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.     

Genetic relatedness among some wild cherry (<Emphasis Type="Italic">Prunus</Emphasis> subgenus <Emphasis Type="Italic">Cerasus</Emphasis>) genotypes native to Iran assayed by morphological traits and random amplified polymorphic DNA analysis

Subgenus Cerasus species are useful genetic resources for cherry breeding programs. A total of 17 morphological traits together with 19 random amplified polymorphic DNA (RAPD) primers were used to study 39 accessions including 34 wild Cerasus subgenus genotypes belonging to Prunus avium L., P. cerasus L., P. mahaleb L., P. microcarpa Boiss., P. incana Pall., and P. brachypetala Boiss. species, along with an unknown wild Cerasus sample, two advanced cherry cultivars (‘Lambert’ and ‘Bulgar’), and two rootstocks (‘Colt’ and ‘Gisela 6’). Genotypes were separated into different groups according to their species and collection sites using cluster analysis performed by Ward’s clustering method based on morphological data. Nineteen RAPD primers from 60 screened produced 304 polymorphic reproducible bands (98.15% polymorphism). According to the similarity matrix, the lowest similarity was obtained between P. avium and P. microcarpa samples. A dendrogram was prepared by the unweighted pair-group method with arithmetic average (UPGMA), and the accessions were separated according to their species and geographic origin. In both morphological and molecular results, the advanced cultivars and rootstocks were separated from wild genotypes, and the unknown genotype was grouped with P. mahaleb accessions. Grouping by morphological characteristics was compared with the results of RAPD analysis, with no significant correlations between morphological and molecular data being found. This is the first report of molecular (RAPD) genetic diversity study in wild Cerasus subgenus genotypes from Iran, and the results demonstrate the high potential of RAPD analysis for discrimination of Cerasus subgenus genotypes.     

Assessment of cultivated cherry germplasm in Iran by multivariate analysis

Key message

This work is an important step in the conservation of genetic cherry resources, which showed distinctive and interesting agronomical characters. Also it introduces suitable genotypes for cultivation and breeding studies.

Abstract

The purpose of this study was to characterize cherry germplasm that is cultivated in Iran. Thirty-three morphopomological parameters were studied in this germplasm, consisting of 70 cherry genotypes (41 sweet cherry, 24 sour cherry and 5 duke cherry genotypes). A wide variation was found in blooming time, ripening time, fruit weight, fruit color, anthocyanin, total soluble solids (TSS), titratable acidity (TA), fruit dimensions and flesh firmness and stone size. There were close positive correlations between fruit weight and fruit dimensions, and between fruit weight and fruit stalk weight, fruit flesh firmness and cracking and also a negative correlation between pH and TA. Dendrogram gave a clear separation between the sour, duke and sweet cherry species and also showed existing intraspecific morphological variation. Based on fruit size and organoleptic properties, the sweet cherry genotypes ‘Siah-Mashhad’, ‘Takdaneh-Mashhad’, ‘Shabestar’, ‘Siah-Daneshkade’, ‘Ghazvin’ and ‘Droongezna’ are recommended for fresh consumption. Good fruit chemical composition and late-ripening time stands out genotypes ‘Dirres-Italia’, ‘Dirres-Pardis’, ‘Maremoot’, ‘Abardeh’ and ‘Rorshon’ and make them suitable for processing. Also, ‘Gilas46’ and ‘Gilas49’ were substantially late-ripening, a characteristic that makes these genotypes highly suitable for breeding studies in case of ripening time. Furthermore, sour cherries ‘Hashtgerd2’ and ‘Hashtgerd3’ and duke cherries ‘Pardis1’ and ‘Pardis3’ were the best genotypes. This work is an important step in the conservation of genetic cherry resources in Iran, which showed distinctive and interesting agronomical characters such as low susceptibility to fruit cracking, high levels of total soluble solids, early fruit maturity and high fruit quality.     

