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Abstract Evolutionary studies of plant groups which are distributed in vast geographical regions and face different ecological and environmental conditions are important as they through light on different mechanisms of local adaptation and species divergence through time. The genus Avicennia is one of these plant groups which inspire of few species show interesting geographical distribution with some degree of species-specific geographical isolations. In general, very limited molecular phylogenetic investigations have been carried out in the genus Avicennia, and therefore we conducted the present study with the following aims: 1. To estimate the species divergence time based on different nuclear and chloroplast DNA regions, separately. This will illustrate how different genetic regions evolved in this genus, 2. To identify the sequences with potential adaptive value against geographical variable by latent factor mixed models (LFMM) analysis, 3. To illustrate the phylogenetic signal of these DNA regions and their role in speciation within the genus and, 4. To introducing a new computational strategy for estimating adaptive time for the sequences. The results showed that different genetic regions may produce different species divergent time, both the nuclear ribosomal internal transcribed spacer (ITS) region and chloroplast DNA sequences, contained potentially adaptive single nucleotide polymorphisms (SNPs).We could present a suggestive time for these adaptive sequences for the first time. In conclusion both local adaptation and independent mutations seem to have played role in Avicennia speciation and evolution.

Abstract Conservation and management of medicinally important plants are among the necessary tasks all over the world. The genus Dracocephalum (Lamiaceae) contains about 186 perennials, or annual herb species that have been used for their medicinal values in different parts of the world as an antihyperlipidemic, analgesic, antimicrobial, antioxidant, as well as anticancer medicine. Producing detailed data on the genetic structure of these species and their response against climate change and human landscape manipulation can be very important for conservation purposes. Therefore, the present study was performed on six geographical populations of two species in the Dracocephalum genus, namely, Dracocephalum kotschyi, and Dracocephalum oligadenium, as well as their inter-specific hybrid population. We carried out, population genetic study, landscape genetics, species modeling, and genetic cline analyses on these plants. We present here, new findings on the genetic structure of these populations, and provide data on both geographical and genetic clines, as well as morphological clines. We also identified genetic loci that are potentially adaptive to the geographical spatial features and genocide conditions. Different species distribution modeling (SDM) methods, used in this work revealed that bioclimatic variables related to the temperature and moisture, play an important role in Dracocephalum population’s geographical distribution within IRAN and that due to the presence of some potentially adaptive genetic loci in the studied plants, they can survive well enough by the year 2050 and under climate change. The findings can be used for the protection of these medicinally important plant.

Abstract Background Male infertility is rapidly growing, and single nucleotide polymorphism (SNP) association studies are of critical importance. Tumor suppressor candidate 1 (TUSC1) gene is associated with azoospermia. We investigated association between rs1462218557 in TUSC1 with azoospermia. Methods We performed tetra-ARMS PCR analysis and sequencing on healthy and infertile individuals. Results Tetra-ARMS PCR results revealed that the allele frequency of the SNP for T alleles was 0.66, while the same value for C allele was 0.36. It was different from the previous reports of the other countries because they reported the allele C as the frequent allele and it was considered an ancestral allele. The genotype frequencies obtained showed that 67% of the samples were heterozygotes (T/C), while 33% were homozygotes (TT). SNP-STAT analysis showed a significant association (p = 0.04) with the studied SNP and azoospermia in Iranian samples. Conclusions The present study reports a new allele frequency of rs1462218557 in TUSC1 gene, which may be associated with azoospermia in Iranian people. Moreover, no association was observed between neighboring sequences/SNPs with male infertility.

Abstract Mangrove forests grow in coastal areas, lagoons, estuaries, and deltas and form the main vegetation in tidal and saline wetlands. Due to the mankind activities and also changes in climate, these forests face degradations and probably extinction in some areas. Avicennia marina is one of the most distributed mangrove species throughout the world. The populations of A. marina occur in a limited region in southern parts of Iran. Very few genetic and spatial analyses are available on these plants from our country. Therefore, the present study was planned to provide detailed information on Avicennia marina populations with regard to genetic diversity, gene flow versus genetic isolation, effects of spatial variables on connectivity and structuring the genetic content of trees populations and also identifying adaptive genetic regions in respond too spatial variables. We used SCoT molecular markers for genetic analyses and utilized different computational approaches for population genetics and landscapes analyses. The results of present study showed a low to moderate genetic diversity in the studied populations and presence of significant Fst values among them. Genetic fragmentation was also observed within each province studied. A limited gene flow was noticed among neighboring populations within a particular province. One population was almost completely isolated from the gene flow with other populations and had peculiar genetic content.Spatial PCA analysis revealed both significant global and local genetic structuring in the studied populations. Spatial variables like humidity, longitude and altitude were the most important spatial features affecting genetic structure in these populations.

