Conserved DNA-derived Polymorphism Research Articles

Molecular Variation in Some Taxa of Genus Astragalus L. (Fabaceae) in the Iraqi Kurdistan Region

Astragalus L. is one of the main genera of blossoming plants, and its diversity of species and forms is well known. The Astragalus L. taxa make a significant contribution to the mountainous and steppe ecosystems of the Kurdistan region of Iraq. Although the species within this genus have been the subject of several molecular studies, the evolutionary relationships among these species remain unidentified. Despite extensive research, little is known about the phylogenetic relationships among the various subgenera of Astragalus. This research is intended to investigate the molecular variation of 33 species of the genus Astragalus L. found in the Kurdistan area of Iraq. For molecular validations, three separate techniques (nuclear ribosomal DNA (rDNA), inter simple sequence repeats (ISSR), and conserved DNA-derived polymorphism (CDDP)) were used. With respect to Astragalus L. indentations, universal ITS1 and ITS4 gene sequencing was used, and the discovered sequences were subjected to BLAST searches in the NCBI database. A phylogenetic tree was generated with two main clades. Regarding detecting genetic diversity between the taxa, 24 molecular markers (14 ISSR and 10 CDDP) were used. High values of polymorphic materials and gene diversity were detected. ISSR markers had an average of 22.71 polymorphic bands per primer, while CDDP markers had the highest mean values for polymorphic information content (0.37), Shannon’s information index (0.27), expected heterozygosity (0.19), and unbiased expected heterozygosity (0.23). Cluster and principal coordinate analyses divided the Astragalus L. taxa into four main groups using the two molecular data sets. According to the results of the molecular variance analysis, the highest variation was detected within sections, with values of 92.01 and 89.48% for ISSR and CDDP markers, respectively. These outcomes suggest the effectiveness of molecular markers and the ITS region in determining and identifying genetic correlations between Astragalus species.

Assessment of genetic variation and population structure in Iraqi barley accessions using ISSR, CDDP, and SCoT markers

The objective of this study was to investigate the diversity of 59 accessions of barley using inter simple sequence repeat (ISSR), conserved DNA-derived polymorphism (CDDP), and start codon targeted (SCoT) markers. A total of 391 amplified polymorphic bands were generated using 44 ISSR, 9 CDDP, and 12 SCoT primers that produced 255, 35, and 101 polymorphic bands, respectively. The average values of gene diversity were 0.77, 0.67, and 0.81 for ISSR, CDDP, and SCoT markers, respectively. The mean values of polymorphism information content for ISSR, CDDP and SCoT markers were 0.74, 0.63, and 0.80 respectively. The discrimination power of the three approaches for assessing allelic diversity in barley accessions ranked as follows: SCoT > ISSR > CDDP. The barley accessions were classified and clustered into two main groups. Molecular variance analysis revealed 15, 9, and 14% variability among populations with ISSR, CDDP, and SCoT markers, respectively. The Mantel test results revealed that the three molecular marker matrices had significant positive relationships. The SCoT markers might be useful tools for selecting appropriate parents for a breeding program.

Colchicine-mediated in vitro polyploidization in gerbera hybrid.

An efficient in vitro protocol for high-frequency polyploidization for the first time in gerbera hybrid (BGC-2019-01) was developed in the present study. Two-week-old in vitro-developed shoots (tips) were treated individually with 0.1%, 0.25% and 0.5% (w/v) colchicine solutions for 4, 6, 8, and 12h. The colchicine-treated shoot tips were then inoculated on Murashige and Skoog (MS) medium fortified with 1.5mg/l meta-Topolin for multiple shoot proliferation and later transferred into 1.5mg/l indole-3-acetic acid-fortified MS medium for rooting of shoots. The ploidy levels of the colchicine-treated and regenerated plantlets along with the non-treated oneswere confirmed via flow cytometry analysis and metaphasic chromosome count. The highest frequency oftetraploid plantlets (50%) were obtained when shoot tips were treated with 0.1% colchicine for 4h. Morphological observations revealed that inducedtetraploidplantlets exhibited delayed fresh shoot initiation, fewer but longer shoots, as well as fewer but broader leaves. Likewise, the studyof stomata revealed that in comparison to their diploid counterparts, the tetraploidplantlets exhibited less frequent yet significantly larger stomata, and higher number of chloroplasts. The tetraploids were recorded with significantly higher chlorophyll, carotenoid, and anthocyanin content during the photosynthetic pigment analyses. During ex vitro acclimatization and field growth, the tetraploid plants exhibited delayed proliferation but with higher vigor and thickened broad leaves. The genetic uniformity among the diploid and the tetraploidplants was confirmed using conserved DNA-derived polymorphism(CDDP), directed amplification of minisatellite-region DNA(DAMD), inter simple sequence repeats(ISSR), and start codon targeted(SCoT) polymorphism marker systems. The tetraploids developed in the present study would be of immense importance for the genetic improvement of gerbera as far as its ornamental values are concerned.