Genetic variation and identification of promising sour cherries inferred from microsatellite markers

The aim of this study was to identify the group of highly polymorphic microsatellite markers for identification of promising sour cherries. From among 30 tested microsatellite (SSR) markers, 19 were selected to profile genetic variation in sour cherries due to high polymorphisms. Results indicated a high level of polymorphism of the accessions based on these markers. Totally 148 alleles were generated at 19 SSR loci which 122 alleles were polymorphic. The number of total alleles per locus ranged from 2 to 15 with an average of 7.78 and polymorphism percentage varied from 50 to 100% with an average of 78.76%. Also, PIC varied from 0.47 to 0.89 with an average of 0.79 and heterozygosity ranged from 0.35 to 0.55 with a mean of 0.45. According to these results, these markers specially PMS3, PS12A02, PceGA34, BPPCT021, EMPA004, EMPA018, and Pchgms3 produced good and various levels of amplifications and showed high heterozygosity levels. By the way, the genetic similarity showed a high diversity among the sour cherries. Cluster analysis separated improved cultivars from promising sour cherries, and the PCoA supported the cluster analysis results. Since the studied sour cherries were superior to the improved cultivars and were separated from them in most groups, these sour cherries can be considered as distinct genotypes for further evaluations in the framework of breeding programs and new cultivar identification in cherries. Results also confirmed that the set of microsatellite markers employed in this study demonstrated usefulness of microsatellite markers for the identification of sour cherry genotypes.     

Estimation of genetic diversity in some Iranian wild Prunus subgenus Cerasus accessions using inter-simple sequence repeat (ISSR) markers

As Iran is one of the main origins of Prunus germplasm. In this study, ISSR markers were used for genetic diversity evaluation of 39 accessions of subgenus Cerasus belonging to six species i.e. Prunus avium L., Prunus cerasus L., Prunus mahaleb L., Prunus incana Pall., Prunus microcarpa Boiss., and Prunus brachypetala Boiss.. With 12 ISSR primers, 151 polymorphic bands were detected with polymorphism ratio range of 81.8%–100%. The lowest similarity (0.04) was found between P. avium and P. microcarpa genotypes and the mean of similarity between all genotypes was 0.28. Cluster analysis separated improved cultivars from wild accessions. Improved cherry cultivars and rootstocks were placed closer to the P. avium than the other species. The principal coordinate analysis (PCoA) supported the cluster analysis results. The wild accessions were separated according to their species and collection sites. ISSR markers are useful techniques for genetic diversity evaluation in Prunus subgenus Cerasus.     

Genotypic and Phenotypic Diversity of Cherry Species Collected in Serbia

Genetic diversity of cherry species collected in Serbia has been investigated using 26 simple sequence repeat (SSR) markers developed in Prunus. This material consisted of 77 cherry accessions corresponding to the five following species, Prunus cerasus, Prunus avium, Prunus fruticosa, Prunus mahaleb, and Prunus serrulata. A total of 98 alleles were detected, with an average of 3.7 putative alleles per primer combination. Sixteen unique, species-specific, alleles were detected with nine primer pairs in four species, P. avium, P. cerasus, P. mahaleb, and P. serrulata. The highest number of unique alleles, 8, was observed in P. mahaleb and no species-specific alleles were detected in P. fruticosa. SSR markers generated unique fingerprints for all cherry accessions. Cluster analysis classified accessions into four groups according to their taxonomy, where P. avium and P. cerasus were grouped together, supporting P. avium as one of the progenitors of sour cherry. The highest genetic variability and potential value in rootstock breeding was observed in P. mahaleb and P. serrulata material. Principal component (PC) analysis explained more than 50 % of the total observed phenotypic variability using the first two components. The most important characteristics of PC1 were leaf length and width, fruit taste, color of leaf nectaries, fruit weight, leaf blade margin incisions, petiole length, size of vegetative buds, and length of internode. The most important characteristics of PC2 were shape of leaf blade at base, fruit skin color, and leaf blade length and tip angle. The investigated germplasm proved to be sufficiently genetically diverse for use in breeding programs and development of new cherry cultivars and rootstocks.     