The genus Ulva L. (Sea lettuce), one of the most valuable marine macroalgae, is found in shallow coastal areas and in brackish and fresh water around the world. Ulva species have nutritional and medicinal values in addition to other applications, and contain various compounds such as lipids, proteins and carotenoids. These species have high phenotypic plasticity and varied in response to different environmental conditions. In this study, 38 populations of 10 species of Ulva from the coastal areas of the Persian Gulf and Oman Sea, from different areas of Bushehr, Hormozgan and Sistan and Baluchestan provinces, were studied and identified on the basis of morphological and anatomical traits. Different populations showed variations in characteristics such as height, shape and color of thallus, number of pyrenoids and cell dimensions. Metabolites such as total protein, total oil, chlorophyll a, b and carotenoids contents were measured and compared among the different populations. The results should that the percentage of protein was highest in U. prolifera of Shif Island from Bushehr province as compared with the Ulva species studied, with about 26.5% of dry weight, and the percentage of total oil was lowest in U. flexuosa of Hakhamanesh region from Hormozgan province as compared with the species studied, with about 4.8% of dry weight. These results show that different environmental conditions affect the morphological and anatomical structure of species and the content of their metabolites. Due to the high-protein and low-calorie content of the Ulva genus and the importance of finding new and sustainable resources for food and pharmaceutical industries, the species of this genus have valuable potentials.

Abstract Medicinal plants are an important source for treatment of diseases in many countries. Today, controlling the quality of the products of medicinal plants is an important task. Customer health may be in danger due to the fraud and misconduct by the sales associates in the sales centers. Melissa officinalis L. (Lamiaceae) is an important medicinal plant used for treatment of several diseases. In Iran, the species of Dracocephalum, Hymencrater, Nepeta and Stachys are mistakenly sold under the name of Badranjboye that have different pharmaceutical properties. For avoiding this mistake, this investigation was performed with the following aims: 1) Checking for the cheating and identifying the Badranjboye in the Iran’s market of medicinal plants, 2) Providing the molecular barcode for the medicinal species of Melissa. For this purpose, Market-sold plant samples (leaves) and original reference plant species were compared by morphology, odor as well as Internal transcribed spacer (ITS) and chloroplast DNA ((psbA–trnH) and (trnL–trnF)) sequences. Various molecular analyses, such as sequencing, determination of genetic distance, and construction of phylogenetic tree were performed. These reports have shown that internal transcribed spacer (ITS) and chloroplast DNA (psbA–trnH) sequences are an efficient molecular marker to produce barcode gap and differentiating Melissa officinalis from other species.

Este estudio presenta algunas observaciones detalladas sobre el comportamiento meiótico y un estudio palinológico comparativo de algunas especies seleccionadas de Salvia L. sect. Aethiopis. Se usa la prueba ANOVA para comparar la frecuencia, la distribución y las asociaciones cromosómicas de los quiasmas, lo que revela una diferencia significativa en todas las características meióticas entre las especies S. hypoleuca, S. limbata, S. reuteriana, S. spinosa y S. xanthocheila. Además, en estas especies se producen algunas anomalías meióticas, como la adherencia de los cromosomas, los cromosomas rezagados, así como la formación frecuente de células tripolares, multipolares y citomixis. Se usa microscopía de luz (LM) y microscopía electrónica de barrido (SEM) para analizar el polen. Algunas características micromorfológicas como la forma del polen, el tamaño, la longitud del eje polar, la longitud del eje ecuatorial, el número de aperturas y la ornamentación de la exina, exhiben diferencias notables entre las especies estudiadas.

Abstract Background Citrus species are among the most important and widely consumed fruit trees in the world and are subjected to increasing global cultivation. Sweet orange (Citrus sinensis L. Osbeck) is one of 30 species of citrus which is cultivated in different regions of Iran. In this study, 80 trees of 13 sweet orange cultivars of Mazandaran province were studied for genetic diversity and fingerprinting by five short simple repeat (SSR) marker. Results The studied cultivars showed a high degree of genetic variability with an average genetic polymorphism of 98.46%. Behshahr and Jadeh Ghadim2 genotypes had the highest and lowest values in Nei genetic diversity, number of effective alleles, and Shannon index, respectively. Based on k-means clustering, the studied genotypes were divided into two main different groups. The high magnitude of genetic similarity between replicates of different cultivars indicated a potential case of homonymy or synonymy. DAPC analysis showed genetic admixture among some of the cultivars. The heatmap plot illustrated the alleles involved in cultivar differentiation. The CAPs analysis of monomorphic alleles of SSR loci indicated that these alleles differ in their sequences which add up to the genetic variability of citrus germplasm. Conclusion In general, SSR markers, due to their codominant nature and abundance in genome, are a good indicator for cultivar fingerprinting and hybrid prediction in orange cultivars. The present results showed the high diversity of sweet orange trees in different cultivars in the north of the country.

The genus Avicennia contains of 8 species which show a great extent of morphological and genetic variability, which make taxonomy of the genus difficult. Molecular barcoding along with advancement in computational approaches may be proper methods to investigate and assess the efficiency of different molecular genetic regions in Avicennia species delineation and also produce data on species evolution and divergence. The aims of present study were to utilize multiple genetic data for the species delineation and study the phylogeny of the genus. Moreover, we developed a hypothesis on biogeography of these species with respect to barcode divergence. The results showed that both Internal transcribed spacer (ITS) and trnHG–psbA intergenic spacer (trnHG-psbA) sequences may be used in Avicennia species delineation. Barcode gap analysis and nucleotide difference of the studied taxa showed significant Fst for pair-wise species comparison and the role of nucleotide changes in Avicennia speciation.

