Assessing the Genetic Diversity and Population Structure of a Tunisian Melon (Cucumis melo L.) Collection Using Phenotypic Traits and SSR Molecular Markers

The assessment of genetic diversity and structure of a gene pool is a prerequisite for efficient organization, conservation, and utilization for crop improvement. This study evaluated the genetic diversity and population structure of 24 Tunisian melon accessions, by using 24 phenotypic traits and eight microsatellite (SSR) markers. A considerable phenotypic diversity among accessions was observed for many characters including those related to agronomical performance. All the microsatellites were polymorphic and detected 30 distinct alleles with a moderate (0.43) polymorphic information content. Shannon’s diversity index (0.82) showed a high degree of polymorphism between melon genotypes. The observed heterozygosity (0.10) was less than the expected heterozygosity (0.12), displaying a deficit in heterozygosity because of selection pressure. Molecular clustering and structure analyses based on SSRs separated melon accessions into five groups and showed an intermixed genetic structure between landraces and breeding lines belonging to the different botanical groups. Phenotypic clustering separated the accessions into two main clusters belonging to sweet and non-sweet melon; however, a more precise clustering among inodorus, cantalupensis, and reticulatus subgroups was obtained using combined phenotypic–molecular data. The discordance between phenotypic and molecular data was confirmed by a negative correlation (r = −0.16, p = 0.06) as revealed by the Mantel test. Despite these differences, both markers provided important information about the diversity of the melon germplasm, allowing the correct use of these accessions in future breeding programs. Together they provide a powerful tool for future agricultural and conservation tasks.Publishe

Morphological evaluation of Tunisian garlic (Allium sativum L.) landraces for growth and yield traits

Purpose: Despite the significance of garlic as a food product and high annual income, until now there are no local commercialized Tunisian cultivars with registered names, which lead to the lack of recommended varieties of high yielding. This work is aimed to create the first garlic gene bank collection in Tunisia, evaluate the variation, identify yield related traits and structure genetic diversity among them. Research method: Thirty six local garlic landraces from the main production regions of Tunisia were collected and recorded in the National Gene Bank of Tunisia database, then grown in a gene bank field for multiplication. The phenotypic diversity was conducted on the basis of fourteen quantitative characteristics add to flowering ability. Findings: High diversity among Tunisian garlic landraces was detected. The bulb weight and bulb diameter explain the most significant variation of the yield. The cluster analysis sorted the 36 genotypes into three main groups as cluster 1 (11 accessions), cluster 2 (20 accessions), and cluster 3 (5 accessions). However, the grouping of genotypes did not correspond with their geographic origin. The highest genetic distance was reported between NGBTUN442 and NGBTUN452, however NGBTUN429 and NGBTUN434 found to be most similar with the lowest dissimilarity. Research limitation: Morphological traits need to be investigated overtime. Originality/Value: This study is interesting since it presents the first creation of the garlic gene bank in Tunisia. The results will provide basis information for the efficient use of the local garlic germplasm and help breeders to easily select out the desirable materials

Variations in the sugars and antioxidant compounds related to root colour in tunisian carrot (daucus carota subsp. sativus) landraces

Carrot (Daucus carota L.) is the most widely consumed root vegetable since it is an important source of nutritional compounds, mainly antioxidants and sugars. In Tunisia, despite the genetic diversity observed in carrot germplasm, including landraces and wild relatives, no research has been conducted on the biochemical composition of carrot. Thus, this study aims to analyse carotenoids, soluble sugars, total phenols, total flavonoids and colour properties of 14 carrot landraces, in order to determine the diversity among them and evaluate the relationships among their biochemical contents. The main carotenoids identified were a-carotene, B-carotene and lutein. Orange carrots were richer in B-carotene and a-carotene than yellow carrots. The major sugars were sucrose, glucose, fructose and galactose. Significant differences were observed among the Tunisian carrot landraces with respect to their biochemical composition and colour characteristics. Total carotenoids and total sugars ranged from 155.74 to 511.44 ug/g of dw and from 368.77 to 546.79 mg/g of dw, respectively. Total phenols and total flavonoids varied from 24.13 to 41.39 mg GAE/100 g of dw and from 16.51 to 24.85 ug CE/100 g of dw, respectively. Significant, positive and negative correlations were found among the measured parameters. A principal component analysis (PCA) and agglomerative hierarchical clustering (AHC) were performed to classify the Tunisian carrot landraces on the basis of colour properties and biochemical compounds. The PCA divided the landraces into four main groups and AHC classified them into two major clusters. The Tunisian carrot landraces were found to be rich in bioactive compounds; they could be good candidates for future breeding programs