Comparative analysis of genetic structure and variability in wild and cultivated pomegranates as revealed by morphological variables and molecular markers

In this study, the genetic variability and relationships among wild and cultivated pomegranate genotypes from the north of Iran were investigated by morphological characters and RAPD molecular markers. Principal component analysis showed that the first three components explained 61.64 % of the total morphological variation for studied genotypes. Fruit neck diameter, anthocyanin index, TSS, aril juice, fruit flavor index, petiole length, fruit peel thickness and seed hardness were predominant in the first component and contributed most of the total variation. Fruit characteristics such as titratable acidity were negatively correlated (r = ?0.56) with TSS (r = ?0.56) and pH (r = ?0.86) and also, seed hardness showed negative correlation with aril length and aril diameter. Clustering from morphological data allocated individuals into two main clusters with high variation. Two hundred and twenty-nine fragments were scored of which 174 of them were polymorphic with 76.9 % polymorphism. Genetic similarity ranged from 0.15 to 0.78 with an average of 0.42, indicating high genetic variation among studied genotypes. High molecular and morphological variability indicated that this germplasm includes rich and valuable plant materials for pomegranate breeding.     

Identification and genetic diversity of plum cultivars grown in Belarus

A study of the collection of sour cherry, sweet cherry, common plum, diploid and tetraploid types of plums, and apricots grown in Belarus carried out using 20 SSR markers showed that they are characterized by high genetic diversity. Among 106 genotypes, 524 polymorphic alleles were identified. The average number of alleles was 15.4 in common plum samples, 11.3 in diploid and tetraploid plum, 9.3 in sour cherry, 6.0 in apricot, and 4.9 in sweet cherry. The greatest genetic diversity is characteristic of common plum cultivars (PD = 0.811). The genetic diversity decreases as follows: diploid plum (PD = 0.741), sour cherry (PD = 0.721), apricot (PD = 0.673), and sweet cherry (PD = 0.655). Cluster analysis shows that the degree of intraspecific divergence in sour cherry and sweet cherry cultivars is less than that of common plum, diploid plum, and apricot plum. Although apricots and plums belong to the subgenus Prunophora, according to the results of SSR analysis, apricot cultivars form a cluster that is more distant from both Cerasus and Prunophora. A set of seven SSR markers (EMPA001, EMPA005, EMPA018, EMPA026 and BPPCT025, BPPCT026, BPPCT039) was selected for DNA identification of cultivars of sour cherry, sweet cherry, common plum, diploid plum, and apricot, as well as species and interspecies hybrids.     

Genetic Relationships Among Some Hawthorn (Crataegus spp.) Species and Genotypes

The genus Crataegus is well distributed in Turkey as a wild plant, with numerous, inherently variable species and genotypes. RAPD markers were used to study 17 hawthorn genotypes belonging to Crataegus monogyna ssp. monogyna Jacq (2 genotypes), C. monogyna ssp. azarella Jacq (1), Crataegus pontica K.Koch (3), Crataegus orientalis var. orientalis Pallas Ex Bieb (3), Crataegus pseudoheterophylla Pojark (1), Crataegus aronia var. dentata Browicz (1), C. aronia var. aronia Browicz (4), and Crateagus × bornmuelleri Zabel (2). The 10 RAPD primers produced 72 polymorphic bands (88% polymorphism). A dendrogram based on Jaccard’s index included four major groups and one outgroup according to taxa. The lowest genetic variability was observed within C. aronia var. aronia genotypes. The study demonstrated that RAPD analysis is efficient for genotyping wild-grown hawthorns.     

