Characterizations of plant genetic resources based on molecular markers have been increased in the last years. Studies using a broad range of markers applied on hundreds of plant species are the theoretical basis for inferring genetic diversity to propose both breeding and conservation strategies. Despite increased importance of molecular characterization in plant genetic resources, there is scarce information about analysis of this type of data. To fill this gap of information, this review discuss the rationale behind analyses achieved to study genetic relationship among accessions (within and between groups) and to identify accession, and also discuss the adequacy of some analyses and/or parameters for specific purposes. Genetic diversity within groups may be either quantified for the whole group (parameters to choose will depend on type of marker), or quantified and visualized for the relationships among individuals. Quantification parameters will be chosen depending on type of marker, reproduction mode and relatedness of individuals. Visualization is achieved by hierarchical and non-hierarchical methods. Genetic diversity between groups should be quantified either by analysis of molecular variance, or Nei’s parameters, or Wright’s F-statistics. Efficiency of accession identification can be evaluated by maximal probability of identical match by chance and number of resolved genotypes.

Data analysis for molecular characterization of plant genetic resources

There are limited numbers of pistachio (Pistacia vera L.) cultivars in the world and their phenotypic appearance and productivity are variable. Understanding such variation would facilitate their use in cultivar breeding programs. Therefore, in this study, 69 pistachio cultivars and genotypes originating from seven countries were characterized by randomly amplifi ed polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR), and amplifi ed fragment-length polymorphism (AFLP) markers. The results showed that all three marker systems were able to reveal variability between pistachio cultivars and genotypes. The correlation coeffi cients for genetic distances were statistically signifi cant among all three molecular marker types. The correlation between RAPD and AFLP data was the highest (r = 0.73) and the value between RAPD and ISSR data was the lowest (r = 0.58). AFLP proved to be the best technique among them. ISSR and AFLP assays were reliable and produced reproducible bands. ISSR was preferred over RAPD, especially when fi nancial investment and technical knowledge are limited. The constructed unweighted pair group method with arithmetic averages (UPGMA) dendrogram obtained from combined data separated the genotypes into two main clusters: one cluster ("Iranian") included genotypes originating from Iran and the second cluster ("Mediterranean") contained most other genotypes. The "Mediterranean" cluster further divided into three subclusters: one ("Siirt") consisted of the cultivars Siirt and Hacireso with a few other selections; the second subcluster ("Turkish") included Turkish cultivars; and the third subcluster contained Syrian, Italian, and the remaining cultivars. The closeness of the clusters was "Iranian" - "Siirt" - "Turkish"/"Syrian." These fi ndings reveal a new understanding in the diffusion of pistachio cultivation from its center of origin, the Iranian-Caspian region, via southeastern Turkey to Syria, the Mediterranean region of Europe, and northern Africa.

/pdf/detecting-dna-polymorphism-and-genetic-diversity-in-a-wide-54h343cre2.pdf

Detecting DNA Polymorphism and Genetic Diversity in a Wide Pistachio Germplasm: Comparison of AFLP, ISSR, and RAPD Markers

Water-phase extract of bamboo shavings (WEBS), by supercritical carbon dioxide extraction, was evaluated for its antimicrobial action against the range of food borne and food spoilage pathogens using agar disc diffusion assay in nutrient agar and Czapek Dox Agar media. The WEBS exhibited antimicrobial activity against Staphylococcus aureus, Bacillus subtilis, Escherichia coli, Aspergillus niger, Penicilliun citrinum and Saccharomyces cerevisiae with a concentration-dependent relationship. The minimum inhibitory  concentrations (MICs) of the WEBS against the tested bacterial strains were found in the range of 4.9 - 32 mg/ml using the two-fold dilution method. Different heat treatment conditions have no significant influence on the antibacterial activity. Emodin was taken as the standard sample to test for the content of total  anthraquinone compound and preliminarily verify its antibacterial mechanism, so as to lay a theoretical foundation for development of its natural preservatives. Key words: Water-phase extract of bamboo shavings (WEBS), antimicrobial activity, natural preservative.

/pdf/antibacterial-activity-of-water-phase-extracts-from-bamboo-1awslf3bzx.pdf

Antibacterial activity of water-phase extracts from bamboo shavings against food spoilage microorganisms

The systematic position and intrageneric relationships of the economically important Pistacia species (Anacardiaceae) are controversial. The phylogeny of Pistacia was assessed using five data sets: sequences of nuclear ribosomal ITS, the third intron of the nuclear nitrate reductase gene (NIA-i3), and the plastid ndhF, trnL-F and trnC-trnD. Significant discordance was detected among ITS, NIA-i3, and the combined plastid DNA data sets. ITS, NIA-i3, and the combined plastid data sets were analyzed separately using Bayesian and parsimony methods. Both the ITS and the NIA-i3 data sets resolved the relationships among Pistacia species well; however, these two data sets had significant discordance. The ITS phylogeny best reflects the evolutionary relationships among Pistacia species. Lineage sorting of the NIA-i3 alleles may explain the conflicts between the NIA-i3 and the ITS data sets. The combined analysis of three plastid DNA data sets resolved Pistacia species into three major clades, within which only a few subclades were supported. Pistacia was shown to be monophyletic in all three analyses. The previous intrageneric classification was largely inconsistent with the molecular data. Some Pistacia species appear not to be genealogical species, and evidence for reticulate evolution is presented. Pistacia saportae was shown to be a hybrid with P. lentiscus (maternal) and P terebinthus (paternal) as the parental taxa.

