-quality de novo reference genome for V. sylvestris, onto which we map whole-genome re-sequencing data of a cross to locate the sex locus. Assembly of the full X, Y, and Yh haplotypes of V. sylvestris and V. vinifera sex locus and examining their gene content and expression profiles during flower development in wild and cultivated accessions show that truncation and deletion of tapetum and pollen development genes on the X haplotype likely causes male sterility, while the upregulation of a Y allele of a cytokinin regulator (APRT3) may cause female sterility. The downregulation of this cytokinin regulator in the Yh haplotype may be sufficient to trigger reversal to hermaphroditism. Molecular dating of X and Y haplotypes is consistent with the sex locus being as old as the Vitis genus, but the mechanism by which recombination was suppressed remains undetermined. Conclusions We describe the genomic and evolutionary characterization of the sex locus of cultivated and wild grapevine, providing a coherent model of sex determination in the latter and for transition from dioecy to hermaphroditism during domestication.
    Keywords Grapevine ; Dioecy ; Sex chromosomes ; Sex-determining genes ; Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
    Subject code 590
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome

    Navdeep Gill / Matteo Buti / Nolan Kane / Arnaud Bellec / Nicolas Helmstetter / Hélène Berges / Loren H. Rieseberg

    Biology, Vol 3, Iss 2, Pp 295-

    2014  Volume 319

    Abstract: Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, ...

    Abstract Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is >78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are “novel” to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence.
    Keywords sunflower ; genome ; whole genome duplication ; transposable elements ; Class I LTR-retrotransposons ; Class II DNA transposons ; transcriptome ; expressed sequence tags ; expression pattern ; Biology (General) ; QH301-705.5
    Subject code 580
    Language English
    Publishing date 2014-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

    Michael Abrouk / Hanin Ibrahim Ahmed / Philippe Cubry / Denisa Šimoníková / Stéphane Cauet / Yveline Pailles / Jan Bettgenhaeuser / Liubov Gapa / Nora Scarcelli / Marie Couderc / Leila Zekraoui / Nagarajan Kathiresan / Jana Čížková / Eva Hřibová / Jaroslav Doležel / Sandrine Arribat / Hélène Bergès / Jan J. Wieringa / Mathieu Gueye /
    Ndjido A. Kane / Christian Leclerc / Sandrine Causse / Sylvie Vancoppenolle / Claire Billot / Thomas Wicker / Yves Vigouroux / Adeline Barnaud / Simon G. Krattinger

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 13

    Abstract: Fonio millet is a fast growing orphan cereal crop with a great potential for dryland agriculture. Here, the authors report chromosome-scale reference genome assembly and population genomic resources to shed light on genetic diversity, population ... ...

    Abstract Fonio millet is a fast growing orphan cereal crop with a great potential for dryland agriculture. Here, the authors report chromosome-scale reference genome assembly and population genomic resources to shed light on genetic diversity, population structure and domestication of fonio millet.
    Keywords Science ; Q
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: High-quality genome sequence of white lupin provides insight into soil exploration and seed quality

    Bárbara Hufnagel / André Marques / Alexandre Soriano / Laurence Marquès / Fanchon Divol / Patrick Doumas / Erika Sallet / Davide Mancinotti / Sébastien Carrere / William Marande / Sandrine Arribat / Jean Keller / Cécile Huneau / Thomas Blein / Delphine Aimé / Malika Laguerre / Jemma Taylor / Veit Schubert / Matthew Nelson /
    Fernando Geu-Flores / Martin Crespi / Karine Gallardo / Pierre-Marc Delaux / Jérôme Salse / Hélène Bergès / Romain Guyot / Jérôme Gouzy / Benjamin Péret

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 12

    Abstract: White lupin is an annual crop cultivated for protein rich seeds and can produce cluster roots for efficient phosphate acquisition. Here, the authors generate high quality genome assemblies of a cultivated accession, a landrace, and a wild relative and ... ...

    Abstract White lupin is an annual crop cultivated for protein rich seeds and can produce cluster roots for efficient phosphate acquisition. Here, the authors generate high quality genome assemblies of a cultivated accession, a landrace, and a wild relative and provides insight into soil exploration and seed quality.
    Keywords Science ; Q
    Language English
    Publishing date 2020-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

    Michael Abrouk / Hanin Ibrahim Ahmed / Philippe Cubry / Denisa Šimoníková / Stéphane Cauet / Yveline Pailles / Jan Bettgenhaeuser / Liubov Gapa / Nora Scarcelli / Marie Couderc / Leila Zekraoui / Nagarajan Kathiresan / Jana Čížková / Eva Hřibová / Jaroslav Doležel / Sandrine Arribat / Hélène Bergès / Jan J. Wieringa / Mathieu Gueye /
    Ndjido A. Kane / Christian Leclerc / Sandrine Causse / Sylvie Vancoppenolle / Claire Billot / Thomas Wicker / Yves Vigouroux / Adeline Barnaud / Simon G. Krattinger

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 13

    Abstract: Fonio millet is a fast growing orphan cereal crop with a great potential for dryland agriculture. Here, the authors report chromosome-scale reference genome assembly and population genomic resources to shed light on genetic diversity, population ... ...

    Abstract Fonio millet is a fast growing orphan cereal crop with a great potential for dryland agriculture. Here, the authors report chromosome-scale reference genome assembly and population genomic resources to shed light on genetic diversity, population structure and domestication of fonio millet.
    Keywords Science ; Q
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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