Molecular phylogeny of Lathyrus species: insights from sequence-related amplified polymorphism markers.

Sequence-related amplified polymorphism (SRAP) markers were used to evaluate the intra- and interspecific variation among 40 Lathyrus genotypes (four species) (Fabaceae). Ten SRAP primer combinations resulted in a total of 94 bands, and they exhibited high interspecific variability. The genetic differentiation among Lathyrus, estimated using AMOVA, was highly significant. The results indicated that 58% of the total genetic variation existed among species, and 42% of the differentiation was within species. This was explained by the high level of genome conservation of these species as well as the recent and slow evolution of this genus. These results were confirmed by the topology of the neighbor-joining cladogram and the results of the principal coordinate analysis. Our data support previous results based on seed protein diversity. These results make SRAP markers choice markers for the study of functional polymorphism that is directly related to the transcriptomic data. The SRAP markers used in this study provide an accurate picture of the population structure within Lathyrus germplasm, which is critically important information for the design of genetic diversity and structure analyses. Moreover, further extensive studies are necessary to fully examine other Lathyrus species and tests that adopt the SRAP technique to enrich the Lathyrus library for next-generation sequencing, thus providing a potent protocol for the study of polymorphism.

Pheno-morphological variation, genetic diversity and population structure of Tunisian Echinus Medic (Medicago ciliaris L.).

Medicago ciliaris L., considered as a valuable genetic resource, is a good candidate for the improvement of marginal or degraded lands with low fertility or high salinity. In this study, the pheno-morphological and genetic diversity were investigated in 14 Tunisian populations of M. ciliaris for the first time. Fourteen morphological traits showed significant differentiation between populations and high levels of diversity. Two amplified fragment length polymorphism primer combinations (E-AGC/M-CAA; E-AAG/M-CTG) were analyzed using an automated capillary electrophoresis system. A total of 528 loci were generated, of which 54% were polymorphic. Allelic polymorphism ranged from 0.02 to 0.5. Significant variation between populations was found for gene diversity, mean number of alleles per locus and Shannon index for which mean values were 0.17, 0.26, and 1.57, respectively. Analysis of molecular variance revealed a high rate of genetic variation within populations. Principal component analysis and genotypic clustering discriminated M. ciliaris populations according to their geographical origin. M. ciliaris clustered into three main groups. The first group was associated with high inland and cold areas, the second was defined by low areas with mild winters while the third described low coastal areas. Similarity of morphological and molecular results indicated that either markers could be used for the study of genetic diversity in this species.

Genetic diversity analysis in Tunisian perennial ryegrass germplasm as estimated by RAPD, ISSR, and morpho-agronomical markers.

Tunisia is rich in diverse forage and pasture species including perennial ryegrass. In order to enhance forage production and improve agronomic performance of this local germplasm, a molecular analysis was undertaken. Random amplified polymorphic DNA (RAPD), inter simple sequence repeats (ISSR) and morpho-agronomical traits markers were used for genetic diversity estimation of ryegrass germplasm after screening 20 spontaneous accessions, including a local and an introduced cultivars. Same mean polymorphism information content values were obtained (0.37) for RAPD and ISSR suggesting that both marker systems were equally effective in determining polymorphisms. The average pairwise genetic distance values were 0.57 (morpho-agronomical traits), 0.68 (RAPD), and 0.51 (ISSR) markers data sets. A higher Shannon diversity index was obtained with ISSR marker (0.57) than for RAPD (0.54) and morpho-agronomical traits (0.36). The Mantel test based on genetic distances of a combination of molecular markers and morpho-agronomical data exhibited a significant correlation between RAPD and ISSR data, suggesting that the use of a combination of molecular techniques was a highly efficient method of estimating genetic variability levels among Tunisian ryegrass germplasm. In summary, results showed that combining molecular and morpho-agronomical markers is an efficient way in assessing the genetic variability among Tunisian ryegrass genotypes. In addition, the combined analysis provided an exhaustive coverage for the analyzed diversity and helped us to identify suitable accessions showed by Beja and Jendouba localities, which present large similarities with cultivated forms and can be exploited for designing breeding programmes, conservation of germplasm and management of ryegrass genetic resources.

Variation and genetic structure of Tunisian Festuca arundinacea populations based on inter-simple sequence repeat pattern.

