Construction of a potato consensus map and QTL meta-analysis offer new insights into the genetic architecture of late blight resistance and plant maturity traits

<p>Abstract</p> <p>Background</p> <p>Integrating QTL results from independent experiments performed on related species helps to survey the genetic diversity of loci/alleles underlying complex traits, and to highlight potential targets for breeding or QTL cloning. Potato (<it>Solanum tuberosum </it>L.) late blight resistance has been thoroughly studied, generating mapping data for many Rpi-genes (R-genes to <it>Phytophthora infestans</it>) and QTLs (quantitative trait loci). Moreover, late blight resistance was often associated with plant maturity. To get insight into the genomic organization of late blight resistance loci as compared to maturity QTLs, a QTL meta-analysis was performed for both traits.</p> <p>Results</p> <p>Nineteen QTL publications for late blight resistance were considered, seven of them reported maturity QTLs. Twenty-one QTL maps and eight reference maps were compiled to construct a 2,141-marker consensus map on which QTLs were projected and clustered into meta-QTLs. The whole-genome QTL meta-analysis reduced by six-fold late blight resistance QTLs (by clustering 144 QTLs into 24 meta-QTLs), by <it>ca</it>. five-fold maturity QTLs (by clustering 42 QTLs into eight meta-QTLs), and by <it>ca</it>. two-fold QTL confidence interval mean. Late blight resistance meta-QTLs were observed on every chromosome and maturity meta-QTLs on only six chromosomes.</p> <p>Conclusions</p> <p>Meta-analysis helped to refine the genomic regions of interest frequently described, and provided the closest flanking markers. Meta-QTLs of late blight resistance and maturity juxtaposed along chromosomes IV, V and VIII, and overlapped on chromosomes VI and XI. The distribution of late blight resistance meta-QTLs is significantly independent from those of Rpi-genes, resistance gene analogs and defence-related loci. The anchorage of meta-QTLs to the potato genome sequence, recently publicly released, will especially improve the candidate gene selection to determine the genes underlying meta-QTLs. All mapping data are available from the Sol Genomics Network (SGN) database.</p

PROTOCOLS AND GUIDELINES TO MAXIMIZEORGANIC SEED PRODUCTION FOR BROCCOLI, TOMATO AND SNAP BEAN

With the goal to increase organically managed farmland to 25% by 2030 together with the upcoming requirement to use exclusively organic seeds for organic farming, more seeds produced under organic conditions are needed on the market. Seed production underorganic conditions is even more challenging than in conventional production systems, mainly due to the restricted access to regular products for fertilization and plant protection. To increase the number of healthy seeds, we tested different agronomic factors which could influence the number of seeds produced in several organic farms in Europe and provide recommendations on relevant factors in these guidelines

A high-resolution map of the Grp1 locus on chromosome V of potato harbouring broad-spectrum resistance to the cyst nematode species Globodera pallida and Globodera rostochiensis

The Grp1 locus confers broad-spectrum resistance to the potato cyst nematode species Globodera pallida and Globodera rostochiensis and is located in the GP21-GP179 interval on the short arm of chromosome V of potato. A high-resolution map has been developed using the diploid mapping population RHAM026, comprising 1,536 genotypes. The flanking markers GP21 and GP179 have been used to screen the 1,536 genotypes for recombination events. Interval mapping of the resistances to G. pallida Pa2 and G. rostochiensis Ro5 resulted in two nearly identical LOD graphs with the highest LOD score just north of marker TG432. Detailed analysis of the 44 recombinant genotypes showed that G. pallida and G. rostochiensis resistance could not be separated and map to the same location between marker SPUD838 and TG432. It is suggested that the quantitative resistance to both nematode species at the Grp1 locus is mediated by one or more tightly linked R genes that might belong to the NBS-LRR class

Diversité structurale des locus de résistance à Phytophthora infestans chez la pomme de terre et synténie chez les Solanacées