Sex determination of date palm seedlings is the challengeable effort for breeders. Different studies based on molecular markers and genome sequencing have provided some insight in to the genetic regions related to sex determination in date palms in general. But due to differences in cultivar population structure and also cost of whole genome sequencing, we may need a more suitable approach in developing countries for this task. Therefore, we suggest using a combination of different available molecular markers and a computational approach to identify the genetic regions involved in sex differentiation in date palm cultivars. In this study we used twenty-three cultivars including 7 male and 16 female cultivars that were examined by 30 different dominant and co-dominant molecular markers which deal with different genomic regions. Grouping of the tree samples based on 178 loci resulted in genetic differentiation of the studied male and female palm trees. Multiple correspondence analysis (MCA) bi-plot also showed genetic difference within male and female trees. Heatmap plot specified those markers which differentiate date palm trees. SSR (simple sequence repeats) and IRAP (inter retrotransposon amplified polymorphism) markers provided sex linked markers for male cultivars. In present study, we introduced sex specific alleles for Iranian male date palm cultivars as a fast track in seedlings. Different association studies performed identified the candidate genetic regions which are significantly associated with sex differentiation in date palm cultivars.

The genus Crocus L. of Iridaceae family contains about 160 species and is considered as a complex group of plant taxa with regard to evolutionary and phylogenetic events. Inter-specific hybridization and gene flow contribute to species genetic homogeneity in one hand and high within species genetic variability and species genetic content overlaps caused species resolution a problem. In spite of extensive molecular phylogenetic studies in this genus, nothing is known about DNA sequences or Single nucleotide polymorphisms (SNPs) which are of adaptive nature. Moreover, nothing is known about which geographical or environmental factors plays role in species local adaptation and speciation events within Crocus L. genus. Therefore, the present study was conducted to answer the above said questions. We used a combined molecular data set of internal transcribed spacer (ITS) nuclear gene and trnL-F intergenic spacer (trnL-F) sequences of chloroplast genome. A multiple analytical method of Canonical correlation (CCA), Redundency analysis (RDA), and Latent Factor Mixed Model (LFMM)identified a few potential adaptive SNPs. Moreover, population criterions like Tajimas’ D, molecular clock test, as well as skyline-plot revealed a smooth and continuous genetic changes for most of the Crocus species, but the occurrence of a sudden deep nucleotide substitution for Crocus taxa of Iran. The impact of latitude was significantly higher on nucleotide changes compared to that of longitudinal distribution of Crocus species.

Tamarix is the largest genus in the family Tamaricaceae with about 54 species. T. tetragyna var. meyeri and T. tetragyna var. deserti were previously reported from Iran. Due to the presence of overlapping features in the previously designed identification keys for the separation of these two varieties, it could be helpful to use other characters and character states derived from other sources, such as anatomical and molecular studies, in addition to find more effective morphological features for the separation of the two varieties. Therefore, the present study aimed to differentiate these two presumed varieties by multiple approaches using morphological, anatomical and molecular data. For morphological study, 6 quantitative and qualitative characters were examined in 12 samples of the two varieties. ANOVA analysis showed a significant difference between the studied characters. For anatomical study, 10 traits were examined in 4 samples of the two varieties, which also showed a significant difference. AMOVA analysis based on molecular studies using Scot marker showed a significant difference between the two varieties. The PCA biplot show the most variable traits in morphological and anatomical studies. For varieties delimitation, different clustering methods were drawn in all three studies. The results of this study showed that the use of appropriate diagnostic traits in morphological and anatomical studies as well as the use of molecular markers can be effective in showing the separated boundaries of the two varieties studied.

The pomegranate is an economically important fruit plant species which has been utilized since ancient time as a source of food and medicine by mankind. This plant although is cultivated in certain geographical regions, but its fruits are imported and sold throughout the world. Iran is the center of origin for pomegranate and contains huge number of known cultivars. However, genetic studied on these cultivars are very limited and much detailed information has to be produced for better hybridization and breeding tasks in the country. A fingerprinting study was performed on 178 Punica trees in 47 known cultivars by using SCoT molecular markers. We obtained 61 SCoT bands/ loci which were used for genetic diversity analyses and grouping of the cultivars. A low genetic variability was obtained within and among Punica cultivars, but as revealed by AMOVA, this was quiet enough to produce significant genetic difference among them. DAPC analysis revealed a trace of genetic admixture among the cultivars either due to gene flow or as a result of common ancestral shared alleles. Discriminating SCoT loci may be used in germplasm evaluation of Punica. The genetic difference of these cultivars can be utilized for hybridization and breeding programs

The pomegranate fruit is one of the most important horticultural products due to the presence of polyphenolic, antioxidant and anti-fungal compounds. In the present study, morphological and phytochemical compounds diversity was investigated in eight Iranian commercial pomegranate cultivars. Fourteen morphological characters and 10 chemical compounds were measured. Based on PCA analysis the most variable morphological characteristics among Punica cultivars studied were the wood surface, the leaf tip, the leaf incision, growth power and rained condition. High-performance liquid chromatograms of chlorgenic acid, caffeic acid, Para Coumaric acid as well as titrable acidity, total soluble solid, total phenolic contents, antioxidant activity in juice and peel of cultivars differentiated the cultivars studied. Comparing the two UPGMA dendrograms of Punica cultivars based on morphological data and chemical contents indicated certain disagreement between them. The correlation between morphological and chemical compounds and geographical distances of Punica cultivars was not statistically significant by the Mantel test. These findings indicate that Punica cultivars studied differ in their genetic content, however, this genetic difference is not correlated with their geographical distance.