Tunisian tall fescue (Festuca arundinacea Schreb.) is an important grass for forages or soil conservation, particularly in marginal sites. Inter-simple sequence repeats were used to estimate genetic diversity within and among 8 natural populations and 1 cultivar from Northern Tunisia. A total of 181 polymorphic inter-simple sequence repeat markers were generated using 7 primers. Shannon's index and analysis of molecular variance evidenced a high molecular polymorphism at intra-specific levels for wild and cultivated accessions, showing that Tunisian tall fescue germplasm constitutes an important pool of diversity. Within-population variation accounted for 39.42% of the total variation, but no regional differentiation was discernible to designate close relationships between regions. Most of the variation (GST = 67%) occurred between populations, rather than within populations. The ɸST (0.60) revealed high population structuring. Additionally, the population structure was independent of the geographic origin and was not affected by environmental factors. The unweighted pair group method with arithmetic mean tree based on genetic similarity and principal coordinate analysis based on coefficient similarity illustrated that continental populations from the proximate localities of Beja and Jendouba were genetically closely related, while the wild Skalba population from the littoral Tunisian locality was the most diverse from the others. Moreover, great molecular similarity of the spontaneous population Sedjnane originated from the mountain areas was revealed with the local cultivar Mornag. The observed genetic diversity can be used to implement conservation strategies and breeding programs for improving forage crops in Tunisia.

Evolution of rbcL among Lathyrus and Kupicha's classification.

Phylogenetic relationships in the Lathyrus genus were examined using cpDNA data, particularly data attributed to the "barcode" rbcL gene to construct a possible evolutionary scenario. Plant barcoding can be used to differentiate between species within a genus and to conserve DNA within the same species. We assessed the phylogeny of 29 species of Lathyrus using maximum parsimony, maximum likelihood and unweighted pair-group method and arithmetic mean. The classifications did not agree with current morphological and basic Lathyrus classification. Lathyrus belinensis is a new species that was not described by Kupicha; according to rbcL analysis, the species belongs in the Lathyrus genus. Additionally, the genus Lathyrus has undergone a rapid population expansion as indicated by neutral selection indices.

Sequence divergence of microsatellites for phylogeographic assessment of Moroccan Medicago species.

Six Medicago species were investigated to characterize and valorize plant genetic resources of pastoral interest in Morocco. Samples were obtained from the core collection of the South Australian Research and Development Institute (SARDI). The transferability of single sequence repeat markers of Medicago truncatula was successful with 97.6% efficiency across the five species. A total of 283 alleles and 243 genotypes were generated using seven SSR markers, confirming the high level of polymorphism that is characteristic of the Medicago genus, despite a heterozygosity deficit (HO = 0.378; HE = 0.705). In addition, a high level of gene flow was revealed among the species analyzed with significant intra-specific variation. The unweighted pair group method with arithmetic mean dendrogram generated by the dissimilarity matrix revealed that M. polymorpha and M. orbicularis are closely related, and that M. truncatula is likely the ancestral species. The Pearson correlation index revealed no significant correlations between the geographic distribution of the Moroccan species and genetic similarities, indicating local adaptation of these species to different ecological environments independent of their topographical proximities. The substantial genetic variation observed was likely due to the predominance of selfing species, the relative proximity of prospected sites, human impacts, and the nature of the SARDI core collections, which are selected for their high genetic diversity. The results of this first report on Moroccan Medicago species will be of great interest for establishing strategies aiming at reasonable management and selection programs for local and Mediterranean germplasm in the face of increasing environmental change.

Relative efficiency of morphological characters and molecular markers in the establishment of an apricot core collection.

In order to optimize the management of genetic resources, in most cases a representative sample of the germplasm collections needs to be developed. The establishment of a core collection is thus of major importance either to minimize the cost associated with the management of the associated germplasm or to apply analysis onto representative bases. In order to select a representative core collection among the Tunisian apricot germplasm of 110 accessions large, the Maximization strategy algorithm was used. This algorithm was shown to be the most convenient when using both morphological traits and molecular markers. Three core collections based on morphological characters, molecular markers or the combined data were compared. Our data indicate that both the molecular and the morphological markers have to be considered to obtain a core collection that represents the global diversity of the 110 accessions. Using this method, a subset of 34 selected accessions was found to represent accurately the 110 accessions present in the whole collection (75 to 100% for the morphological characters and 97% of the molecular markers). These results show that the combination of molecular and morphological markers is an efficient way to characterize the apricot core collection and provides an exhaustive coverage for the analyzed diversity on morphological and genetic bases.

Amplified fragment length polymorphism (AFLP) is useful for finding markers associated with QTL for architectural trait in Hedysarum coronarium L.

Amplified fragment length polymorphism (AFLP) has been proposed as a valuable tool for finding molecular markers linked to QTL controlling architectural trait. Segregation of polymorphic AFLP fragments was followed in F2 offsprings Hedysarum coronarium derived from two native wild accesions crossing: Jebel Zit x El Haouaria, which had previously characterised by morphological and AFLP markers. A comparison of profiles from the morphologically contrasted parental individuals and F2 offspring has been assessed using five AFLP primer combinations. These generated 178 bands revealed by silver-stained denaturing polyacrylamide gels, of which 150 were polymorphic. Several AFLP markers appeared to be implied in the orthotropic form that can assist the selection and improve Hedysarum forage crop.