Pauline Lasserre‐Zuber

Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement

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Frédéric Choulet

Génétique, Diversité, Écophysiologie des Céréales

Hélène Rimbert

Génétique, Diversité, Écophysiologie des Céréales

Nathan Papon

Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement

Etienne Paux

Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement

Charles‐Eric Durel

Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement

Romain De Oliveira

University of Copenhagen

Caroline Denancé

Institut de recherche en horticulture et semences

Valérie Caffier

Institut Agro Rennes-Angers

François Laurens

Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement

Philippe Leroy

Génétique, Diversité, Écophysiologie des Céréales

Cooperative Institutions

Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement

Institut National de la Recherche Agronomique

Institut de recherche en horticulture et semences

Centre National de la Recherche Scientifique

Génétique, Diversité, Écophysiologie des Céréales

Université d'Angers

Université Clermont Auvergne

Institut Agro Rennes-Angers

Université Nantes Angers Le Mans

L'Institut Agro

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ExIGE : Évaluation multi-environnementale de blé tendre « exotique »prédictions génomiques GxE et génétique d'association-projet FSOV 2018 P

Justin Blancon Jonathan Kitt Pauline Lasserre‐Zuber David Álvarez Sibille Perrochon

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The added value of –omic approach to dissect phytopathogenicity of Fusarium graminearum: from genomic to genetic

HAL (Le Centre pour la Communication Scientifique Directe) (2015)

Benoît Laurent Magalie Moinard Cathy Spataro Pauline Lasserre‐Zuber Nadia Ponts

Value (mathematics)

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CONTROLLING HOMOLOGOUS AND HOMOEOLOGOUS RECOMBINATION IN BREAD WHEAT TO ENHANCE THE DEVELOPMENT OF ORIGINAL AND PRODUCTIVE WHEAT VARIETIES

Pierre Sourdille Heïdi Serra Jeanne Bazile Chiara Di Dio Isabelle Nadaud

Wheat germ

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High-resolution genetic and physical map of the Rvi1 (Vg) apple scab resistance locus

Molecular Breeding (2015)

Valentina Cova Pauline Lasserre‐Zuber Stefano Piazza Alessandro Cestaro Riccardo Velasco

Venturia inaequalis

Apple scab

Malus

Bacterial artificial chromosome

10.1007/s11032-015-0245-1

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Citations (24)

All families of transposable elements were active in the recent wheat genome evolution and polyploidy had no impact on their activity

The Plant Genome (2023)

Nathan Papon Pauline Lasserre‐Zuber Hélène Rimbert Romain De Oliveira Etienne Paux

Bread wheat (Triticum aestivum L.) is a major crop and its genome is one of the largest ever assembled at reference-quality level. It is 15 Gb, hexaploid, with 85% of transposable elements (TEs). Wheat genetic diversity was mainly focused on genes and little is known about the extent of genomic variability affecting TEs, transposition rate, and the impact of polyploidy. Multiple chromosome-scale assemblies are now available for bread wheat and for its tetraploid and diploid wild relatives. In this study, we computed base pair-resolved, gene-anchored, whole genome alignments of A, B, and D lineages at different ploidy levels in order to estimate the variability that affects the TE space. We used assembled genomes of 13 T. aestivum cultivars (6x = AABBDD) and a single genome for Triticum durum (4x = AABB), Triticum dicoccoides (4x = AABB), Triticum urartu (2x = AA), and Aegilops tauschii (2x = DD). We show that 5%-34% of the TE fraction is variable, depending on the species divergence. Between 400 and 13,000 novel TE insertions per subgenome were detected. We found lineage-specific insertions for nearly all TE families in di-, tetra-, and hexaploids. No burst of transposition was observed and polyploidization did not trigger any boost of transposition. This study challenges the prevailing idea of wheat TE dynamics and is more in agreement with an equilibrium model of evolution.

10.1002/tpg2.20347

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Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding

GigaScience (2022)

Jean‐Marc Aury Stéfan Engelen Benjamin Istace Cécile Monat Pauline Lasserre‐Zuber

Abstract Background The sequencing of the wheat (Triticum aestivum) genome has been a methodological challenge for many years owing to its large size (15.5 Gb), repeat content, and hexaploidy. Many initiatives aiming at obtaining a reference genome of cultivar Chinese Spring have been launched in the past years and it was achieved in 2018 as the result of a huge effort to combine short-read sequencing with many other resources. Reference-quality genome assemblies were then produced for other accessions, but the rapid evolution of sequencing technologies offers opportunities to reach high-quality standards at lower cost. Results Here, we report on an optimized procedure based on long reads produced on the Oxford Nanopore Technology PromethION device to assemble the genome of the French bread wheat cultivar Renan. Conclusions We provide the most contiguous chromosome-scale assembly of a bread wheat genome to date. Coupled with an annotation based on RNA-sequencing data, this resource will be valuable for the crop community and will facilitate the rapid selection of agronomically important traits. We also provide a framework to generate high-quality assemblies of complex genomes using ONT.