Taxonomy and molecular phylogeny of the genus Cousinia are complicated and unresolved mainly because of disagreement between morphological and molecular phylogenetic studies. The genus Cousinia has approximately 700 species, which makes it one of the most varied genera found in central and southwest Asia. Section Cynaroideae, containing 89 species, is considered the largest section of the genus. While evidence on the phytochemical and biological features of the Cousinia genus has been reported, identification and delineation as well as classifying the section and the species’ relationships within the genus Cousinia generally remain debatable. Therefore, the present study aims to: 1) identify and delineate the species within the two sections Cynaroideae and Platyacanthae; 2) study the species relationships based on both morphological and molecular features (Internal Transcribed Spacer (ITS) marker); 3) study the sectional delimitation and its monophyly; and 4) estimate the divergence time of the studied sections. To this end, 50 Cousinia species occurring in Iran were investigated for the first time. A maximum parsimony tree of the morphological features separated the species of the two sections from each other. However, the ITS-based phylogenetic tree did not delimit the two studied sections. The relationships among the studied Cousinia species in the genetic trees were generally not congruent with the obtained morphological tree. The divergence time of the studied species within the Cynaroideae and Platyacanthae sections determined using Bayesian Evolutionary Analysis Sampling Trees (BEAST) was estimated to be around 3.5 million years ago (Mya).

Lallemantia is a medicinally important plant in the world. Due to interspecific hybridization and horizontal gene transfer, spices relationship and delimitation on the genus Lallemantia is difficult based on different molecular markers. Therefore, selecting the appropriate marker can be important. Fingerprinting techniques continue to be used for genomic profiling for the characterization of germplasm and the establishment of the identity of varieties/hybrids/parental sources of aromatic and medicinal plants. For this, we need to produce detailed information on genetic diversity available in Lallemantia as well as investigate spices relationship and delimitation. Therefore, the present study was performed on Lallemantia species in Iran. We used SCoT and REMA molecular marker for our genetic investigation with the following aims: 1- To reveal the species delimitation and species relationship in Lallemantia, and 2- To investigate discriminating power of the SCoT and REMAP markers by Gst and NM analysis. The results obtained revealed that the SCoT marker is the best to show the relationships between species while the REMAP marker is the best for species delimitation. we found the loci with the high value of Gst (1.00) in SCoT and REMAP markers that can be used in barcoding and fingerprinting of L. royleana.

Persian walnut (Juglans regia L.), is very auspicious plant species of Iran from both economical and food points of views. Both wildly grown as well as cultivated forms of this plant species are scattered in different geographical regions of the country and are a valuable source for edible nut as well as job employment. Scattered published data on genetic diversity of this important plant species are mainly based on different molecular data analyses, therefore a meta-analysis of the same cultivars based on several different molecular markers including DNA-sequences and multi-locus markers was conducted to provide detailed insight on genetic structure of walnuts. The results indicated a moderated genetic variability of about 40 percent in the studied cultivars, however these cultivars are genetically differentiated as revealed by Fst and AMOVA. HGT analyses revealed that the cultivars phylogeny differs to some degree by different markers and therefore a heat map was constructed. to reveal the cultivars relationships based on combined molecular data. A higher Pst value was obtained compared to that of Fst genetic differentiation, therefore, it seems that local adaptation and selection have played role in the walnut cultivars’ morphological divergence. LFMM analysis identified some of multi-locus alleles to be adaptive in walnut cultivars studied.

Date Palm (Phoenix dactylifera L.) is one of the oldest domesticated fruit trees. For future breeding program, knowledge on genetic structure of cultivars is necessary. Therefore, the present study was performed with the following aims: 1- To provide data on genetic diversity and genetic structure of 36 date palm cultivars, 2- To provide data on the association between fruit characteristics and the genetic features of the cultivars. We used nine SSRs and EST-SSR loci for our genetic investigation. The most of SSR loci obtained have a high Gst value (0.70), and therefore have a good discrimination power for date palm cultivar differentiation task. K-Means clustering grouped date palm cultivars either in two broad clusters, or in 16 smaller genetic groups. This was supported by delta K = 2 of the STRUCTURE analysis. AMOVA produced significant genetic difference among date palm cultivars (PhiPT = 0.70, P = 0.001). New genetic differentiation parameters estimated also produced significant difference among date palm cultivars (G’st(Nei) = 0.673, P =0.001; G’st(Hed) = 0.738, P = 0.001). Test of assignment revealed that some of the cultivars have 33-66% misassignment, probably due to genetic admixture. Heatmaps of genetic versus morphological/or agronomical characters in date palm cultivars differed from each other showing the cultivars morphological changes is not merely related to their genetic content. It points toward the potential role played either by environmental conditions or local selection practice. The new findings can be utilized in future conservation and breeding of date palms in the country.

