Génomique fonctionnelle et marqueurs de qualité chez l'abricot

En lien avec la sélection assistée par marqueurs de la qualité des fruits chez l'abricotier (Prunus armeniaca), 71 marqueurs moléculaires impliqués dans la régulation hormonale et dans le contrôle de l'acidité, du taux de sucre, de la texture, de la biosynthèse des arômes, et des pigments, ont été mis en évidence par étude conjointe de l'évolution du transcriptome et du protéome au cours de la maturation et entre génotypes contrastés. Une base de données a été construite contenant 5200 unigènes formés à partir de 18000 EST, fonctionnellement annotés et regroupés par familles multigèniques. Des lames de microarray ont été construites sur lesquelles 1800 unigènes pertinents ont été déposés sous forme d'oligonucléotides 50 mères définis dans la région 3' non codante des transcrits. Celles-ci ont permis de mener l'étude de l'expression des gènes au cours du développement de la variété Bergeron et au travers différentes variétés contrastées pour la vitesse de maturation, la production d'éthylène et la couleur. L'évolution de l'abondance des protéines totales de Bergeron a été étudiée au cours de son développement par électrophorèse bidimensionnelle. Pour faciliter l'identification des spots protéiques, une base de données de protéines végétales chimériques incluant les mutations spécifiques du genre Prunus au sein des séquences complètes de leurs meilleurs orthologues à été construite à partir des données EST. ABSTRACT : In order to improve apricot (Prunus armeniaca) quality with markers assisted selection, 71 molecular markers involved in hormonal regulation and control of acidity and sugar content, texture, flavours and pigments biosynthesis were highlighted by transcriptomics and proteomics comparison of ripening stages and contrasted genotypes. Thus a database, containing 5200 unigenes extracted from 18000 functionally annotated and multigenic families gathered EST, was designed. Microarrays slides were built, and 1800 relevant unigenes were spotted as specific 50mers oligonucleotides designed in the 3' untranslated region of transcripts. Gene expression study was performed on Bergeron cultivar development and between contrasted cultivars for ethylene outburst and color. Total proteins abundance during Bergeron development was analyzed on two-dimensional gel electrophoresis. For improving identification, a plant proteins database including mutations from conceptually translated expressed sequence tags from Prunus into best matches, was designed

Proteomic analysis of shoot tissue during photoperiod induced growth cessation in V. riparia Michx. grapevines

<p>Abstract</p> <p>Background</p> <p>Growth cessation, cold acclimation and dormancy induction in grapevines and other woody perennial plants native to temperate continental climates is frequently triggered by short photoperiods. The early induction of these processes by photoperiod promotes winter survival of grapevines in cold temperate zones. Examining the molecular processes, in particular the proteomic changes in the shoot, will provide greater insight into the signaling cascade that initiates growth cessation and dormancy induction. To begin understanding transduction of the photoperiod signal, <it>Vitis riparia </it>Michx. grapevines that had grown for 35 days in long photoperiod (long day, LD, 15 h) were subjected to either a continued LD or a short photoperiod (short day, SD, 13 h) treatment. Shoot tips (4-node shoot terminals) were collected from each treatment at 7 and 28 days of LD and SD for proteomic analysis via two-dimensional (2D) gel electrophoresis.</p> <p>Results</p> <p>Protein profiles were characterized in <it>V. riparia </it>shoot tips during active growth or SD induced growth cessation to examine physiological alterations in response to differential photoperiod treatments. A total of 1054 protein spots were present on the 2D gels. Among the 1054 proteins, 216 showed differential abundance between LD and SD (≥ two-fold ratio, p-value ≤ 0.05). After 7 days, 39 protein spots were more abundant in LD and 30 were more abundant in SD. After 28 days, 93 protein spots were more abundant in LD and 54 were more abundant in SD. MS/MS spectrometry was performed to determine the functions of the differentially abundant proteins.</p> <p>Conclusions</p> <p>The proteomics analysis uncovered a portion of the signal transduction involved in <it>V. riparia </it>grapevine growth cessation and dormancy induction. Different enzymes of the Calvin-Benson cycle and glutamate synthetase isoforms were more abundant either in LD or SD treatments. In LD tissues the significantly differentially more abundant proteins included flavonoid biosynthesis and polyphenol enzymes, cinnamyl alcohol dehydrogenase, and TCP-1 complexes. In the SD tissue photorespiratory proteins were more abundant than in the LD. The significantly differentially more abundant proteins in SD were involved in ascorbate biosynthesis, photosystem II and photosystem I subunits, light harvesting complexes, and carboxylation enzymes.</p