Subspecies Variation of Daucus carota Coastal (“Gummifer”) Morphotypes (Apiaceae) Using Genotyping-by-Sequencing

The genus Daucus is widely distributed worldwide, but with a concentration of diversity in the Mediterranean Region. The D. carota complex presents the greatest taxonomic problems in the genus. We focus on a distinctive phenotypic group of coastal morphotypes of D. carota, strictly confined to the margins to within about 0.5 km of the Mediterranean Sea and the Atlantic Ocean, which we here refer to as coastal morphotypes or D. carota subsp. “gummifer” complex. They are loosely morphologically coherent, sharing a relatively short stature, thick, broad, sometimes highly glossy leaf segments, and usually flat or convex fruiting umbels. We analyzed 288 accessions obtained from genebanks in England, France, and the USA, and an expedition to Spain in 2016, covering the Mediterranean and Atlantic coasts and Balearic Islands, where much of the gummifer complex variation occurs. Our study includes 112 accessions not examined before in this context. Genotyping-by-sequencing identified 29,041 filtered SNPs. Based on high bootstrap support from maximum likelihood and Structure analysis we highlight three main clades. The gummifer morphotypes are intercalated with members of Daucus carota subspecies carota and subspecies maximus in two of these main clades, including a clade containing accessions from Tunisia (also including D. carota subsp. capillifolius) and a clade containing accessions from western Europe (including the British Isles), southern Europe (including the Balearic Islands and the Iberian Peninsula) and Morocco. These results support five independent selections of the gummifer morphotypes in these restricted maritime environments in the Mediterranean and nearby Atlantic coasts. Daucus annuus (=Tornabenea annua) and Daucus tenuissimus (=Tornabenea tenuissima) also fall firmly within D. carota, supporting their classification as morphologically well-defined subspecies of D. carota, which are accepted here under the new combinations Daucus carota subsp. annuus and D. carota subsp. tenuissimus , respectively. Types are indicated for most of treated names, including designation of four lectotypes and three epitypes, which fix their further use.This research was partly funded by the research grant UA2004-47056131 (University of Alicante) to FMF and by the USDA

Genetic Diversity Analysis of Onion (Allium cepa L.) from the Arid Region of Tunisia Using Phenotypic Traits and SSR Markers

The present study was carried out to evaluate and characterize, for the first time, the genetic potential of a collection of onion (Allium cepa L.) local accessions from the arid region of southern Tunisia. The genetic diversity among 135 onion individuals, belonging to 23 accessions, was evaluated using microsatellite (SSR) markers and phenotypic information. A total of 35 alleles were generated with 11 SSRs. The polymorphic information content (PIC) value ranged from 0.08 to 0.95, with an average PIC of 0.43. The expected heterozygosity averaged 0.37, and the observed heterozygosity averaged 0.42. The analysis of molecular variance (AMOVA) revealed that 79% of genetic variation existed within individuals. Structure and cluster analysis grouped the accessions into two major clusters: landraces and pre-breeding lines. For the phenotypic traits evaluated, field trials were conducted in two different environments. Significant differences among accessions were shown, and for most traits, there was also a significant environmental effect and a significant interaction between environment and accession. Great variability was found for all the traits that could be exploited to create new varieties of onion adapted to local conditions by selecting appropriate parents in hybridization breeding.Esta investigación fue financiada en parte por el laboratorio de investigación LR21AGR03-Producción y Protección para una Horticultura Sostenible, financiado por el Ministerio de Educación Superior e Investigación Científica de Túnez y parcialmente financiado por el proyecto A11-20R financiado por el Gobierno de Aragón y por el programa AGROALNEXT apoyado por MCIN con financiación de la Unión Europea NextGenerationEU (PRTR-C17.I1).diversitylandracesmicrosatellitesbreedingphenotypicG × E interactionPublishe

The Effects of Salt Stress on Germination, Seedling Growth and Biochemical Responses of Tunisian Squash (Cucurbita maxima Duchesne) Germplasm