Determination of genetic diversity among Saccharina germplasm using ISSR and RAPD markers

Various species of genus Saccharina are economically important brown macroalgae cultivated in China. The genetic background of the conserved Saccharina germplasm was not clear. In this report, DNA-based molecular markers such as inter simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD) were used to assess the genetic diversity and phylogenetic relationships among 48 Saccharina germplasms. A total of 50 ISSR and 50 RAPD primers were tested, of which only 33 polymorphic primers (17 ISSR and 16 RAPD) had an amplified clear and reproducible profile, and could be used. Seventeen ISSR primers yielded a total of 262 bands, of which 256 were polymorphic, and 15.06 polymorphic bands per primer were amplified from 48 kelp gametophytes. Sixteen RAPD primers produced 355 bands, of which 352 were polymorphic, and 22 polymorphic bands per primer were observed across 48 individuals. The simple matching coefficient of ISSR, RAPD and pooled ISSR and RAPD dendrograms ranged from 0.568 to 0.885, 0.670 to 0.873, and 0.667 to 0.862, revealing high genetic diversity. Based on the unweighted pair group method with the arithmetic averaging algorithm (UPGMA) cluster analysis and the principal components analysis (PCA) of ISSR data, the 48 gametophytes were divided into three main groups. The Mantel test revealed a similar polymorphism distribution pattern between ISSR and RAPD markers, the correlation coefficient r was 0.62, and the results indicated that both ISSR and RAPD markers were effective to assess the selected gametophytes, while matrix correlation of the ISSR marker system (r = 0.78) was better than that of the RAPD marker system (r = 0.64). Genetic analysis data from this study were helpful in understanding the genetic relationships among the selected 17 kelp varieties (or lines) and provided guidance for molecular-assisted selection for parental gametophytes of hybrid kelp breeding.     

Genetic variability and relationships among thirty genotypes of finger millet (Eleusine coracana L. Gaertn.) using RAPD markers

Ragi or finger millet (Eleusine coracana L.) is an important crop used for food, forage, and industrial products. It is distributed in tropical and temperate regions of the world. The germplasm identification and characterization is an important link between the conservation and utilization of plant genetic resources. Traditionally, species or varieties identification has relied on morphological characters like growth habit, leaf architecture or floral morphology. Investigation through RAPD (random amplified polymorphic DNA) markers was undertaken for identification and determination of the genetic variation among thirty genotypes of ragi of the family Poaceae. Thirteen selected decamer primers were used for genetic analysis. A total of 124 distinct DNA fragments ranging from 300-3000 bp was amplified by using selected random RAPD marker. The genetic similarity was evaluated on the basis of the presence or absence of bands. Cluster analysis was made by the similarity coefficient. It indicated that the 30 genotypes of ragi form two major clusters, first, a major cluster having only one genotype, i. e. Dibyasinha and a second major cluster having twenty-nine genotypes. The second major cluster again subdivides into two minor clusters. A first minor cluster has only three varieties, i. e. Neelachal, OEB-56 and Chilika. The genotypes Neelachal and OEB-56 exhibit a 86% similarity with each other and 80% similarity with Chilika. A second minor cluster has 26 genotypes and is divided into two sub-minor clusters. The first sub-minor cluster has only one genotype (VL-322). The second sub-minor cluster again subdivides into two groups. One group has one genotype and the second group again is divided into two sub-groups, one with 13 genotypes and the other with 11 genotypes. The highest similarity coefficient was detected in a genotype collected from southern India and the least from northern India. The genotypes of finger millet collected from diverse agroclimatic regions of India constitute a wide genetic base. This is helpful in breeding programs and a major input into conservation biology of cereal crop.     

