Donia Abdallah

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Francesco Sottile

Università degli Studi di Palermo

Daniela Giovannini

Jose I Hormaza

Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" CSIC-UMA

Magdolna Tóth

Corvinus University of Budapest

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Papers by Donia Abdallah

Genetic Characterization of a Plum Landrace Collection from La Palma, Canary Islands

Agronomy, Sep 14, 2022

This article is an open access article distributed under the terms and conditions of the Creative... more

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Analysis of genetic diversity and water-stress tolerance in Tunisian plums [Prunus.spp; Rosacea]

Scientia Horticulturae, 2021

Abstract Prunus L. (Rosaceae), a genus of over 230 species, exhibits gametophytic self-incompatib... more Abstract Prunus L. (Rosaceae), a genus of over 230 species, exhibits gametophytic self-incompatibility system (GSI). In this study, we explored the patterns of variability in Plum genotypes carrying different reproductive systems, using 36 microsatellite markers (SSRs) and the S-locus. The analysis of genetic diversity showed a rich genetic variability of the studied genotypes. Linkage Disequilibrium decayed rapidly in analyzed plums reaching the significant value (r² = 0.1) at 7.5 cM. Also, we examined the patterns of variability at the end of the sixth linkage group to emphasize the effect of the S-locus on the surrounding region. The genetic diversity in the genomic neighborhood of the S-locus is related to the negative frequency dependent selection (NFDS) which can extend the high polymorphism at the selected locus to closely linked neutral sites. We conducted a drought stress on Tunisian plum to test their response. The analysis of five morphological parameters tested under drought conditions allowed selecting five plum genotypes (one hexploid and four diploid) characterized by their important tolerance to drought stress. These genotypes may be selected as important rootstock for varietal improvement.

Identification of conserved genes linked to responses to abiotic stresses in leaves among different plant species

Functional Plant Biology, 2021

As a consequence of global climate change, certain stress factors that have a negative impact on ... more As a consequence of global climate change, certain stress factors that have a negative impact on crop productivity such as heat, cold, drought and salinity are becoming increasingly prevalent. We conducted a meta-analysis to identify genes conserved across plant species involved in (1) general abiotic stress conditions, and (2) specific and unique abiotic stress factors (drought, salinity, extreme temperature) in leaf tissues. We collected raw data and re-analysed eight RNA-Seq studies using our previously published bioinformatic pipeline. A total of 68 samples were analysed. Gene set enrichment analysis was performed using MapMan and PageMan whereas DAVID (Database for Annotation, Visualisation and Integrated Discovery) was used for metabolic process enrichment analysis. We identified of a total of 5122 differentially expressed genes when considering all abiotic stresses (3895 were upregulated and 1227 were downregulated). Jasmonate-related genes were more commonly upregulated by d...

Self-compatibility in peach [Prunus persica (L.) Batsch]: patterns of diversity surrounding the S-locus and analysis of SFB alleles

Horticulture Research, 2020

Self-incompatibility (SI) to self-compatibility (SC) transition is one of the most frequent and p... more Self-incompatibility (SI) to self-compatibility (SC) transition is one of the most frequent and prevalent evolutionary shifts in flowering plants. Prunus L. (Rosaceae) is a genus of over 200 species most of which exhibit a Gametophytic SI system. Peach [Prunus persica (L.) Batsch; 2n = 16] is one of the few exceptions in the genus known to be a fully self-compatible species. However, the evolutionary process of the complete and irreversible loss of SI in peach is not well understood and, in order to fill that gap, in this study 24 peach accessions were analyzed. Pollen tube growth was controlled in self-pollinated flowers to verify their self-compatible phenotypes. The linkage disequilibrium association between alleles at the S-locus and linked markers at the end of the sixth linkage group was not significant (P > 0.05), except with the closest markers suggesting the absence of a signature of negative frequency dependent selection at the S-locus. Analysis of SFB1 and SFB2 protein...

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Genetic Diversity of Local Peach (Prunus persica) Accessions from La Palma Island (Canary Islands, Spain)

Agronomy, 2020

Peach (Prunus persica) is an economically important temperate fruit crop due to its edible fruits... more Peach (Prunus persica) is an economically important temperate fruit crop due to its edible fruits. Due to the need to develop new varieties better adapted to climate change, it is of great interest to find germplasm adapted to warmer conditions, such as those found in the Canary Islands. Peach was an important crop during the last century in one of those islands (La Palma), but its cultivation has been abandoned in recent years. Currently, commercial production is relict and isolated trees are relegated to family orchards with little management. With the objective to characterize and prevent the loss of local varieties of this crop, peach trees were sampled along La Palma. A total of 89 local peach accessions were prospected and analyzed with 10 single-sequence repeat (SSR) loci, which permitted 28 different genotype profiles to be detected. These genotypes were compared to 95 Spanish peach landraces conserved in an ex situ collection, and 26 additional samples from eight different ...