Salt stress is considered as one of the most common abiotic stresses reducing the productivity and fruit quality of crop plants. The present study was carried out to assess the salt tolerance among 15 local squash (Cucurbita maxima Duchesne) landraces. Different salt (NaCl) concentrations of 0, 100, 200 and 300 mM were selected in order to evaluate the response of the study germplasm to salt stress based on 12 agronomic parameters and 3 biochemical traits, proline, malondialdehyde (MDA) and chlorophylls. A varied effect of the salt stress level was observed among the studied landraces based on germination potential, as well as on growth and biochemical parameters at seedling stage. Results showed that all landraces were drastically affected at high stress level with a significant variation in their stress response, indicating the existence of considerable genetic variability. Landraces “746” and “747” were the best performing cultivars across stress levels, whereas “1007”, “1008” and “1009” were the most negatively affected. Based on the tested landrace performance, four landraceswere selected and further evaluated at biochemical level, focusing on the determination of compounds that play a key role in the ability to withstand salt stress. The mean MDA content across landraces was generally increased in stressed plants, as compared to the control treatment; the increase was attributed to a peak in MDA content at specific stress levels. In particular, “746” and “1007” showed the maximum content at 100 mM NaCl, while in landrace “751”, MDA content reached its peak at 300 mM NaCl. In addition, the response of most landraces to salt stress involved an increase in free proline content, with the exception of “746”, with the maximum content being observed either at 200 mM (“748” and “751” landraces) or at 300 mM NaCl, where only “747” expressed the highest content. These findings can be extrapolated into efforts to develop more salt-tolerant squash landraces and exhaust the possibilities of using saline water or soils under changing climate conditions

Distributions and Conservation Status of Carrot Wild Relatives in Tunisia: A Case Study in the Western Mediterranean Basin

Crop wild relatives, the wild progenitors and closely related cousins of cultivated plant species, are sources of valuable genetic resources for crop improvement. Persisting gaps in knowledge of taxonomy, distributions, and characterization for traits of interest constrain their expanded use in plant breeding and likewise negatively affect ex situ (in genebanks) and in situ (in natural habitats) conservation planning. We compile the state of knowledge on the taxonomy and distributions of the wild relatives of carrot (genus Daucus L.) natively occurring within Tunisia—a hotspot of diversity of the genus, containing 13 taxa (27% of species worldwide). We use ecogeographic information to characterize their potential adaptations to abiotic stresses of interest in crop breeding and assess their ex situ and in situ conservation status. We find substantial ecogeographic variation both across taxa and between populations within taxa, with regard to adaptation to high temperatures, low precipitation, and other traits of potential interest. We categorize three of the taxa high priority for further conservation both ex situ and in situ, five medium priority, and five low priority, with none currently considered sufficiently conserved. Geographic hotspots for species diversity, especially in the northern coastal areas, represent particularly high value regions for efficient further collecting for ex situ conservation and for in situ protection in Tunisia

Identification of novel pathogenic MSH2 mutation and new DNA repair genes variants: investigation of a Tunisian Lynch syndrome family with discordant twins

International audienceBackground: Lynch syndrome (LS) is a highly penetrant inherited cancer predisposition syndrome, characterized by autosomal dominant inheritance and germline mutations in DNA mismatch repair genes. Despite several genetic variations that have been identified in various populations, the penetrance is highly variable and the reasons for this have not been fully elucidated. This study investigates whether, besides pathogenic mutations, environment and low penetrance genetic risk factors may result in phenotype modification in a Tunisian LS family. Patients and methods: A Tunisian family with strong colorectal cancer (CRC) history that fulfill the Amsterdam I criteria for the diagnosis of Lynch syndrome was proposed for oncogenetic counseling. The index case was a man, diagnosed at the age of 33 years with CRC. He has a monozygotic twin diagnosed at the age of 35 years with crohn disease. Forty-seven years-old was the onset age of his paternal uncle withCRC. An immunohistochemical (IHC) labeling for the four proteins (MLH1, MSH2, MSH6 and PMS2) of the MisMatchRepair (MMR) system was performed for the index case. A targeted sequencing of MSH2, MLH1 and a panel of 85 DNA repair genes was performed for the index case and for his unaffected father. Results: The IHC results showed a loss of MSH2 but not MLH1, MSH6 and PMS2 proteins expression. Genomic DNA screening, by targeted DNA repair genes sequencing, revealed an MSH2 pathogenic mutation (c.1552C>T; p.Q518X), confirmed by Sanger sequencing. This mutation was suspected to be a causal mutation associated to the loss of MSH2 expression and it was found in first and second degree relatives. The index case has smoking and alcohol consumption habits. Moreover, he harbors extensive genetic variations in other DNA-repair genes not shared with his unaffected father. Conclusion: In our investigated Tunisian family, we confirmed the LS by IHC, molecular and in silico investigations. We identified a novel pathogenic mutation described for the first time in Tunisia. These results come enriching the previously reported pathogenic mutations in LS families. Our study brings new arguments to the interpretation of MMR expression pattern and highlights new risk modifiers genes eventually implicated in CRC. Twins discordance reported in this work underscore that disease penetrance could be influenced by both genetic background and environmental factors