Diplôme : Dr. d'UniversitéPolygenic resistances to plant pathogens, controlled by QTLs (Quantitative Trait Loci), appear as a durable alternative to monogenic resistances, which are often quickly overcome by new virulences. To facilitate the use of polygenic resistances in plant breeding and in an attempt to better understand their potential durability, the exploration of the host diversity is necessary to inventory the resistance sources and describe the involved loci in the most comprehensive way, according to their genomic distribution and their allelic variability. The aim of this work was to clarify the structural organization of resistance loci to Phytophthora infestans on the potato genome and to make more precise their syntenic relationships with the QTLs of two other Solanaceae. Phytophthora are oomycetes responsible for late blight, and provoke tremendous damages in Solanaceae crops. Many loci of quantitative and qualitative resistances have been described, mostly in potato, but also in tomato and pepper. Three kinds of QTL analyses were used. The analyses in bi-parental independent populations and in connected multi-populations using a factorial mating design allowed the identification of new resistance QTLs in three potato-related wild species, S. sparsipilum, S. spegazzinii and S. berthaultii, with quantitative tests on stems and foliage. A meta-analysis of all available QTL mapping data coming from the present work and from literature highlighted QTL congruency between the different studies, and made colocations clearer between QTLs and major genes of resistance, and with maturity QTLs. Candidate genes of the obtained meta-QTLs have been proposed. From a more prospective point of view, in order to make the syntenic relationships between the three Solanaceae more precise in a region of QTL colinearity, an inter-specific meta-analysis was achieved. Hypotheses were proposed about the molecular nature of the genes underlying the QTLs of the different species, their possible origins and evolution during speciation.Les résistances polygéniques aux bioagresseurs des plantes, contrôlées par des QTL (Quantitative Trait Locus), seraient une alternative durable aux résistances monogéniques, souvent rapidement contournées par de nouvelles virulences. Pour faciliter l’exploitation des résistances polygéniques en sélection variétale et tenter de comprendre leur potentielle durabilité, l'exploration de la diversité de l'espèce hôte est nécessaire pour inventorier les sources de résistance et décrire de la façon la plus complète possible les locus impliqués, selon leur distribution sur le génome et selon leur variabilité allélique. L’objectif de la thèse est de clarifier l’organisation structurale des locus de résistance à Phytophthora infestans sur le génome de la pomme de terre et de préciser leurs relations synténiques avec les QTL de deux autres Solanacées. Les Phytophthora sont des oomycètes responsables du mildiou et provoquent des dégâts considérables dans les cultures de Solanacées. Plusieurs locus de résistance qualitative ou quantitative ont été décrits, majoritairement chez la pomme de terre, mais aussi chez le piment et la tomate. Au cours de la thèse, trois approches d'analyse QTL ont été suivies. L'analyse de populations biparentales indépendantes et connectées selon un plan factoriel a permis d'identifier de nouveaux QTL de résistance chez trois espèces apparentées à la pomme de terre, S. sparsipilum, S. spegazzinii et S. berthaultii, avec des tests quantitatifs sur tige et feuillage. Une méta-analyse de l’ensemble des données de cartographie produites et publiées a montré la congruence des QTL des différentes études, et précisé les colocalisations entre QTL et gènes majeurs de résistance et avec les QTL liés à la maturité. Des gènes candidats aux méta-QTL obtenus ont pu être proposés. Sur un plan plus prospectif, afin de préciser les relations synténiques entre les trois Solanacées dans une zone de colinéarité fonctionnelle de QTL, une méta-analyse inter-spécifique a été réalisée. Des hypothèses ont été proposées sur la nature possible des gènes sous-jacents aux QTL des différentes espèces, leurs origines et leur évolution possible au cours de la spéciation

Major-effect late blight resistance QTLs in Solanum sparsipilum and Solanum spegazzinii map in resistance gene clusters of chromosomes VIII and X

International audienc

Re-evaluation of the Globodera pallida resistance QTLs originating from the wild potato species Solanum spegazzinii

International audienc

A pex1 Missense Mutation Improves Peroxisome Function in a Subset of Arabidopsis pex6 Mutants Without Restoring pex5 Recycling

Peroxisomes are eukaryotic organelles critical for plant and human development because they house essential metabolic functions, such as fatty acid β-oxidation. The interacting ATPases PEX1 and PEX6 contribute to peroxisome function by recycling PEX5, a cytosolic receptor needed to import proteins targeted to the peroxisomal matrix. Arabidopsis pex6 mutants exhibit low PEX5 levels and defects in peroxisomal matrix protein import, oil body utilization, peroxisomal metabolism, and seedling growth. These defects are hypothesized to stem from impaired PEX5 retrotranslocation leading to PEX5 polyubiquitination and consequent degradation of PEX5 via the proteasome or of the entire organelle via autophagy. We recovered a pex1 missense mutation in a screen for second-site suppressors that restore growth to the pex6-1 mutant. Surprisingly, this pex1-1 mutation ameliorated the metabolic and physiological defects of pex6-1 without restoring PEX5 levels. Similarly, preventing autophagy by introducing an atg7-null allele partially rescued pex6-1 physiological defects without restoring PEX5 levels. atg7 synergistically improved matrix protein import in pex1-1 pex6-1, implying that pex1-1 improves peroxisome function in pex6-1 without impeding autophagy of peroxisomes (i.e., pexophagy). pex1-1 differentially improved peroxisome function in various pex6 alleles but worsened the physiological and molecular defects of a pex26 mutant, which is defective in the tether anchoring the PEX1–PEX6 hexamer to the peroxisome. Our results support the hypothesis that, beyond PEX5 recycling, PEX1 and PEX6 have additional functions in peroxisome homeostasis and perhaps in oil body utilization