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Conserved DNA-derived polymorphism, new markers for genetic diversity analysis of Tunisian Pistacia vera L

Physiology and Molecular Biology of Plants, 2019

Pistachio trees (Pistacia vera L.) have been cultivated in Tunisia for decades and the plantation... more Pistachio trees (Pistacia vera L.) have been cultivated in Tunisia for decades and the plantation was extended mostly in the center of the country contributing to the economic growth of marginalized areas. Herein we used conserved DNA derived polymorphism (CDDP) technique, which target specifically conserved sequences of plant functional genes, to assess the genetic diversity and construct genetic relationships among 65 Tunisian pistachio trees. A set of nine primers were used and 157 CDDP markers were revealed with an average of 17.44 showing a high degree of polymorphism (99.37%). The average of polymorphism information content of CDDP markers was of 0.86, which indicates the efficiency of CDDP primers in the estimation of genetic diversity between pistachios. UPGMA dendrogram and the principal component analysis showed four clusters of analyzed pistachios trees. Our results showed that the genetic structure depends on: (1) the gene exchanges between groups, (2) the geographical origin and (3) the sex of the tree. The same result was revealed by the Bayesian analysis implemented in STRUCTURE at K = 4, in which the pistachio genotypes of El Guettar, Kasserine and Sfax were assigned with more than 80% of probability. Our results prove polymorphism and efficiency of CDDP markers in the characterization and genetic diversity analysis of P. vera L. genotypes to define conservation strategy.

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Analysis of Self-Incompatibility and Genetic Diversity in Diploid and Hexaploid Plum Genotypes

Frontiers in Plant Science, 2019

During the last decade, S-genotyping has been extensively investigated in fruit tree crops such a... more During the last decade, S-genotyping has been extensively investigated in fruit tree crops such as those belonging to the Prunus genus, including plums. In plums, S-allele typing has been largely studied in diploid species but works are scarcer in polyploid species due to the complexity of the polyploid genome. This study was conducted in order to analyze the S-genotypes of 30 diploid P. salicina, 17 of them reported here for the first time, and 29 hexaploid plums (24 of P. domestica and 5 of P. insititia). PCR analysis allowed identifying nine S-alleles in the P. salicina samples allocating the 30 accessions in 16 incompatibility groups, two of them identified here for the first time. In addition, pollen tube growth was studied in self-pollinated flowers of 17 Tunisian P. salicina under the microscope. In 16 samples, including one carrying the Se allele, which has been correlated with self-compatibility, the pollen tubes were arrested in the style. Only in one cultivar ("Bedri"), the pollen tubes reached the base of the style. Twelve S-alleles were identified in the 24 P. domestica and 5 P. insititia accessions, assigning accessions in 16 S-genotypes. S-genotyping results were combined with nine SSR loci to analyze genetic diversity. Results showed a close genetic relationship between P. domestica and P. salicina and between P. domestica and P. insititia corroborating that S-locus genotyping is suitable for molecular fingerprinting in diploid and polyploid Prunus species.

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Combination of Simple Sequence Repeat, S-Locus Polymorphism and Phenotypic Data for Identification of Tunisian Plum Species (Prunus spp.)

Biochemical Genetics, 2019

Plums (Prunus spp.) are among the first fruit tree species that attracted human interest. Artific... more Plums (Prunus spp.) are among the first fruit tree species that attracted human interest. Artificial crosses between wild and domesticated species of plums are still paving the way for creation of new phenotypic variability. In Tunisia, despite a considerable varietal richness of plum as well as a high economic value, the plum sector is experiencing a significant regression. The main reason of this regression is the absence of a national program of plum conservation. Hence, this work was aimed to phenotypically and genetically characterize 23 Tunisian plum accessions to preserve this patrimony. Closely related Prunus species from the same subgenus may be differing at two characteristics: ploidy level and phenotypic traits. In this study, single sequence repeat (SSR) markers allowed distinguishing between eighteen diploid accessions and five polyploid accessions, but SSR data alone precluded unambiguous ploidy estimation due to homozygosity. In contrast, S-allele markers were useful to identify the ploidy level between polyploid species, but they did not distinguish species with the same ploidy level. Seven out of 12 phenotypic traits were shown to be discriminant traits for plum species identification. Molecular and phenotypic traits were significantly correlated and revealed a powerful tool to draw taxonomic and genotypic keys. The results obtained in this work are of great importance for local Tunisian plum germplasm management.

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DNA variation and polymorphism in Tunisian plum species (Prunus spp): contribution of flow cytometry and molecular markers

Genetics and Molecular Research, 2015

Plums (Prunus spp) are among the most important stone fruit crops in the world. European (Prunus ... more Plums (Prunus spp) are among the most important stone fruit crops in the world. European (Prunus domestica) and Japanese (Prunus salicina) plums are characterized by different levels of ploidy. Because genetic variability is the prerequisite for any plant-breeding program, we aimed to establish the taxonomic status of Tunisian plums and study their genetic variability. The nuclear DNA content of 45 wild and cultivated Tunisian plums was determined by flow cytometry. Two arbitrary primers (AD10, AD17) were used to elaborate SCAR markers useful to identify plum species. Three wild trees, Zenou 1, Zenou 6, and Zenou 3, which had 2C nuclear DNA contents of 1.99, 2.05, and 2.13 pg, were shown to be hexaploid (2n = 6x = 48), whereas the others were diploid (2n = 2x = 16). These results suggest that the three hexaploid wild plums 18035 DNA variation in Tunisian plum species ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (4): 18034-18046 (2015) belong to Prunus insititia, and the others belong to Prunus salicina. No SCAR markers were revealed using the AD10 and AD17 RAPD primers in relation to the ploidy of plums. We note also that AD17 primer appears to be the most informative concerning the genetic diversity. Morphological and pomological traits revealed similarity between introduced and Tunisian plum cultivars. Despite the significant morphological differences found, all the cultivars studied belong to P. salicina. The information obtained in this analysis provided on local plum genetic resources will be helpful to establish a core collection, to evaluate genetic diversity, and to initiate an improvement and selection program.