Development and Evaluation of a Genome-Wide 6K SNP Array for Diploid Sweet Cherry and Tetraploid Sour Cherry

High-throughput genome scans are important tools for genetic studies and breeding applications. Here, a 6K SNP array for use with the Illumina Infinium® system was developed for diploid sweet cherry (Prunus avium) and allotetraploid sour cherry (P. cerasus). This effort was led by RosBREED, a community initiative to enable marker-assisted breeding for rosaceous crops. Next-generation sequencing in diverse breeding germplasm provided 25 billion basepairs (Gb) of cherry DNA sequence from which were identified genome-wide SNPs for sweet cherry and for the two sour cherry subgenomes derived from sweet cherry (avium subgenome) and P. fruticosa (fruticosa subgenome). Anchoring to the peach genome sequence, recently released by the International Peach Genome Initiative, predicted relative physical locations of the 1.9 million putative SNPs detected, preliminarily filtered to 368,943 SNPs. Further filtering was guided by results of a 144-SNP subset examined with the Illumina GoldenGate® assay on 160 accessions. A 6K Infinium® II array was designed with SNPs evenly spaced genetically across the sweet and sour cherry genomes. SNPs were developed for each sour cherry subgenome by using minor allele frequency in the sour cherry detection panel to enrich for subgenome-specific SNPs followed by targeting to either subgenome according to alleles observed in sweet cherry. The array was evaluated using panels of sweet (n = 269) and sour (n = 330) cherry breeding germplasm. Approximately one third of array SNPs were informative for each crop. A total of 1825 polymorphic SNPs were verified in sweet cherry, 13% of these originally developed for sour cherry. Allele dosage was resolved for 2058 polymorphic SNPs in sour cherry, one third of these being originally developed for sweet cherry. This publicly available genomics resource represents a significant advance in cherry genome-scanning capability that will accelerate marker-locus-trait association discovery, genome structure investigation, and genetic diversity assessment in this diploid-tetraploid crop group.     

RAPD and essential oil characterization of Turkish basil (Ocimum basilicum L.)

Sweet basil (Ocimum basilicum L., Lamiaceae), an important medicinal plant and culinary herb due to its delicate aroma and fragrance, shows great variation in both morphology and essential oil components. Genetic variation among basil accessions in Turkey has not been extensively examined with molecular markers. Genetic diversity was determined using random amplified polymorphic DNA (RAPD) markers of 14 genotypes of basil. A total of 375 bands were obtained from the RAPD analysis, and 273 of them (70.3 %) were polymorphic. The RAPD analysis allowed the grouping of samples into two main clusters. Genetic similarity values among the basil genotypes ranged between 0.46 and 0.87. Considerable genetic diversity was determined among basil genotypes. Essential oils were obtained by hydro-distillation and were characterized by gas chromatography. A total of 17 chemical components were identified. The evaluated genotypes of O. basilicum can be classified into seven chemotypes: (1) Linalool (7, 12, 16, 22, 25A and 33), (2) Methyl chavicol (6, 10A), (3) Citral/methyl chavicol (10L, 17), (4) Methyl eugenol (11), (5) Methyl cinnamate/linalool (23), (6) Linalool/methyl eugenol (25K), and (7) Methyl chavicol/linalool (Let). The chemical variability obtained from the essential oil composition of the genotypes in the study was remarkable. The chemical characterization of genotypes 10L and 17 was rich in citral (42.17 and 44.80 %) and methyl chavicol (30.56 and 32.03 %). Citral/methyl chavicol can be assessed as a new chemotype of basil cultivated in Turkey. The basil genotypes were grouped into two major clusters for both the RAPD analysis and chemical characterization with very few exceptions (genotype n. 6). A correlation analysis of the genetic distance matrix and the Euclidian distance matrix showed relatively low values (r = ?0.40). The results demonstrated a certain degree of correspondence between chemical and molecular data.     

Miscanthus: Genetic Diversity and Genotype Identification Using ISSR and RAPD Markers