Rice (Oryza sativa L.), is a staple food and cash crop in many countries and studies on genetic structure and differentiation patterns of rice landraces along with the cultivated rice, provide important data for future rice breeding. Therefore, the aims of present investigation were 1-To study the genetic diversity present within Iranian rice genotypes, 2-To study genetic relatedness of these rice genotypes, and 3-To provide barcoding of the rice genotypes based on SSR molecular markers and produce data for rice varieties authentication. In total, 201 rice samples originated from 10 geographical regions of Iran were studied in this project. All rice samples underwent fragment analysis in every 64 SSR loci and different clustering and ordination methods performed. In general, four major clusters were formed. Both landraces as well as rice cultivars were distributed in different clusters due to their genetic difference. STRUCTURE analysis of the studied genotypes followed by Evanno test produced the optimal number of genetic groups K = 2. The mean Nm = 13.6, for the studied genotypes indicates that a high degree of gene flow/ ancestral common alleles are present in the rice genotypes studied. Mantel test indicated a significant positive association between genetic distance and geographic distance of the rice genotype studied and presence of an overall isolation by distance (IBD) model of differentiation across the geographical regions of Iran. Overall, the significant genetic difference observed between rice landraces and rice cultivars of the country may be used in future hybridization and breeding of rice in the country. The landrace rice genotypes may contain useful genes to be transferred to the popular rice cultivars. Moreover, SSR loci that can differentiate rice genotypes are identified and can be used in rice cultivars authentication.

The genus Cousinia Cass. of the tribe Cardueae with about 700 species is one of the most diverse genera in Central and SW Asia. Section Cynaroides Bunge with 89 species is the largest section of the genus.Due to controversy in the number of Cousinia species and their delineation, the first step in studying the genus is to identify and delimit presumed species. Species delimitation is usually difficult in the species with overlaps in their morphological features. We therefore, used a combination of morphological and molecular markers (ISSRs) to carry out delimitation in 204 taxa of 68 Cousinia species sections Cynaroideae Bunge and Platyacanthae Rech. f.. The species delineation based on morphometry and ISSR data were done by UPGMA clustering. The samples of each species were placed close to each other and formed a single sub-cluster, separated from the other studied Cousinia species. This clearly reveals application of ISSR molecular markers in taxonomy and species differentiation. Based on ISSR and morphological data, the members of two sections Cynaroideae Bunge and Platyacanthae Rech. f. are separated from each other. The Mantel test performed between morphological distance and Nei genetic distance produced non-significant correlation. This result also supports distance analyses of the trees and reveals that the two dendrograms are not correlated. One of the possible causes of this discordance between the two morphological and genetic trees can be reticulation and horizontal gene transfer (HGT) between closely related species.

X-chromosome and its independent loci, recently has gained importance in genetic investigations that are concerned with diseases control-case studies, as well as in population genetic analyses and phylogenetic investigations. The present study was performed as a preliminary investigation on X-chromosome sequence variability as a source of genetic diversity within Iranian population and to investigate potential use of these sequences for differentiating the ethnic groups within the country. A limited random sample could be obtained from four different ethnic populations, which were sequenced for TEX-11 gene of the X-chromosome. At the beginning we used seven specific primers related to seven known SNPs within TEX-11 gene. Later on we searched for the other known as well as new potential SNPs or sequence variants in the studied samples. We could identify 87 potential SNPs or sequence variants. Genetic diversity analysis revealed the presence of five haplotype groups within the studied sequences. AMOVA revealed no significant genetic differentiation among sample driven from the ethnic populations. Moreover, Mantel test did not show significant association between geographical distance and genetic distance of these samples, indicating that gene flow occurred among these populations with no geographical obstacle. This is the first report on X-chromosome sequence diversity analysis in Iran.

Plantago afra (Plantaginaceae) is the most medicinally important species in genus Plantago and it is native to the western Mediterranean region, West Asia and North Africa, and cultivated extensively in Asia and Europe for seed husk known as black Psyllium. We have no data on the population genetic structure of this species in the world. Therefore a population genetic and morphological investigation was performed through light on genetic and morphological variability in this taxa. We used ISSR molecular markers for population genetic investigation. Genetic diversity analyses revealed a moderate genetic variability within Plantago afra, while PCoA showed some degree of genetic admixture among populations. AMOVA produced significant genetic difference among populations. The Mantel test showed a positive significant correlation between the genetic and geographic distance of the studied populations. STRUCTURE analysis showed that there are different genetic groups in the studied populations. Morphometric analysis showed that one population differed in seed color and mean stem diameter. The same population contained specific allele combinations and differed genetically from the rest of the studied populations. Therefore, we considered it as a new variety within Plantago afra.

