Genetic relationships among cherry species with transferability of simple sequence repeat loci.

Sweet and sour cherries are two economically important species in the world. The capability to distinguish among cherry genotypes in breeding, cultivation and germplasm collection is extremely important for scientific as well as economic reasons. In the present research, sixteen simple sequences repeat (SSR) loci were used to estimate the relationships among sweet, sour, duke and wild cherries. All of the SSR markers showed high transferability across the studied species that allowed us to study genetic diversity in them. Totally 96 alleles were generated with SSR loci, of which 93 were found polymorphic with 97.57 % polymorphism. Values of genetic similarity between genotypes varied from 0.16 to 0.97 which indicated high level of genetic diversity. On the basis of their genetic similarities, SSR analysis allowed to group the genotypes into three main clusters according to their species. These results have an important implication for cherry germplasm characterization, improvement, and conservation.

Comprehensive genetic discrimination of Leonurus cardiaca populations by AFLP, ISSR, RAPD and IRAP molecular markers.

Leonurus cardiaca is well known for its medicinal importance. In this investigation, genotypic characterization of this species from six eco-geographical regions of Iran was evaluated by four molecular techniques (AFLP, RAPD, ISSR and IRAP). A total of 899 polymorphic fragments were detected by used molecular markers (AFLP = 356, RAPD = 325, ISSR = 113 and IRAP = 105) with an overall average polymorphism of 81.24%. Genetic variation calculated using Shannon's Information index (I) and Nei's gene diversity index (H) showed high genetic diversity in studied germplasm. Also, analysis of molecular variance showed high genetic variation among (55%) and within populations (45%). UPGMA dendrogram constructed from combined data of molecular markers distinguished studied populations in accordance with the results obtained by each marker which all individuals were clearly differentiated into two major clusters. The correlation coefficients were statistically significant for all marker systems with the highest correlation between similarity matrixes of RAPD and ISSR markers (r = 0.82). The present results have an important implication for L. cardiaca germplasm characterization, improvement, and conservation. Furthermore, the characterized individuals exhibited a great deal of molecular variation and they seem to have a rich gene pool for breeding programs.

Assessment of genetic and chemical variability in Thymus caramanicus.

Thymus caramanicus is an endemic species grown in Iran with interesting pharmacological and biological properties. In the present work, essential oil compositions and inter-simple sequences repeat (ISSR) markers were used to estimate the relationships among and within seven populations of T. caramanicus, belonging to three provinces in Iran. The studied individuals were distinguished on the basis of ISSR markers and constituents of essential oil. A total of 127 band positions were produced by 12 ISSR primers, of which 105 were found polymorphic with 82.68% polymorphism. Genetic similarity values among individuals ranged between 0.15 and 0.82 which was indicative of a high level of genetic variation. On the basis of their genetic similarities, ISSR analysis allowed to group the samples into two main clusters. One of these included populations originated from Kerman and Isfahan provinces, and the other cluster consists of populations from Semnan province. Chemical compounds of essential oils were found variable in the various individuals and all samples were principally composed of phenolic constituents (carvacrol and/or thymol). As a consequence, the plants were classified into two major chemotypes including carvacrol and thymol/carvacrol. A relationship between genetic and chemical variability and geographic distribution has been observed in studied populations of T. caramanicus.

Evaluation of genetic variability, rust resistance and marker-detection in cultivated Artemisia dracunculus from Iran.

Artemisia dracunculus L. (tarragon), a small shrubby perennial herb, is cultivated for the use of its aromatic leaves in seasoning, salads, etc., and in the preparation of tarragon vinegar. In the present work, genetic analysis of 29 cultivated individuals of this species was carried out employing 12 ISSR and 11 SRAP markers. A total of 59 (71.64%) and 79 (83.14%) polymorphic bands were detected by 12 ISSR primers and 11 SRAP primer pairs, respectively. High similarity for patterns of genetic diversity and clustering of individuals was observed using two ISSR and SRAP marker systems and combined data. Range of genetic similarity by ISSR markers was 0.14 to 0.95, by SRAP markers was 0.14 to 0.90, while this range varied from 0.18 to 0.91 by ISSR+SRAP. In the UPGMA cluster analysis (ISSR, SRAP and ISSR+SRAP), we always found two clusters, the first cluster included 22 individuals and the second contained seven individuals. The results demonstrated that both ISSR and SRAP methods were suitable for discriminating among the studied individuals and the SRAP markers were more efficient and preferable. The results of multiple regression analysis revealed statistically significant association between rust resistance and some molecular markers that they can provide clues for identification of the individuals with higher rust resistance. The molecular marker-based study of genetic diversity suggests that the germplasm studied representing the kind of variability would be a valuable genetic resource for future breeding. In addition, in situ conservation measures are recommended to preserve the valuable A. dracunculus genetic resources as the most effective and economical approach.