Identification and characterization of DAMs mutations associated with early blooming in sweet cherry, and validation of DNA-based markers for selection

Dormancy release and bloom time of sweet cherry cultivars depend on the environment and the genotype. The knowledge of these traits is essential for cultivar adaptation to different growing areas, and to ensure fruit set in the current climate change scenario. In this work, the major sweet cherry bloom time QTL qP-BT1.1m (327 Kbs; Chromosome 1) was scanned for candidate genes in the Regina cv genome. Six MADS-box genes (PavDAMs), orthologs to peach and Japanese apricot DAMs, were identified as candidate genes for bloom time regulation. The complete curated genomic structure annotation of these genes is reported. To characterize PavDAMs intra-specific variation, genome sequences of cultivars with contrasting chilling requirements and bloom times (N = 13), were then mapped to the ‘Regina’ genome. A high protein sequence conservation (98.8–100%) was observed. A higher amino acid variability and several structural mutations were identified in the low-chilling and extra-early blooming cv Cristobalina. Specifically, a large deletion (694 bp) upstream of PavDAM1, and various INDELs and SNPs in contiguous PavDAM4 and -5 UTRs were identified. PavDAM1 upstream deletion in ‘Cristobalina’ revealed the absence of several cis-acting motifs, potentially involved in PavDAMs expression. Also, due to this deletion, a non-coding gene expressed in late-blooming ‘Regina’ seems truncated in ‘Cristobalina’. Additionally, PavDAM4 and -5 UTRs mutations revealed different splicing variants between ‘Regina’ and ‘Cristobalina’ PavDAM5. The results indicate that the regulation of PavDAMs expression and post-transcriptional regulation in ‘Cristobalina’ may be altered due to structural mutations in regulatory regions. Previous transcriptomic studies show differential expression of PavDAM genes during dormancy in this cultivar. The results indicate that ‘Cristobalina’ show significant amino acid differences, and structural mutations in PavDAMs, that correlate with low-chilling and early blooming, but the direct implication of these mutations remains to be determined. To complete the work, PCR markers designed for the detection of ‘Cristobalina’ structural mutations in PavDAMs, were validated in an F2 population and a set of cultivars. These PCR markers are useful for marker-assisted selection of early blooming seedlings, and probably low-chilling, from ‘Cristobalina’, which is a unique breeding source for these traits. © Copyright © 2021 Calle, Grimplet, Le Dantec and Wünsch

Dynamics of almond (Prunus amygdalus (L.) Batsch, syn P. dulcis (Mill.)) tree architecture and scion/rootstock interaction

La importancia económica del almendro (Prunus amygdalus (L.) Batsch, syn P. dulcis (Mill.)) ha crecido en los últimos años, especialmente en la península ibérica y países mediterráneos, y en España, la producción ha aumentado significativamente. Sin embargo, aunque es el primer país en área dedicada a su cultivo, está todavía muy lejos de EEUU en términos de producción de almendra. Por ello, se han introducido nuevos sistemas de cultivo en el área mediterránea, que requieren de variedades con un hábito erecto, ramificaciones productivas y un bajo vigor. Debido a esto, ha adquirido relevancia comprender que procesos biológicos modulan la estructura tridimensional del árbol. Todas las características que la definen se engloban en el término arquitectura del árbol, la cual está regulada por varios factores, desde ambientales hasta otros relacionados con el manejo del cultivo, como la poda, los nutrientes o la elección del patrón. El objetivo de este trabajo es caracterizar los factores fisiológicos y moleculares que regulan la arquitectura del almendro, así como el efecto en la misma de la comunicación entre variedad y patrón. La participación de la familia IGT en la diversidad del hábito de crecimiento fue analizada en un conjunto de variedades de almendro y especies silvestres. Aunque en varias especies se ha descrito que regula el ángulo de las ramas y raíces, en almendro, no se ha encontrado ninguna correlación entre la variabilidad de esta familia de genes y la diversidad en hábito. La complejidad de la arquitectura del árbol, involucrando múltiples aspectos del desarrollo del árbol, ha hecho necesario establecer un protocolo de fenotipado cuantitativo enfocado a estudios moleculares. Siete parámetros fueron seleccionados como descriptores de la arquitectura del árbol y del efecto del patrón en su variabilidad. Con estos analizamos el efecto de la interacción entre variedad y patrón en treinta combinaciones con seis variedades comerciales y cinco híbridos interespecíficos. Se observó que el patrón tenía una influencia significativa en los parámetros asociados a la dominancia apical. Por otro lado, variedades con fenotipos extremos de dominancia apical (alta, ‘Isabelona’, o baja, ‘Lauranne’) se veían menos afectadas. Este efecto se transmite a la formación de ramas, viéndose alterada la producción de ramas inmediatas (silépticas) por el genotipo del patrón. Solo se observó expresión diferencial de genes en ápices de ramas en individuos de ‘Diamar’, donde existía una influencia fenotípica del patrón. Estos genes están asociados a la formación de brotes, la diferenciación de meristemos, la división celular, la reorganización de la pared celular o la captación de nutrientes. Mientras que la interacción entre variedad y patrón influye en la arquitectura de la variedad, también la variedad puede afectar al desarrollo del patrón. Observamos una prevalencia de genes expresados diferencialmente asociados a la regulación hormonal, la disponibilidad de nitrógeno o el desarrollo radicular, demostrando que la variedad puede igualmente modificar el perfil molecular del patrón. Esto ratifica la importancia de considerar el efecto mutuo que tienen variedad y patrón en la regulación de un rasgo tan complejo como la arquitectura del almendro.<br /