Ziziphora clinopodioides Lam., (Lamiaceae), is a perennial herb which is used as traditional medicine in Iran. Different authors disagree on the number of subspecies. In general, taxonomic and biosystematic studies of Ziziphora clinopodioides have been limited and no molecular phylogenetic or biogeographic study of the species has been carried out. Therefore, the aims of this study were (1) to determine the number of subspecies, (2) to produce information on the species’ genetic structure and intra-specific genetic variability, and (3) to produce data on the probable date of appearance of Ziziphora clinopodioides in Iran. We used a combination of morphological and molecular data to study plants randomly collected from 5 geographical regions. Both analyses revealed a high level of within population variability and grouping of the studied provinces produced an admixture that indicated the absence of any subspecies within the species. STRUCTURE analysis and K-Means clustering identified two gene pools within the country. The probable date of divergence obtained was 5-10 Mya for the appearance of this species in the mountainous regions of Qazvin and Mazandaran.

Olive is an important horticultural plant having both cultivated and wild forms. The aim of the present study was investigating genetic diversity of 13 wild olive trees belonging four geographical populations in IRAN using SRAP neutral molecular markers as well as cp-DNA rpl intergenic sequences and ITS region. Genetic diversity parameters determined for 76 SRAP loci within the studied olive populations identified the most variable loci. Population differentiation parameters determined for SRAP loci, identified 13 SRAP loci with Gst value of 1, that means they differentiate the studied trees. PCoA analysis based on SRAP data separated olive trees from each other due to genetic difference. Distribution of the samples in PCoA plot indicated that the population 1 are more spread due to population genetic variability. However, the SRAP result reveals that these molecular markers can be used in population genetic investigations and germ plasm analysis. AMOVA showed significant genetic difference among the studied olive populations. Cp-DNA analysis produced 366 bp long sequences, out of which 224 sites were segregating among the studied plants. The mean nucleotide diversity was 0.32. TCS network based on cp-DNA separated most of the studied populations. Therefore, it seems that cp-DNA rpl sequences is a suitable barcode molecular marker for population genetic studies. Phylogenetic tree of ITS data could partially differentiate wild olive population. In conclusion, a combined use of SRAPs and cp-DNA sequences are suggested for wild olive population genetic investigation.

Lallemantia is a small genus of Lamiaceae with five herbaceous annual or biennial species. Some of these species are of medicinal value, while others have been used as the source of food. All five Lallemantia species occur in Iran. Although, there are many discussions about infra-generic variations in the genus, very scarce comprehensive studies are found about its taxonomy. Therefore, in the current study, pollen grain morphology was investigated using scanning electron microscopy. We used SPSS ver. 15 and PAST ver. 2.17 for multivariate statistical analyses of data. In total, we studied eleven qualitative and quantitative traits. Pollen equatorial and polar views were similar among the species and were prolate and circular, respectively. Pollen ornamentations differed as bireticulate (L. royleana and L. iberica), microreticulatm (L. peltata and L. Baldshuanica) and reticulate- faveolate (L. canescens). PCA-biplot showed some traits such as pori length/width ratio were important in identifications of species. The studied species created two groups in the WARD method tree of palynological data. L. royleana and L. baldshuanica were grouped together, and in the other group L. canescens and L. iberica placed nearly and L. peltata placed far from them. Our obtained results were similar to previous morphological study of the genus. The present study revealed taxonomic implication of the micromorphological study in the interspecific classification of the genus.

Lallemantia is a small genus with 5 species, which one of them is Lallemantia peltata. This aromatic plant grows in a limited area of the Iran and is known as medicinal herb in folk medicine. We have no information on the infraspecific variations on morphological, anatomical and molecular features of this species. Therefore, in the current study; we investigated these variations on six geographical populations of it. These plants were used for morphological, anatomical and molecular investigations. GenAlex, GenoDive and PAST softwares were used for statistical analyses. In morphological study, we used fifteen characteristics. PCA bi-plot revealed some characteristics had diagnostic value in separation of the populations. The studied populations were clustered into two groups. We examined fifteen qualitative and quantitative anatomical variables. PCA loading revealed that some anatomical variables had the highest positive correlation and were the most variable anatomical characters among the studied populations. Based on the anatomical traits, theses populations divided into two groups. Ten ISSR primers were used for examination of genetic variations among the populations. The STRUCTURE analyses of ISSR data revealed two groups in theses populations that they were divided into two groups in MDS plot. The results of morphological, anatomical and also ISSR studies were similar. Clustering and ordination of the studied populations separated some of these populations from the others and suggest the existence of two groups within this species.

Ziziphus jujuba (jujube) of buckthorn family (Rhamnaceae) is an important medicinal crop plant cultivated in different provinces of Iran. It has also wild populations in some geographical areas. We carried out population genetic study on 8 populations of cultivated versus wild jujuba by using ISSR molecular markers to produce data on population genetic structure, gene flow, and genetic variability in the studied populations. We also aimed to investigate genetic differentiation between wild and cultivated plants and identify the potential gene pools of this medicinal plant species. The studied populations had a moderate genetic variability and were grouped in two major groups by PCoA plot. AMOVA revealed significant genetic difference among these cultivars. Mantel test showed significant correlation between genetic distance and geographical distance in the studied populations. PCoA analysis showed genetic differentiation between wild and cultivated plants within each province. STRUCTURE analysis identified two potential gene pools for jujube cultivars. Data obtained may be used in genetic conservation and future breeding programs of this medicinal plant species in the country.