Population structure and genotypic variation of Crataegus pontica inferred by molecular markers.

Information about the natural patterns of genetic variability and their evolutionary bases are of fundamental practical importance for sustainable forest management and conservation. In the present study, the genetic diversity of 164 individuals from fourteen natural populations of Crataegus pontica K.Koch was assessed for the first time using three genome-based molecular techniques; inter-retrotransposon amplified polymorphism (IRAP); inter-simple sequence repeats (ISSR) and start codon targeted (SCoT) polymorphism. IRAP, ISSR and SCoT analyses yielded 126, 254 and 199 scorable amplified bands, respectively, of which 90.48, 93.37 and 83.78% were polymorphic. ISSR revealed efficiency over IRAP and SCoT due to high effective multiplex ratio, marker index and resolving power. The dendrograms based on the markers used and combined data divided individuals into three major clusters. The correlation between the coefficient matrices for the IRAP, ISSR and SCoT data was significant. A higher level of genetic variation was observed within populations than among populations based on the markers used. The lower divergence levels depicted among the studied populations could be seen as evidence of gene flow. The promotion of gene exchange will be very beneficial to conserve and utilize the enormous genetic variability.

Population genetic structure and trait associations in forest savory using molecular, morphological and phytochemical markers.

In this investigation, morphological, phytochemical and ISSR markers were used to estimate the relationships among and within seven populations of white savory (Satureja mutica), belonging to four provinces in Iran. The individuals were phenotypically diverse, which stamen length, corolla length, corolla diameter, calyx length, bract length, inflorescence length, calyx length and bracteole width were characteristics with the highest variation. Leaf dimensions were in significant correlation with flower and inflorescence characteristics. Chemical compounds of essential oils were found variable in various individuals and all samples were principally composed of phenolic constituents (carvacrol and/or thymol). As a consequence, the plants were classified into two major chemotypes including carvacrol and thymol. A total of 197 band positions were produced by 14 ISSR primers, of which 176 were found polymorphic with 88.91% polymorphism. ISSR genetic similarity values among individuals ranged between 0.45 and 0.94 which was indicative of a high level of genetic variation. Multiple regression analysis (MRA) revealed that phytochemical compositions as dependent variable, showed statistically significant correlation and in association with leaf and flower traits as independent variable, indicating a main role of leaf and flower on production of these compounds. Also, several ISSR fragments were found associated with some morphological traits and phytochemical compositions. The high diversity within and among populations of S. mutica according to different data systems could provide useful information for conservation and selection of cross-parents in breeding programs.

Genetic variability and structure of Quercus brantii assessed by ISSR, IRAP and SCoT markers.

Persian oak (Quercus brantii Lindl.) is one of the most important woody species of the Zagros forests in Iran. Three molecular marker techniques: start codon targeted (SCoT), inter-simple sequence repeat (ISSR) and inter-retrotransposon amplified polymorphism (IRAP) markers were compared for fingerprinting of 125 individuals of this species collected from different geographical locations of north-west of Iran. A total of 233 bands were amplified by 18 ISSR primers, of which 224 (96.10%) were polymorphic, and 126 polymorphic bands (97.65%) were observed in 129 bands amplified by 10 IRAP primers. Besides, 118 bands were observed for all 10 SCoT primers, of which 113 were polymorphic (95.71%). Average polymorphism information content (PIC) for ISSR, IRAP and SCoT markers was 0.30, 0.32 and 0.38, respectively, and this revealed that SCoT markers were more informative than IRAP and ISSR for the assessment of diversity among individuals. Based on the three different molecular types, cluster analysis revealed that 125 individuals taken for the analysis can be divided into three distinct clusters. The Jaccard's genetic similarity based on the combined data ranged from 0.23 to 0.76. These results suggest that efficiency of SCoT, IRAP and ISSR markers was relatively the same in fingerprinting of individuals. All molecular marker types revealed a low genetic differentiation among populations, indicating the possibility of gene flow between the studied populations. These results have an important implication for Persian oak (Q. brantii) germplasm characterization, improvement, and conservation.