Correction: Montesinos et al. Phenotyping almond orchards for architectural traits influenced by rootstock choice. Horticulturae 2021, 7, 159

Error in Figure/Table. In the original publication [1], there was a mistake in Figure 2 as published; it contained incorrect names for the cultivars. The correct figure is shown below this paragraph..

Gene expression analysis in cold stress conditions reveals BBX20 and CLO as potential biomarkers for cold tolerance in almond

Late spring frosts can become one of the limiting factors for the expansion of cultivation area towards a harsher climate for the almond [Prunus amygdalus Batsch syn P. dulcis (Mill.) D.A. Webb] crop as spring frost can damage up to 90% of the harvest. In order to identify key genes favoring cold tolerance in almonds, branches from three late-blooming genotypes: ‘Guara’, ‘Soleta’ and ‘Belona’ were exposed at -4¿C during 24 h in a constant climate chamber. Phenotype analysis showed that ‘Guara’ and ‘Soleta’ had a greater acclimation capacity to cold than ‘Belona’. The qRT-PCR BioMark System technology was used to monitor the relative expression of 30 candidate genes with a potential relation to cold response, which are either involved in the ICE-CBF-COR pathway or the independent CBF pathway, and also genes not yet characterized or with unknown function in almond genome. Differences in the gene expression profiles were found among the three studied genotypes and the three time-points of cold exposure (0, 2 and 24 h). BBX20 and CLO genes behaved as differentiator genes between tolerant and susceptible genotypes in cold stress response in almond pistils. In addition, the differences of expression among the tolerant genotypes suggested the intervention of different mechanisms responding to cold stress in almonds. © 2021 by the authors. Licensee MDPI, Basel, Switzerland

The LATERAL ORGAN BOUNDARIES Domain gene family in grapevine: Genome-wide characterization and expression analyses during developmental processes and stress responses

LATERAL ORGAN BOUNDARIES (LOB) DOMAIN (LBD) constitute a family of plant-specific transcription factors with key roles in the regulation of plant organ development, pollen development, plant regeneration, pathogen response, and anthocyanin and nitrogen metabolisms. However, the role of LBDs in fruit ripening and in grapevine (Vitis vinifera L.) development and stress responses is poorly documented. By performing a model curation of LBDs in the latest genome annotation 50 genes were identified. Phylogenetic analysis showed that LBD genes can be grouped into two classes mapping on 16 out of the 19 V. vinifera chromosomes. New gene subclasses were identified that have not been characterized in other species. Segmental and tandem duplications contributed significantly to the expansion and evolution of the LBD gene family in grapevine as noticed for other species. The analysis of cis-regulatory elements and transcription factor binding sites in the VviLBD promoter regions suggests the involvement of several hormones in the regulation of LBDs expression. Expression profiling suggest the involvement of LBD transcription factors in grapevine development, berry ripening and stress responses. Altogether this study provides valuable information and robust candidate genes for future functional analysis aiming to clarify mechanisms responsible for the onset of fruit ripening and fruit defense strategies. © 2017 The Author(s)