Differential Selection on Carotenoid Biosynthesis Genes as a Function of Gene Position in the Metabolic Pathway: A Study on the Carrot and Dicots

Background: Selection of genes involved in metabolic pathways could target them differently depending on the position of genes in the pathway and on their role in controlling metabolic fluxes. This hypothesis was tested in the carotenoid biosynthesis pathway using population genetics and phylogenetics. Methodology/Principal Findings: Evolutionary rates of seven genes distributed along the carotenoid biosynthesis pathway

Résistance du pommier à la tavelure (Venturia inaequalis) : Recherche de nouveaux loci et construction de génotypes "prototypes" en vue d'une gestion durable de la résistance

Worldwide, most of cultivated apple varieties (Malus x domestica) are susceptible to scab (fungus Venturia inaequalis). Genetic resistance is a major tool to reduce the amounts of fungicides in commercial orchards. Current strategies of genetic control are mainly based on the use of few major genes. The breakdown of the Vf major gene, introgressed from the wild species M. floribunda, clearly shows the limits of such breeding strategies. In such a context, the objective of this thesis is to study apple scab resistance factors for a durable management of the resistance in front of pathogen adaptation capacity. Two approaches were applied: (i) searching new resistance loci in the resistant variety ‘Dülmener Rosenapfel' and within a pedigreed population of the INRA breeding programme; (ii) recombination of different (major and partial) resistance factors in a half-diallel design, and comparison of the relative efficiency of these genetic combinations towards pathogen variability. A new major gene, Rvi14, was characterised in the variety ‘Dülmener Rosenapfel', together with two QTL: the first one co-localised with Rvi14, and the second one with a broad-spectrum QTL already identified in other genetic backgrounds. The study of the pedigreed population confirmed the frequent polymorphism at this second QTL and revealed different alleles at a third QTL co-localising with the Vf gene. The analysis of different genetic combinations allowed us to develop a model assessing the resistance level of apple genotypes according to the resistance factors they carry and the fungal isolates/races they face. The gained results induced a general discussion on the efficiency of resistance loci detection methods and the use of these loci for a durable management of the resistance.A l'échelle mondiale, la majorité des variétés de pommier cultivées (Malus x domestica) sont sensibles à la tavelure (champignon Venturia inaequalis). La lutte génétique est une des voies privilégiées pour réduire drastiquement le nombre d'applications fongicides en verger commercial. Les stratégies actuelles de lutte génétique reposent principalement sur l'utilisation de quelques gènes majeurs. Le contournement du gène majeur Vf, introgressé de l'espèce sauvage M. floribunda, montre clairement les limites de telles stratégies de sélection. Dans un tel contexte, ce projet de thèse visait à étudier les facteurs de résistance du pommier à la tavelure dans l'optique d'une gestion durable de la résistance face aux capacités d'adaptation de l'agent pathogène. Deux axes ont été abordés : (i) recherche de nouveaux loci de résistance chez la variété résistante ‘Dülmener Rosenapfel' et dans un ensemble de descendances du programme d'amélioration INRA connectées par leur pedigree ; (ii) combinaison de différents facteurs de résistance (majeure et partielle) dans un plan de croisement demi-diallèle, et comparaison de l'efficacité relative de ces constructions génétiques vis-à-vis de la variabilité de l'agent pathogène. Un nouveau gène majeur, Rvi14, a été caractérisé chez la variété ‘Dülmener Rosenapfel', ainsi que deux QTL : le premier co-localise avec Rvi14, et le second avec un QTL à large spectre d'action déjà identifié dans d'autres fonds génétiques. L'étude de la population en pedigree a confirmé l'occurrence fréquente d'un polymorphisme à ce second QTL et a mis en évidence différents allèles à un troisième QTL co-localisant avec le gène Vf. L'analyse des différentes combinaisons génétiques a permis d'initier la modélisation du niveau de résistance des génotypes de pommier en fonction des loci de résistance portés et face aux souches/races du champignon auxquelles ils sont confrontés. Les résultats obtenus au cours de ce travail sont le support d'une réflexion sur l'efficacité des méthodes de détection de loci de résistance et sur l'utilisation de ces loci en vue d'une gestion durable de la résistance

Differential Selection on Carotenoid Biosynthesis Genes as a Function of Gene Position in the Metabolic Pathway: A Study on the Carrot and Dicots

