Genetic diversity and relationships among wild and cultivated Ficus carica L.: Usefulness of RGA markers

Disease resistance and the maintenance of genetic diversity in wild and cultivated populations are very important challenges to implement breeding program and markers assisted selection of Ficus carica L. facing climate change and its consequences. Resistance gene analogs (RGA) markers were used for variety discrimination and assessment of genetic structure and diversity of wild and cultivated Ficus carica L. species in Tunisia. The RGA markers were efficient and reliable markers for discriminating wild and cultivated fig. The high level of polymorphism (95.65) detected suggests the effectiveness of RGAs for both genetic fingerprinting and relationships assessment in wild and cultivated fig. The detected markers may represent candidate genes for disease resistance and could be further used to facilitate the identification of candidate genes and accelerate the genetic improvement of disease resistance in breeding programs of Ficus carica species

The Date Palm (Phoenix dactylifera L.) leaf proteome: identification of a gender biomarker to screen male parents

Abstract To establish a proteomic reference map of date palm leaves (Deglet Nour cultivar), we separated and identified leaf proteins using two-dimensional polyacrylamide gel electrophoresis and mass spectrometry, respectively. In total, 284 spots were excised from gel and analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS). Among them, 158 were successfully identified (i.e, a success rate of 55.6%) conducting to the identification of 126 unique proteins. These proteins were then clustered according to their functional annotations. Identified proteins were involved in metabolism, electron transport, photosynthesis, protein synthesis, cell structure or defence. However, 29.4 % of the identifications gave unknown function. We then compared the proteome map of female and male trees. Only one discriminated spot was found to be specific of the gender. We identified the corresponding protein as an ABC superfamily ATP binding cassette transporter, ABC protein, a protein whose an ortholog in Arabidopsis thaliana was already reported as required for male fertility and pollen formation. The relevance of this protein as gender biomarker was then confirmed in four other cultivars, i.e., Aligue, Khouet Aligue, Kentichi and Kenta. Such biomarker should be helpful in rapidly distinguishing date palm gender of immature trees

Effects of Natural and Anthropogenic Stressors on Fucalean Brown Seaweeds Across Different Spatial Scales in the Mediterranean Sea

Este artículo contiene 14 páginas, 8 figuras, 3 tablas.Algal habitat-forming forests composed of fucalean brown seaweeds (Cystoseira, Ericaria, and Gongolaria) have severely declined along the Mediterranean coasts, endangering the maintenance of essential ecosystem services. Numerous factors determine the loss of these assemblages and operate at different spatial scales, which must be identified to plan conservation and restoration actions. To explore the critical stressors (natural and anthropogenic) that may cause habitat degradation, we investigated (a) the patterns of variability of fucalean forests in percentage cover (abundance) at three spatial scales (location, forest, transect) by visual estimates and or photographic sampling to identify relevant spatial scales of variation, (b) the correlation between semi-quantitative anthropogenic stressors, individually or cumulatively (MA-LUSI index), including natural stressors (confinement, sea urchin grazing), and percentage cover of functional groups (perennial, semi-perennial) at forest spatial scale. The results showed that impacts from mariculture and urbanization seem to be the main stressors affecting habitat-forming species. In particular, while mariculture, urbanization, and cumulative anthropogenic stress negatively correlated with the percentage cover of perennial fucalean species, the same stressors were positively correlated with the percentage cover of the semi-perennial Cystoseira compressa and C. compressa subsp. pustulata. Our results indicate that human impacts can determine spatial patterns in these fragmented and heterogeneous marine habitats, thus stressing the need of carefully considering scale-dependent ecological processes to support conservation and restoration.This study was supported by the European Union’s EASME (Executive Agency for Small and Medium Enterprise) and EMFF (European Maritime and Fisheries fund) as part of the project AFRIMED, “Algal Forest Restoration in the Mediterranean Sea” (under grant agreement no. 789059), http:// afrimed-project.eu/.Peer reviewe

Genetic variability organisation and gene flow in natural populations of Medicago polymorpha L. prospected in Tunisia

International audienc

Genotyping by sequencing reveals the interspecific C. maxima / C. reticulata admixture along the genomes of modern citrus varieties of mandarins, tangors, tangelos, orangelos and grapefruits.