Ziziphus jujuba (jujube) is an important horticultural crop with medicinal value. It is under cultivation in many areas of Iran and also grows as wild in several geographical populations throughout the country. We have no information on genetic variability and population structure of this important plant species in our country. Therefore, the aim of the present study was to perform genetic fingerprinting of 13 geographical populations of jujuba for the first time and provide data on population genetic structure, admixture versus genetic fragmentation of this important crop. We used multilocus molecular markers (ISSRs and SRAPs) for genetic fingerprinting and also compared the results with bioinformatics investigation results we did on jujuba cultivars by using nuclear r-DNA and chloroplast inter-genetic cp-DNA sequences. Genetic diversity parameters and AMOVA test as well as Ivanno test support some kind of genetic distinctness of the jujuba populations studied. We found that cp-DNA inter-genic sequences can also discriminate jujuba cultivars as efficient as multilocus molecular markers and therefore, a multiple molecular approaches may be used for genetic fingerprinting of jujuba. The present study revealed good level of genetic diversity among wild/ uncultivated populations of jujuba which can be used in conservation and breeding of this important horticultural crop plant within the country. As this crop has several wild geographical populations throughout the country, we plan to continue our quest to investigate many more populations in nearby future and try to utilize cp-DNA inter-genic sequences along with multilocus molecular markers for genetic discrimination of wild populations.

The cosmopolitan genus salvia L. (Lamiaceae) consists of nearly 1000 species distributed throughout the Old and New Worlds. America and South- West of Asia are the two most important distribution centers. Of the 70 species reported in the flora Iranica area nearly 56 species belong to Iran. This investigation deals with the morphology of Salvia. The morphological studies were performed on 36 populations of 11 species which grow in Central Alborz Mo-untains. In this analysis 42 quality and quantity characters were used. The results of this analysis have been used for the preparation of the identification key. Clustering, cladistics and PCA ordination reveals the relationships of the species in this genus.

Section Gamosepalum has been reported from Turkey for the first time by Dudley. In recent years, several species of this section were reported as new records for Iran. Four species of Alyssum section are tranfered from sect. Alyssum to sect. Gamosepalum with considering of important characters in each section. These changes made two synonymies. Five species of Gamosepalum section including A. lanceolatum, A. persicum, A. lepidoto-stellatum, A. mulleri and A. baumgartnerianum are present in Iran. Identification key of accepted species and distribution map of them are given. All specimens examined in the present work are deposited at FUMH, G, TARI and W.

Carduus L. of the genus Compositae include about 90 species which are distributed mainly in the Europe, Asia and Africa as the three major centers of diversity of Carduus. About 8 species of Carduus are distributed in Iran among which 1 species is endemic. In this study, 45 quantitative and qualitative morphological characters from vegetative and reproductive parts were considered and evaluated in 37 populations of 8 species of Carduus from different localities in Iran. The aim of this study was to evaluate the species relationship in Iran. To evaluate the species relationships, cluster analysis and ordination based on principal component analysis and PCO were implemented. Statistical analysis indicated that characters as Capitulum shape, Capitulum length, phillary bract spine length, phillary bract width, number of rows phillary bract, number of phillary bract, involucre length, involucres width, length to width ratio involucres had the most important role as diagnostic characters in inter-genus variation. Based on statistical results and diagnostic characters, an identification key was provided for Carduus species in Iran.

Karyotype studies were performed in 18 populations of eight Helichrysum species in Iran. Those species showed chromosome numbers of 2n = 2x = 14; 2n = 4x = 24, 28 and 32; 2n = 6x = 36; 2n = 7x = 42; 2n = 8x = 48; 2n = 9x = 54; and 2n = 10x = 60. The chromosome numbers of H. davisianum, H. globiferum, H. leucocephalum and H. oocephalum are reported here for the first time. New ploidy levels are reported for H. oligocephalum (2n = 4x = 24) and H. plicatum (2n = 4x = 32). The chromosomes were metacentric and submetacentric. An ANOVA among H. globiferum and H. leucocephalum populations showed significant differences for the coefficient of variation for chromosome size, total form percentage and the asymmetry indices, indicating that changes in the chromosome structure of Helichrysum species occurred during their diversification. Significant positive correlations among the species and populations studied, in terms of the total chromosome length, lengths of the short arms and lengths of the long arms, indicate that these karyotypic features change simultaneously during speciation events. The genome sizes of Helichrysum species are reported here for first time. The 2C DNA content ranged from 8.13 pg (in H. rubicundum) to 18.4 pg (in H. leucocephalum and H. davisianum). We found that C-value correlated significantly with ploidy level, total chromosome length, lengths of the long arms and lengths of the short arms (p