Assessment of Genetic Diversity of the Medicinal and Aromatic Crop, Amomum tsao-ko, Using PAAP and CDDP Markers

Amomum tsao-ko (Zingiberaceae) is a well-known medicinal and aromatic crop with a long history of cultivation in China. Food and pharmaceutical industries widely use its dried ripe fruit. In this study, 12 promoter anchored amplified polymorphism (PAAP) primer pairs and 12 conserved DNA-derived polymorphism (CDDP) primers were used to assess the genetic diversity and population structure of 96 A. tsao-ko accessions from eight cultivated populations. A total of 98 polymorphic loci were detected by 12 PAAP primers with 8.167 polymorphic loci per primer, and 203 polymorphic loci were observed using 12 CDDP primers with 16.92 alleles per primer. Nei’s gene diversity (PAAP, H = 0.207; CDDP, H = 0.188) and Shannon’s information index (PAAP, I = 0.329; CDDP, I = 0.305) revealed the relatively high level of genetic diversity in these populations of A. tsao-ko. The genetic differentiation coefficient (Gst) for the populations was 0.151 (PAAP) and 0.128 (CDDP), which indicated that 84.9% and 87.2%, respectively, of the genetic variation was within populations. Analysis of molecular variance (AMOVA) also revealed that genetic differentiation of the A. tsao-ko populations mainly occurred within populations (91% variation within populations for both PAAP and CDDP). Genetic identity among the investigated populations was high for PAAP (0.957) and CDDP (0.967). Cluster and principal coordinate analysis (PCoA) grouped the 96 A. tsao-ko accessions into two major groups. Accession classification was consistent with population structure analysis. Overall, these results will be useful for A. tsao-ko germplasm resource characterization, conservation, and utilization.

Analysis of Biochemical and Genetic Variability of Pleurotus ostreatus Based on the β-Glucans and CDDP Markers.

Oyster mushroom (Pleurotus ostreatus) is still one of the most cultivated edible and medicinal mushrooms. Despite its frequent cultivation around the world, there is currently just a little information available on the variability of strains in terms of the content of β-glucans in them. This work presents an extensive study of 60 strains in terms of the content of α-glucans and β-glucans in their caps and stipes. The authenticity of the production strains based on an analysis of the variability of their genome by CDDP (Conserved DNA-derived polymorphism) markers was confirmed, whereas identical CDDP profiles were identified between samples 45, 89, 95, and 96. Genetic variability of the analyzed production strains showed a high polymorphism and effective discriminative power of the used marking technique. Medium positive correlations were found among the CDDP profiles and β-glucan content in the group of strains that generated the same CDDP profiles, and low negative correlation was found among these profiles in the group of low β-glucan content strains. For the determination of glucans content, Mushroom and Yeast analytical enzymatic kit (Megazyme, Bray, Co. Wicklow, Ireland) were used. The results clearly showed that the stipe contains on average 33% more β-glucans than the cap. The minimum detected β-glucan content in the stipe was in strain no. 72, specifically 22%, and the maximum in strain no. 43, specifically 56%, which after the conversion represents a difference of 155%. From the point of view of β-glucan content, the stated strain no. 43 appears to be very suitable for the commercial production of β-glucans under certain conditions.

