Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L.

peer reviewedThe RADseq technology allows researchers to efficiently develop thousands of polymorphic loci across multiple individuals with little or no prior information on the genome. However, many questions remain about the biases inherent to this technology. Notably, sequence misalignments arising from paralogy may affect the development of single nucleotide polymorphism (SNP) markers and the estimation of genetic diversity. We evaluated the impact of putative paralog loci on genetic diversity estimation during the development of SNPs from a RADseq dataset for the nonmodel tree species Robinia pseudoacacia L. We sequenced nine genotypes and analyzed the frequency of putative paralogous RAD loci as a function of both the depth of coverage and the mismatch threshold allowed between loci. Putative paralogy was detected in a very variable number of loci, from 1% to more than 20%, with the depth of coverage having a major influence on the result. Putative paralogy artificially increased the observed degree of polymorphism and resulting estimates of diversity. The choice of the depth of coverage also affected diversity estimation and SNP validation: A low threshold decreased the chances of detecting minor alleles while a high threshold increased allelic dropout. SNP validation was better for the low threshold (4×) than for the high threshold (18×) we tested. Using the strategy developed here, we were able to validate more than 80% of the SNPs tested by means of individual genotyping, resulting in a readily usable set of 330 SNPs, suitable for use in population genetics applications

Cartographie génétique des composés phénoliques de la pomme

In relation to their antioxidant potential, phenolic compounds are usually associated with a protective effect on the human health of a diet rich in fruits and vegetables. They are also widely associated to the organoleptic quality of ciders since they affect bitterness, astringency, color and aroma. Two studies have recently been published on QTL detection for the phenolic content of dessert apple. No study has yet been published for cider apple, even though they are usually more concentrated in phenolic compounds The objective of this work was to identify genomic regions involved in the phenolic content for a cider apple progeny. In a first time, two quantification methods were developed and compared in UHPLC-UV and UHPLC-MS/MS for major phenolic compounds in juices. Even overestimation of some compounds with one detector were observed, these two methods were highly correlated. Phenolic compounds of whole fruits were also quantified at the INRA station of Rennes. A high variability was observed in both fruits and juices of this progeny, representative of major cider apple varieties grown in Europe. 48 QTL were detected on nine linkage groups (LG). Nine clusters seem particularly stable according to the year or material study. Enzymes of the polyphenol pathway and transcription factors were targeted as candidate gene and identified in silico under major QTL. This work offers new targets for the marker-assisted selection like the QTL for chlorogenic acid on LG17 to improve cider apple varieties.En lien avec leur potentiel antioxydant, les composés phénoliques sont généralement associés à l'effet protecteur sur la santé d'une alimentation riche en fruits et légumes. Ils sont également fortement associés à la qualité organoleptique des cidres puisqu'ils affectent directement leur astringence, leur amertume, leur couleur et leurs arômes. Deux études ont récemment été publiées sur la détection de QTL des composés phénoliques des pommes de table. Aucune étude n'a encore été publiée pour les pommes à cidre, réputées pour leur forte teneur en composés phénoliques. L'objectif de cette thèse est d'identifier les régions génétiques impliquées dans la teneur en composés phénoliques d'une descendance de pommiers à cidre. Dans un premier temps, deux méthodes de quantification ont été développées et comparées en UHPLC-UV et UHPLC-MS/MS pour les principaux composés phénoliques du jus de pomme. Bien qu'il y ait des surestimations avec l'un des détecteurs pour certains composés, ces deux méthodes corrèlent très fortement. Des dosages ont également été réalisés sur fruit entier à l'INRA de Rennes. Une grande variabilité a été observée pour les fruits et les jus de cette descendance, représentative des principales variétés de pommes à cidre cultivées en Europe. 48 QTL ont été détectés sur neuf groupes de liaison (LG). Neuf clusters semblent particulièrement stables, indépendamment de l'année ou du matériel (fruit ou jus) étudié. Les enzymes de la biosynthèse des composés phénoliques et facteurs de transcription ont été ciblés pour l'identification des gènes candidats, réalisée au niveau des principaux QTL. Ces travaux proposent de nouvelles cibles pour la sélection assistée par marqueurs comme le QTL pour l'acide chlorogénique du LG17 pour l'amélioration des variétés de pommes à cidr

Cartographie fine d'un QTL de résistance du pommier à la tavelure, et localisation par rapport au locus du gène majeur Vf

Diffusion du document : A consulter sur place Diplôme : Master RechercheLa tavelure du pommier, maladie fongique causée par Venturia inaequalis, est l'une des maladies les plus importantes en verger commercial. Le gène majeur de résistance Vf, très utilisé en sélection, a été récemment contourné par de nouvelles races du champignon. Il est donc nécessaire de trouver de nouvelles combinaisons génétiques durablement résistantes. Deux QTL de résistance à la tavelure ont été mis en évidence à l'INRA sur le groupe de liaison 1 du pommier à proximité du locus du gène Vf : T1 porté par l'hybride 'TN10-8' et Z1 porté par l'hybride 'Z185'. pour une utilisation en sélection assistée par marqueurs, il est nécessaire de réduire l'intervalle de confiance du QTL T1 et de confirmer la présence du QTL Z1 sur le groupe de liaison 1. Des individus recombinant au voisinage du locus Vf ont été sélectionnés grâce à des marqueurs flanquants dans trois familles issues de 'TN10-8', puis ont été phénotypés pour leur niveau de résistance à la tavelure. Des marqueurs additionnels ont été génotypés pour densifier la carte génétique autour du locus Vf. Ces mêmes marqueurs ont été employés sur une nouvelle famille issue de 'Z185'. Les méthodes de cartographie fine et de méta-analyse employées dans notre étude ont permis de réduire significativement l'intervalle de confiance du QTL T1, détecté à proximité de Vf. En revanche, la présence du QTL Z1 sur le groupe de liaison 1 n'a pu être confirmée