Sequence assembly

10.1093/gigascience/giac034

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Etude de la diversité génétique et de la structure d'une collection française de pommiers

Ludivine Lassois Caroline Denancé Elisa Ravon Pauline Lasserre‐Zuber Laurence Feugey

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All families of transposable elements were active in the recent wheat genome evolution and polyploidy had no impact on their activity

bioRxiv (Cold Spring Harbor Laboratory) (2022)

Nathan Papon Pauline Lasserre‐Zuber Hélène Rimbert Romain De Oliveira Etienne Paux

A bstract Bread wheat ( Triticum aestivum L.) is a major crop and its genome is one of the largest ever assembled at reference-quality level. It is 15 Gb, hexaploid, with 85% of transposable elements (TEs). Wheat genetic diversity was mainly focused on genes and little is known about the extent of genomic variability affecting TEs, transposition rate, and the impact of polyploidy. Multiple chromosome-scale assemblies are now available for bread wheat and for its tetraploid and diploid wild relatives. In this study, we computed base pair-resolved, gene-anchored, whole genome alignments of A, B, and D lineages at different ploidy levels in order to estimate the variability that affects the TE space. We used assembled genomes of 13 T. aestivum cultivars (6x=AABBDD), T. durum (4x=AABB), T. dicoccoides (4x=AABB), T. urartu (2x=AA), and Aegilops tauschii (2x=DD). We show that 5 to 34% of the TE fraction is variable, depending on the species divergence. Between 400 and 13,000 novel TE insertions per subgenome were detected. We found lineage-specific insertions for nearly all TE families in di- tetra- and hexaploids. No burst of transposition was observed and polyploidization did not trigger any boost of transposition. This study challenges the prevailing idea of wheat TE dynamics and is more in agreement with an equilibrium model of evolution.

Aegilops tauschii

Aegilops

Transposition (logic)

10.1101/2022.11.25.517938

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Genetics of resistance to Zymoseptoria tritici and applications to wheat breeding

Fungal Genetics and Biology (2015)

James K. M. Brown Laëtitia Chartrain Pauline Lasserre‐Zuber Cyrille Saintenac

This paper reviews current knowledge about genes for resistance to Septoria tritici blotch (STB) of wheat, caused by Zymoseptoria tritici (formerly Mycosphaerella graminicola). These genes can be placed into two classes, although a few may have characteristics of both classes. Qualitative resistance is controlled by genes which control large fractions of genetic variation, 21 of which have been discovered and mapped so far. Most of them have been shown to be genotype-specific, being effective against the minority of Z. tritici isolates which are avirulent, and Stb6 has been shown to control a gene-for-gene relationship. Most qualitative resistances are unlikely to be durable and some formerly effective genes have been overcome by the evolution of pathogen virulence. Quantitative resistance is generally controlled by genes with small-to-moderate effects on STB. They have generally weaker specificity than qualitative genes and have provided more durable resistance. 89 genome regions carrying quantitative trait loci (QTL) or meta-QTL have been identified to date. Some QTL have been mapped at or near loci of qualitative genes, especially Stb6, which is present in several sources of resistance. Another gene of particular interest is Stb16q, which has been effective against all Z. tritici isolates tested so far. In addition to resistance, the susceptibility of wheat cultivars to STB can also be reduced by disease escape traits, some of which may be undesirable in breeding. The fundamental requirements for breeding for STB-resistance are genetic diversity for resistance in wheat germplasm and a field trial site at which STB epidemics occur regularly and effective selection can be conducted for resistance combined with other desirable traits. If these are in place, knowledge of resistance genes can be applied to improving control of STB.

Mycosphaerella graminicola

Germ plasm

10.1016/j.fgb.2015.04.017

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Citations (221)

Pyramiding Quantitative Resistance with a Major Resistance Gene in Apple: From Ephemeral to Enduring Effectiveness in Controlling Scab

Plant Disease (2018)

Pauline Lasserre‐Zuber Valérie Caffier René Stievenard Arnaud Lemarquand Bruno Le Cam

Genetic resistance is a useful strategy to control plant disease, but its effectiveness may be reduced over time due to the emergence of pathogens able to circumvent the defenses of the plant. However, the pyramiding of different resistance factors in the same plant can improve the effectiveness and durability of the resistance. To investigate the potential for this approach in apple to control scab disease we surveyed scab incidence in two experimental orchards located at a distance of more than 300 km planted with apple genotypes carrying quantitative resistance and major gene resistance alone or in combination. Our results showed that the effectiveness of pyramiding in controlling scab was dependent on the site and could not be completely explained by the effectiveness level of the resistances alone.

Apple scab

10.1094/pdis-11-17-1759-re

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Citations (10)