Phylogenetics and reticulate evolution in Pistacia (Anacardiaceae)

Amplified fragment length polymorphism fingerprinting was applied to survey the genetic diversity of primitive South American Gossypium barbadense cotton for establishing a possible link to its pre-Columbian expansion. New germplasm was collected along coastal Peru and over an Andean transect in areas where most of the archaeological evidence relating to cotton domestication has been recorded. Gene bank material of three diploid (G. raimondii, G. arboreum, and G. herbaceum) and four allotetraploid cotton species (G. hirsutum, G. mustelinum, G. tomentosum and additional G. barbadense) was added for inter- and intra-specific comparison. Eight primer combinations yielded 340 polymorphic bands among the 131 accessions. The obtained neighbor joining and unweighted pair-group method with arithmetic means are in full agreement with the known cytogenetics of the tetraploid cottons and their diploid genome donors. The four tetraploid species are clearly distinct based on taxonomic classification. The genetic diversity within G. barbadense reveals geographic patterns. The locally maintained cottons from coastal Peru display a distinct genetic diversity that mirrors their primitive agro-morphological traits. Accessions from the northernmost coast of Peru and from southwestern (SW) Ecuador cluster basal to the east-of-Andes accessions. The remaining accessions from Bolivia, Brazil, Columbia, Venezuela, and the Caribbean and Pacific islands cluster with the east-of-Andes accessions. Northwestern Peru/SW Ecuador (the area flanking the Guayaquil gulf) appears to be the center of the primitive domesticated G. barbadense cotton from where it spread over the Andes and expanded into its pre-Columbian range.

/pdf/genetic-diversity-and-geographic-pattern-in-early-south-1zofnackau.pdf

Genetic diversity and geographic pattern in early South American cotton domestication

Summary The genus Pistacia (Anacardiaceae) includes 11 species divided into four sections, according to leaf characters and nut morphology. Recently two monophyletic groups have been proposed by using cpDNA, Lentiscus and Terebinthus, containing evergreen and deciduous species, respectively. In the present work molecular markers, derived from two different methods, RAPD and AFLP, are used to study the relationships of native and introduced Pistacia species present in Greece. According to the cophenetic correlation coefficients best results for both methods were obtained by using the Jaccard algorithm and the UPGMA clustering method. However, phenograms were constructed using the NJ method (rcs =0.987 for RAPDs and rcs =0.982 for AFLP), since it is less sensitive against varying mutation rates. Correlation among the genetic similarity (GS) matrices for the two methods was high (r = 0.941). The AFLP and RAPD phenograms were comparable with minor clustering differences. According to our results, two main branches are obtained, one containing the evergreen species P. lentiscus and the resin producing P. lentiscus cv. Chia (cultivated only in the island of Chios), and the other branch containing the deciduous species P. terebinthus, P. palaestina and P. vera. P. chinensis was clustered either with the evergreen species (RAPD data) or with the deciduous species (AFLP data). P. palaestina is clustered to P. terebinthus and can be considered as a subspecies of P. terebinthus, since its GS values are close or smaller than GS values of entries within species (P. vera). The four female cultivars were found to have a narrow genetic basis, probably related to cultivar ‘Nazareth’ with Syrian origin.

Genetic relationships among species and cultivars of Pistacia using RAPDs and AFLPs

Species and genome relationships among 11 diploid (A and C genomes), five tetraploid (AB and AC genomes) and two hexaploid (ACD genome) Avena taxa were investigated using amplified fragment length polymorphisms (AFLPs) and random amplified polymorphic DNA (RAPD) markers. The two primer pairs used for the AFLP reactions produced a total of 354 polymorphic bands, while 187 reproducible bands were generated using ten RAPD primers. Genetic similarities amongst the entries were estimated using the Jaccard and Dice algorithms, and cluster analyses were performed using UPGMA and neighbor joining methods. Principle coordinate analysis was also applied. The highest cophenetic correlation coefficient was obtained for the Jaccard algorithm and UPGMA clustering method (r=0.99 for AFLP and
r=0.94 for RAPD). No major clustering differences were present between phenograms produced with AFLPs and RAPDs. Furthermore, data produced with AFLPs and RAPDs were highly correlated (r=0.92), indicating the reliability of our results. All A genome diploid taxa are clustered together according to their karyotype. The AB genome tetraploids were found to form a subcluster within the As genome diploids (AFLPs), indicating their near-autoploid origin. The AC genome tetraploids are clustered to the ACD genome hexaploids. Finally, the C genome diploids form an outer branch, indicating the major genomic divergence between the A and C genomes in Avena.

Genome and species relationships in genus Avena based on RAPD and AFLP molecular markers

Phylogenetic relationships in Origanum spp. based on rDNA sequences and intra-genetic variation of Greek O. vulgare subsp. hirtum revealed by RAPD

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Genetic relationships among species and cultivars of Pistacia using RAPDs and AFLPs

Genome and species relationships in genus Avena based on RAPD and AFLP molecular markers

Phylogenetic relationships in Origanum spp. based on rDNA sequences and intra-genetic variation of Greek O. vulgare subsp. hirtum revealed by RAPD