Due to the limited number of molecular studies focused on European gene pool investigation, it is necessary to perform plant material recognition. Eighteen accessions of three Miscanthus species, namely, M. × giganteus, M. sinensis, M. sacchariflorus were evaluated with the use of molecular marker systems such as: inter simple sequence repeats (ISSRs), random amplified polymorphic DNA (RAPD), and by estimation of ploidy level based on flow cytometry. As a result, only one ISSR primer (ISSR1) and three RAPD primers (RAPD1, RAPD2, RAPD4) were required to identify all genotypes. Moreover, the use of the above mentioned molecular markers enable the proper species recognition of the interspecific hybrid M. × giganteus “Floridulus,” which has been previously mislabeled as M. floridulus. The highest genetic similarity coefficient (0.94) was observed between M. × giganteus clones, which indicates that the genetic diversity within this species was very low. Whereas M. sinensis genotypes represented a relatively wide diversity with similarity coefficient of 0.58. Cluster analysis using UPGMA grouped the 18 accessions in three clusters according to species affiliation including relabeled M. × giganteus “Floridulus,” which proved to be closely related to M.  × giganteus. Similar groupings were evident in the PCoA analysis.     

Analysis of genetic stability of in vitro propagated potato microtubers using DNA markers

The genetic stability of in vitro propagated potato microtubers was assessed using random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR), simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers. Microtubers were developed through in vitro from potato microplants using standardized protocols. The microtubers were conserved for 1 year under three different culture media and consequently microplants were regenerated for the DNA analyses. During the study, a total of 38 (10 RAPD, 11 ISSR, 12 SSR and 5 AFLP) primers produced a total of 407 (58 RAPD, 56 ISSR, 96 SSR and 197 AFLP) clear, distinct and reproducible amplicons. Cluster analysis revealed 100 % genetic similarity among the mother plant and its derivatives within the clusters by SSR, ISSR and RAPD analyses, whereas AFLP analysis revealed from 85 to 100 % genetic similarity. Dendrogram analysis based on the Jaccard’s coefficient classified the genotypes into five clusters (I–V), each cluster consisting of mother plant and its derivatives. Principal component analysis (PCA) also plotted mother plant and its genotypes of each cluster together. Based on our results, it is concluded that AFLP is the best method followed by SSR, ISSR and RAPD to detect genetic stability of in vitro conserved potato microtubers. The in vitro conservation medium (T2) is a safe method for conservation of potato microtubers to produce true-to-type plans.     

Genetic diversity of Persian shallot (Allium hirtifolium Boiss.) populations based on morphological traits and RAPD markers

Mooseer or Persian shallot (Allium hirtifolium Boiss.) is a bulbous perennial herb belonging to Alliaceae family. Genetic diversity of 16 mooseer populations collected from different parts of Iran were evaluated using 14 morphological traits as well as antioxidant activities and RAPD markers. Statistical analysis showed significant differences among populations for all morphological traits. In a principal component analysis, four components showed 77.5 % of the total morphological variation. Based on the morphological traits, populations were divided into five groups by clustering. Antioxidant capacities differed among all populations, with the Sahneh and Nahavand populations having the highest and the lowest activities, respectively. Genetic diversity of populations was also investigated through RAPD technique using 14 random primers. Cluster analysis based on RAPD markers plus 47 % coefficient of similarity divided the genotypes into six distinct groups. The highest and lowest similarities between populations were detected to be 0.63 and 0.21, respectively. These results indicated that the assessment of genetic diversity in Iranian mooseer populations could be appropriately carried out using RAPD technique which correlates with morphological traits.     

Genetic diversity of <Emphasis Type="Italic">Pistacia khinjuk</Emphasis> Stocks. using RAPD markers and leaf morphological characters

The aim of this research was to study the genetic diversity of Pistacia khinjuk Stocks. and also to reveal the genetic relationships. Leaf morphological characters of 16 genotypes together with Randomly Amplified Polymorphic DNA (RAPD) marker data were used for this purpose. Leaf morphological characters were used for factor analysis, which determined four main factors. Grouping of genotypes by these factors was performed by Ward’s method. Fifteen primers produced a total of 146 fragments, with an average of 9.73 fragments per primer, of which 129 were polymorphic. The unweighted pair group method based on arithmetic average (UPGMA) analysis was performed on Jaccard’s similarity coefficient matrix. According to RAPD data, genotypes were separated into three groups. The first contained the genotypes with round leaflets. Genotypes with three lanceolate leaflets were located in the second and third groups, respectively. This study revealed that high diversity exists among genotypes of P. khinjuk, like in P. vera. Also it could be postulated that genotypes of P. khinjuk with oblique and lanceolate leaflets are probably descendents of the genotypes with acuminate and roundish leaflets.     