The genus Centaurea L. is one of the largest genera in the family Asteraceae. The number of taxa included in this genus ranges from 500 to 600 worldwide. Iran is one of the major centers of diversity for this genus. Pollen morphology has proved useful in the systematics of Asteraceae, as well as in that of some of its genera and species. The pollen morphology of 19 taxa of the genus Centaurea was investigated in detail by light and scanning electron microscopy. Examination under light microscopy showed pollen grains to be tricolporate, isopolar, radially symmetrical, oblate spheroidal, prolate spheroidal, subprolate, tectum perforate and scabrate. Based on the exine ornamentation observed under scanning electron microscopy, we identified two types of pollen grains, designated type I (dense acute spinules) and type II (sparse spinules). All of the taxa evaluated resemble Wagenitz's Jacea type. We present micrographs of pollen grains, together with descriptions of the characteristics of their structure. We found that the pollen characters (shape, exine structure, sculpturing) were useful for classification.

Anchusa )Boraginaceae( includes weedy species in different habitats and cultivations and is composed of four species in Iran. Species delimitation is mainly based on features as zygomorphic or actinomorphic flowers, straight corolla tube and nutlet shape. In this project, morphological features of different accessions of Anchusa species were evaluated. Totally, 33 qualitative and quantitative morphological characters of 12 populations of four species were studied. Statistical analyses were done by SPSS ver. 19.0 Diagnostic value of different features in species delimitation was studied in order to provide an efficient identification key. Results indicated that adopted features were of taxonomic importance. Factor analysis revealed that two main factors had most effects. These factors were location of filaments, calyx length, middle leaf shape, location of anthers, shape of tube of corolla, length of corolla, and diameter of hair tubercles. A new identification key based on obtained results was provided. This was the first morphometric study of Anchusa species in Iran.

Pomegranate (Punica granatum L.) is an important horticultural plant with several cultivated forms planted in different regions of Iran. Due to its economic importance, studies have been carried out to illustrate the genetic diversity at the chromosomal and molecular levels in different pomegranate cultivars growing in this region. This study analyzed chromosome pairing and B-chromosomes of 21 pomegranate cultivars and tried to investigate the effects of geographical parameters like altitude and longitude as well as elevation and the mean annual rainfall on cytogenetic diversity of these taxa. An ANOVA test revealed the presence of a significant difference for chiasmata and chromosome pairing among the cultivars, indicating their genetic differences. A positive significant correlation was observed between total chiasma frequency and terminal chiasmata, intercalary chiasmata and the mean number of quadrivalents. A significant positive correlation was observed between annual rainfall and the mean number of rod bivalents, while a significant negative correlation was found for the number of ring bivalents. Altitude did not show any correlation with the cytogenetic characters studied, but showed a significant negative correlation with the number of univalents. Longitude showed significant positive correlation with the number of ring bivalents and a negative correlation with the number of univalents and intercalary chiasmata. PCA analysis showed that both geographical and cytological features contribute greatly in the diversity observed in the pomegranate cultivars. The occurrence of multipolar cells and unreduced pollen grains were observed in some of the cultivars.A romã (Punica granatum L.) é uma planta hortícola importante com diversas formas de cultura plantadas em diferentes regiões do Irã. Devido à sua importância econômica, alguns estudos genéticos têm sido realizados para ilustrar a diversidade genética em ambos os níveis cromossômico e molecular em diferentes cultivares de romã que crescem neste país. O presente estudo considera as análises de pareamento cromossômico e cromossomo-B em 21 cultivares de romã e tenta investigar os efeitos dos parâmetros geográficos, como altitude e longitude, bem como a elevação e a queda de chuva média anual sobre a diversidade citogenética destes cultivares. O teste ANOVA revelou a presença de uma diferença significativa para quiasmas e emparelhamento de cromossomos entre as cultivares, indicando a sua diversidade genética. A correlação positiva e significativa foi observada entre o freqüência total de quiamas de quiasmas terminais, quiasmas intercalares e o número médio de quadrivalentes. Uma correlação positiva foi observada entre a queda da chuva anual e o número médio de bivalentes haste, com correlação negativa significativa com o número de bivalentes anel. A altitude não mostrou qualquer correlação com caracteres citogenéticos estudados, enquanto a altitude apresentou correlação negativa significativa com o número de monovalentes. A longitude mostrou correlação positiva e significativa com o número de bivalentes anel e correlação negativa com o número de univalentes e chismata intercalares. A análise de PCA mostrou que tanto as características geográficas quanto citológicos podem contribuir grandemente na diversidade observada nas cultivares de romã. A ocorrência de células multipolares e grãos de pólen não reduzidos foram observados em alguns dos cultivares.

Meiotic studies of ploidy level, chromosome paring and chiasma frequency were performed on 11 Cousinia (Asteraceae) species of the section Serratuloideae. The diploid number of the species studied was 2n = 2x = 24 and 26 so these species possess two different basic numbers (x = 12 or 13), a phenomenon common to other sections of the genus. The chromosome numbers of 9 species are reported here for the first time. When the 2n = 24 and 2n = 26 species were subjected to cluster analysis based on relative meiotic characters two different clusters were formed indicating their distinctness. Our data support the results obtained from morphometry, anatomy, pollen morphology and molecular studies of the genus Cousinia.