POLYPHENOL VARIABILITY IN THE FRUITS AND JUICES OF A CIDER APPLE PROGENY

BACKGROUND: Polyphenols have a favorable antioxidant potential on human health, suggesting that their high content in apple is responsible for the beneficial effects of apple consumption. They are also linked to the quality of apple juices and ciders since they are predominantly responsible for astringency, bitterness, color and aroma. Major phenolic compounds were quantified by liquid chromatography in fruits and juices from a cider apple progeny harvested for three years. The total content of procyanidins and their average degree of polymerization (DPn) were also determined in fruits by phloroglucinolysis. Variability and extraction yield of these compounds were determined. RESULTS: The variability observed in the progeny was representative of the variability observed in many cider apple varieties. Hydroxycinnamic acids were the most extractable group, with an average extraction yield of 67%, whereas flavonols and anthocyanins were the least. CONCLUSION: This study is the first one to introduce variability and extraction yields of the main phenolic compounds in both fruits and juices of a cider apple progeny. This dataset will be used for an upcoming QTL mapping study, an original approach that has never been undertaken for cider apple

QTL mapping and candidate gene research for the phenolic content of fruits and juices prepared from a cider apple progeny

Polyphenols have favorable antioxidant potential on human health suggesting that their high content in apple is responsible for the beneficial effects of apple consumption. They are also related to the quality of ciders as they predominantly account for astringency, bitterness, color and aroma. Five groups of phenolic compounds are described in the apple fruit: flavanols, hydroxycinnamic acids, dihydrochalcones, flavonols and anthocyanins. So far, only two studies have been published on the genetic basis of the phenolic content of dessert apples. As cider apples are commonly described to be much more concentrated in phenolic compounds than dessert varieties, the present study focuses on a cider apple progeny. 32 compounds belonging to the five groups were identified and quantified by HPLC-UV and UHPLC-UV-MS/MS in fruit extracts and juices. 53 QTL controlling phenolic compounds concentration were detected on nine linkage groups (LG) on the integrated linkage map, for all phenolic groups except anthocyanins. QTL clusters located on LG1, 12, 14, 15 and 17 were stable across the year or the studied material. QTL detected on LG1, 14 and 17 for quercitrin, p-coumaroylquinic acid, rutin and chlorogenic acid confirmed results of previous studies. However, no significant QTL was obtained on the LG16 where a major locus for flavanols was previously located. With the two previous studies, this study shows the diversity of genomic regions controlling traits of interest in apple.Cartographie génétique des composés phénoliques de la pomm

Prerequisites for a Black locust genomic selection program

The use of renewable resources as an alternative to fossil fuels has become a priority. Efficient use of forest as a resource for energy and green chemistry purposes require the development of suitable selected genotypes that are competitive and ready to meet the challenges of global change. In this context, the black locust, Robinia pseudoacacia L., is a very promising species which has many advantages in the context of current global change: high phenotypic plasticity, drought resistance, high biomass production and fixation of atmospheric nitrogen. The genetic improvement of woody species using traditional methods can take between 20 to 30 years. These times can be greatly reduced with the development of new selection methods such as genomic selection. Before starting a genomic selection program, it is necessary to 1) develop new molecular markers to achieve a very dense genetic map for genomic selection, 2) study the genetic diversity of the species present in Belgium and compare it with that of the native area, 3) study the structure and the relatedness of different populations, 4) establish a core collection gathering the most genetically diverse individuals, and 5) as black locust is an exotic species, verify its invasiveness in Belgium. These 5 steps will be detailed and the first results obtained will be discussed

Phenolic compounds in apple juices - Method of quantification by UHPLC-UV and UHPLC-MS/MS

An UPHLC-UV/MS/MS method was developed for separation and quantification of major polyphenolic compounds present in apple juice. The main classes of polyphenols studied here are monomeric or polymeric flavan-3-ols, phenolic acids, flavonols and dihydrochalcones. compounds were quantified simultaneously with the two detection systems, i.e. with UV-PDA detection and ESI-triple quadrupole mass detection used in the selected reaction monitoring (SRM) mode. Each method (UHPLC-UV and UHPLC-SRM) was assessed with 2 different apple juice samples and linearity, limit of detection and quantification (LOD and LOQ), accuracy and precision tests were realized on the 15 major compounds. Despite the validation of the UHPLC-UV and UHPLC-SRM methods, significantly different results were obtained by comparing UHPLC-UV and UHPLC-SRM quantifications. Three groups of polyphenols were observed, the first one with equivalent results between the two quantification methods (in most cases), and the two others with overestimated or underestimated results when comparing UHPLC-UV and UHPLC-SRM quantifications.Cartographie génétique des composés phénoliques de la pomm

Article Comparison of Two Methods, UHPLC-UV and UHPLC-MS/MS, for the Quantification of Polyphenols in Cider Apple Juices

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