Abstract Background: Selection of genes involved in metabolic pathways could target them differently depending on the position of genes in the pathway and on their role in controlling metabolic fluxes. This hypothesis was tested in the carotenoid biosynthesis pathway using population genetics and phylogenetics

A gene candidate approach to study the control of recurrent blooming in rose

A gene candidate approach to study the control of recurrent blooming in rose. Plant genomics European meeting

Use of carrot genetic resources to understand root carotenoid content: preliminary steps to an association mapping study

Association mapping becomes one of the major genetic methods used to understand genetic control of complex traits. This method allows the use of natural populations with high resolution thanks to ancestral recombinations. Resolution is given by linkage disequilibrium (LD) extend. But false positives can be detected when phenotypic traits are correlated with underlying population stratification at non causal loci. Knowledge of population structure is then a preliminary step for association mapping studies. Here we investigated the population structure in cultivated carrot and the LD extend in the carotenoid isomerase gene, a key gene in the carotenoid biosynthesis pathway. An unexpected high LD for outcrossing species was found in this gene. Population stratification analysis confirmed the differentiation of the carrot germplasm in two clusters. The first one comprised European and American accessions, the second one Asian accessions. These are preliminary steps to perform association mapping studies to understand root carotenoid content in cultivated carrot

Functional gene polymorphism to reveal species history: the case of the CRTISO gene in cultivated carrots.

Carrot is a vegetable cultivated worldwide for the consumption of its root. Historical data indicate that root colour has been differentially selected over time and according to geographical areas. Root pigmentation depends on the relative proportion of different carotenoids for the white, yellow, orange and red types but only internally for the purple one. The genetic control for root carotenoid content might be partially associated with carotenoid biosynthetic genes. Carotenoid isomerase (CRTISO) has emerged as a regulatory step in the carotenoid biosynthesis pathway and could be a good candidate to show how a metabolic pathway gene reflects a species genetic history.In this study, the nucleotide polymorphism and the linkage disequilibrium among the complete CRTISO sequence, and the deviation from neutral expectation were analysed by considering population subdivision revealed with 17 microsatellite markers. A sample of 39 accessions, which represented different geographical origins and root colours, was used. Cultivated carrot was divided into two genetic groups: one from Middle East and Asia (Eastern group), and another one mainly from Europe (Western group). The Western and Eastern genetic groups were suggested to be differentially affected by selection: a signature of balancing selection was detected within the first group whereas the second one showed no selection. A focus on orange-rooted carrots revealed that cultivars cultivated in Asia were mainly assigned to the Western group but showed CRTISO haplotypes common to Eastern carrots.The carotenoid pathway CRTISO gene data proved to be complementary to neutral markers in order to bring critical insight in the cultivated carrot history. We confirmed the occurrence of two migration events since domestication. Our results showed a European background in material from Japan and Central Asia. While confirming the introduction of European carrots in Japanese resources, the history of Central Asia material remains unclear

Role of nonsynonymous and synonymous substitution rates in <i>d_N</i>/<i>d_S</i> ratio variation.

<p>Distribution of (A) <i>d_N</i>/<i>d_S</i> ratio , (B) nonsynonymous substitution rate <i>d_N</i> and (C) synonymous substitution rate <i>d_S</i> calculated from pairwise comparison of seven dicots are displayed as a function of carotenoid biosynthesis genes. The genes are classified according to their pathway position.</p

Constraint relaxation in the carotenoid biosynthesis pathway.

<p>(A) <i>ω₀</i> and (B) ratio of codons with 0<<i>ω</i>₀<1 (<i>p₀</i>) are displayed as a function of carotenoid biosynthesis pathway genes. Values shown were estimated by the M1a model calculated by CODEML <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038724#pone.0038724-Yang2" target="_blank">[65]</a>. The genes are sorted according to their pathway position.</p

Selection in carotenoid biosynthesis pathway in carrot as a function of gene position.

<p>Distribution of p-values obtained according the rank of Tajima’s <i>D</i>, normalized Fay and Wu’s <i>H</i> and <i>F_ST</i> for the seven carotenoid biosynthesis genes in carrot by comparison with the expected distribution obtained by approximate Bayesian computation simulations under the divergence model. Each boxplot combines p-values obtained on pooled, geographic and color samples. The genes are sorted according to their pathway position.</p