Microsatellite marker-based genetic diversity analysis of elite lentil lines differing in grain iron and zinc concentration

Trial comprising fifty lentil genotypes was conducted at three locations in India during year 2013–2014 for estimation of grain Fe and Zn concentrations and to analyze G × E interactions by employing the additive main effect and multiplication interaction model. The study revealed significant effects for genotype, environment and genotype by environment interaction for both grain Fe and Zn concentration. In this model genotypes with the IPCA score of nearly zero and mean greater than grand mean are considered as adaptable to the studied environments. For grain Fe concentration genotypes P13143, P13135, ILL2581, P2130, LL147, L4603, PL101 and Globe mutant and for grain Zn concentration genotypes P13122, P2239, P3204 and L11-245 were found stable. The diversity analysis using 20 genomic and 54 EST-SSR markers indicated that the studied genotypes were diverse. The EST-SSRs revealed lower polymorphism as compare to genomic SSRs. Two major clusters were identified with 37 % similarity. Indigenous genotypes were grouped in cluster I and all exotic accessions were grouped in cluster II indicating the role of geographic origin in diversity. Based on multi location evaluation for grain Fe and Zn concentrations and molecular characterization crosses are proposed for development of grain Fe and Zn rich varieties (P3220 × L4649 and VL103 × P2130) and development of mapping populations (P13122 × L11-287 and LL931 × P3220) for study of genetics and mapping of QTLs/gene(s).     

Assessment of genetic diversity in Lepidium sativum (Chandrasur) a medicinal herb used in folklore remedies in India using RAPD

Lepidium sativum L. is a fast growing edible herb which belongs to family Brassicaceae. The seeds of L. sativum are aperient, diuretic, tonic, demulcent, carminative, galatogogue and emmenagogue. They have been used in the treatment of bacterial and fungal infections, as an aperient and also possess antibacterial and antifungal properties. The seeds of this plant possess rapid bone fracture healing ability. Despite of its diverse medicinal properties no molecular data for diversity analysis is available till date. During this study random amplified polymorphic DNA (RAPD) markers were used to detect genetic variations of L. sativum. Initially 50 decamer primers were screened, out of which only 32 primers showed reproducible fragments with easily recordable bands. A total of 414 reproducible and clear bands were distinguished across the selected primers and statistical analysis showed 361 polymorphic bands and 53 monomorphic bands. Cluster analysis of the genotypes based on UPGMA divided the 18 genotypes into two main clusters, with first cluster having only HCS-20 genotype of L. sativum and other having rest of all 17 genotypes. The dendrogram based on similarity matrix revealed 23–66% genetic relatedness among 18 genotypes. The results of the present study can be used for molecular breeding and improvement of L. sativum for various desired traits through hybridization in future.     

Nuclear and chloroplast DNA variability and phylogeny of Iranian apples (Malus domestica)

This study was conducted to reveal genetic diversity among 23 local apple genotypes using nuclear (RAPD) and chloroplast DNA (PCR-cpRFLP) markers. Eleven RAPD primers and four cpDNA primer combinations were used in this study. RAPD primers produced a total of 77 polymorphic fragments with an average of seven bands per primer. The percentage of polymorphic bands (68.14 %) showed the efficiency of used RAPD primers in distinguishing all the genotypes considered. Genetic similarity between studied genotypes varied from 0.38 to 0.72 and cluster analysis showed the abundant diversity, indicating high intraspecific genetic variation between Iranian apple genotypes. From the four universal chloroplast primer pairs, three primer pairs amplified the fragments and their combinations showed polymorphic patterns and revealed intraspecific chloroplast variation. The information will facilitate germplasm identification, conservation and new cultivar development.