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Cytoplasmic polymorphism and evolutionary history of plum cultivars: Insights from chloroplast DNA sequence variation of trnL-trnF spacer and aggregated trnL intron & trnL-trnF spacer

Genetics and Molecular Research, 2015

We screened for polymorphisms of the non-coding region of plastid DNA in plum trees. Sequencing d... more We screened for polymorphisms of the non-coding region of plastid DNA in plum trees. Sequencing data from the trnL-trnF chloroplast region were used to reveal a pattern of diversity, establish phylogenetic relationships, and test the selection pressure or evolutionary demography scenario for plastome DNA. The size of the non-coding regions varied from 398 to 563 and 865 to 1084 bases pairs for the trnL-trnF spacer and combined sequences, respectively. The average GC contents were 33.8 and 34.4% in the spacer and pooled sequences, respectively. Genetic distances calculated within the plums were 0.077 and 0.254, on average, for the trnL spacer and combined sequences, respectively. The neighbor-joining trees showed clustering relationships among cultivars that were independent of their geographic origins and designations. The neutrality tests and site-frequency spectra Polymorphism of plums using chloroplastic DNA ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (2): 3964-3979 (2015) indicated that spacer and pooled sequences fit the neutral theory model at equilibrium between mutation and genetic drift and reject the hypothesis of a recent demographic expansion. The mismatch distribution shows variation patterns, thus providing evidence of an important genetic diversity explained by an excess of intermediate variants that occurred in the sequences analyzed. Further implications of the findings with regard to plum germplasm management and its utilization in breeding programs are also discussed.

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Genetic diversity and differentiation in Prunus species (Rosaceae) using chloroplast and mitochondrial DNA CAPS markers

Genetics and Molecular Research, 2015

Chloroplast (cpDNA) and mitochondrial DNA (mtDNA) were analyzed to establish genetic relationship... more Chloroplast (cpDNA) and mitochondrial DNA (mtDNA) were analyzed to establish genetic relationships among Tunisian plum cultivars using the polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) technique. Two mtDNA regions (nad 1 b/c and nad 4 1/2) and a cpDNA region (trnL-trnF) were amplified and digested using restriction enzymes. Seventy and six polymorphic sites were revealed in cpDNA and mtDNA, respectively. As a consequence, cpDNA appears to be more polymorphic than mtDNA. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram showed that accessions were distributed independently of their geographical origin, and introduced and local cultivars appear to be closely related. Both UPGMA and principal component analysis grouped Tunisian plum accessions into similar clusters. The analysis of the pooled sequences allowed the detection of 17 chlorotypes and 12 mitotypes. The unique haplotypes detected for cultivars are valuable for management and preservation of the plum ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (2): 4177-4188 (2015) local resources. From this study, PCR-RFLP analysis appears to be a useful approach to detect and identify cytoplasmic variation in plum trees. Our results also provide useful information for the management of genetic resources and to establish a program to improve the genetic resources available for plums.

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A signature of balancing selection in the plastid trnL UAA intron and investigation of the genetic relationships among Tunisian plums (Prunus spp.)

Scientia Horticulturae, 2013

Abstract The trnL (UAA) intron of chloroplast DNA (cpDNA) was amplified using universal primers a... more Abstract The trnL (UAA) intron of chloroplast DNA (cpDNA) was amplified using universal primers and sequenced for 28 accessions of Tunisian plums (Prunus spp.). The aligned sequences show that the length of the trnL intron varied from 553 bp to 712 bp. The average of the GC content is 33.8%. The high level of AT content may explain the high proportion of transversions founded. The genetic distance varied from 0.016 to 0.939. The derived neighbor-joining tree showed a high level of polymorphism that occurred independently from cultivar denominations and their locality of origin. A genetic closeness was observed between local and introduced varieties which proved the performance of local varieties and elucidate their genetic proximity. The maximum parsimony tree with RI index of 0.920 indicates the small homoplasy within the data set. The estimated neutrality tests rejected the neutrality hypothesis and are consistent with a balancing selective pressure in trnL intron as a non coding region of the chloroplast DNA.

Genetic Characterization of a Plum Landrace Collection from La Palma, Canary Islands

Agronomy, Sep 14, 2022

This article is an open access article distributed under the terms and conditions of the Creative... more

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Analysis of genetic diversity and water-stress tolerance in Tunisian plums [Prunus.spp; Rosacea]

Scientia Horticulturae, 2021