The mandarin horticultural group is an important component of world citrus production for the fresh fruit market. This group formerly classified as C. reticulata is highly polymorphic and recent molecular studies have suggested that numerous cultivated mandarins were introgressed by C. maxima (the pummelos). C. maxima and C. reticulata are also the ancestors of sweet and sour oranges, grapefruit, and therefore of all the "small citrus" modern varieties (mandarins, tangors, tangelos) derived from sexual hybridization between these horticultural groups. Recently, NGS technologies have greatly modified how plant evolution and genomic structure are analyzed, moving from phylogenetics to phylogenomics. The objective of this work was to develop a workflow for phylogenomic inference from Genotyping By Sequencing (GBS) data and to analyze the interspecific admixture along the nine citrus chromosomes for horticultural groups and recent varieties resulting from the combination of the C. reticulata and C. maxima gene pools. A GBS library was established from 55 citrus varieties, using the ApekI restriction enzyme and selective PCR to improve the read depth. Diagnostic polymorphisms (DPs) of C. reticulata/C. maxima differentiation were identified and used to decipher the phylogenomic structure of the 55 varieties. The GBS approach was powerful and revealed 30,289 SNPs and 8,794 Indels with 12.6% of missing data. 11,133 DPs were selected covering the nine chromosomes with a higher density in genic regions. GBS combined with the detection of DPs was powerful for deciphering the "phylogenomic karyotypes" of cultivars derived from admixture of the two ancestral species after a limited number of interspecific recombinations. All the mandarins, mandarin hybrids, tangelos and tangors analyzed displayed introgression of C. maxima in different parts of the genome. C. reticulata/C. maxima admixture should be a major component of the high phenotypic variability of this germplasm opening up the way for association studies based on phylogenomics

Molecular detection and characterization of <i>Hop stunt viroid</i> sequence variants from naturally infected pomegranate (<i>Punica granatum </i>L.) in Tunisia

Tunisian pomegranate Hop stunt viroid (HSVd) variants are described. Dot-blot hybridization, S-Page, and reverse transcription polymerase chain reaction (RT-PCR) of RNA extracts from infected tissues were carried out. Results obtained by these techniques were confirmed by cDNA sequencing. The genetic diversity among the Tunisian variants was investigated, which also involved analysis of sequences of previously described HSVd variants from Tunisian citrus var. clementine and fig, and from fruit trees from other Mediterranean countries. Phylogenetic analysis showed that Tunisian pomegranate HSVd variants were clustered into two groups: a cachexia strain within the citrus type group and a recombinant citrus-plum type group. Results also showed a high haplotype diversity which was not related either to the host or to the geographical origin. Selective neutrality and genetic network tests suggest that the HSVd isolates have spread rapidly

Analyse de la diversité génétique de cultivars tunisiens de figuier (

Introduction. Une étude a été réalisée pour évaluer la variabilité génétique d'une collection d'écotypes de figuier (Ficus carica L.) établie dans la région du Sahel, en Tunisie. Elle a été basée sur l'observation de caractères morphologiques relatifs au développement végétatif de l'arbre. Matériel et méthodes. Les mensurations de feuilles et rameaux de 17 écotypes de figuiers tunisiens ont été mesurées à raison de deux arbres échantillonnés par cultivar. Les résultats ont été soumis à une analyse de variance et à des analyses multivariées qui ont permis d'obtenir une matrice des corrélations entre caractères mesurés et une table des distances de Mahalanobis entre les écotypes. Résultats et discussion. La variabilité intracultivar s'est révélée très faible. En revanche, la diversité intercultivar apparaît très importante et cela indépendamment de l'origine géographique et du sexe de la plante. Conclusion. Quelques paramètres morphologiques ont permis de bien différencier les cultivars. Ils pourraient être utilisés comme descripteurs chez cette espèce