CDDP and ISSR markers-assisted diversity and structure analysis in Iraqi Mazu (Quercus infectoria Oliv.) accessions

Mazu, or oak gall (Quercus infectoria Oliv.), a member of the Fabaceae family, is an abundant tree species in Iraq. Because of ongoing habitat damage, this species is on the verge of extinction. However, the genetic diversity of wild oak populations has yet to be measured. Semi-arbitrary [Inter-simple sequence repeat (ISSR)] and gene-targeted [Conserved DNA derived polymorphism (CDDP)] markers were employed separately or in combination to investigate genetic diversity within and among 85 Iraqi Mazu (Q. infectoria) accessions based on geographic origin. A total of 88 polymorphic alleles were produced in this investigation utilizing nine CDDP primers, with an average of 9.78 alleles per primer. The mean values for the major allele frequency (MAF), polymorphism information content (PIC), and marker index were 0.23, 0.29, and 2.79, respectively. Twenty ISSR primers were used to amplify 195 alleles (9.75 bands per primer), with MAF, PIC, and MI values of 0.21, 0.28, and 2.72, respectively. All accessions were divided into two major groups with multiple sub-groups based on Ward clustering and structure analysis. Within-population variance was calculated to be 94.17% using CDDP markers and 92.97% using ISSR markers. As per the fixation index values derived from the STRUCTURE analysis, there was a significant difference within the population. Increased gene flow was found among populations. The correlation (r) between the CDDP-based genetic distance matrix and the ISSR-based genetic distance matrix was 0.54, with a p-value of 0.001. The genetic dissimilarity calculated by CDDP and ISSR data revealed a wide range of diversity, demonstrating substantial genetic variation across accessions originating from various populations. This investigation’s findings could aid in the conservation and further utilization of oak germplasm.

Physiological variation of irradiated red radish plants and their phylogenic relationship using SCoT and CDDP markers

Greenhouse experiment is carried out to explore the outcome of γ-radiation on physiological and genetic variation in red radish (Raphanus sativus) for two generations. Gamma rays from 60Co were used to penetrate red radish seeds with different dose levels (0.0, 10, 20, 40 and 80 Gy). Plants generated from irradiated seeds and from self-pollination of these plants, called M1 and M2 generations, respectively. Some morphological and physiological traits were then determined, and the genetic diversity of both generations was studied using Start Codon Targeted (SCoT) and Conserved DNA-Derived Polymorphism (CDDP) molecular markers. All studied morphological traits (number of leaves/plants, leave height, root diameter, and root weight) were steadily improved by raising irradiation dose rate, reaching a cumulative raise at the irradiation doe level 40 Gy and decreased at dose level 80 Gy. Photosynthetic pigments of red radish plants released a notable increase by increasing gamma rays dose level for chlorophyll (a), chlorophyll (b) and carotenoids for 40 Gy dose rate. Proline content was elevated proportionally to the irradiation dose level, with the greatest increase seen at dose level of 80 Gy. Moreover, phytochemical screening was detected for the both two generations. Fourteen SCoT primers generated a total number of banding patterns of 194 with average 13.86 and the primer SCoT-33 released the highest number banding patterns (21). The percentage mean of polymorphism for all the SCoT primers was 74.66% and was 66.49 and 63.74% for M1 and M2 respectively. Furthermore, fifteen CDDP primers generated a total number of banding patterns of 186 and the primer CDDP-5 relieved the highest number of banding patterns (20). The percentage mean of polymorphism for all the CDDP primers was 73.41% and was 64.38 and 65.91% for M1 and M2 respectively. It could be concluded that gamma irradiation exhibited an appropriate variation in red radish M1 and M2 which was detected by SCoT and CDDP molecular markers.

Genetic Diversity and Population Assessment of Musa L. (Musaceae) Employing CDDP Markers

Sixty-six accessions of Musa genus with different genomic groups that consisted of wild relatives and cultivated lines were obtained from the International Transit Center, Belgium, for DNA extraction using Cetyl trimethylammonium bromide method, followed by amplification with Conserved DNA-derived Polymorphism (CDDP) markers for genetic diversity and population assessment. A total of 421 alleles with major allele frequency of 2.051 were detected from the reproducible markers. High genetic diversity (GD, 11.093) and polymorphic information content (0.918) were revealed. The number of polymorphic loci and percentage of polymorphic loci ranged from 59 to 66 and 89.34 to 100, respectively. Using the potential genetic indicators including effective number of alleles, Nei’s genetic diversity, and Shannon’s information index, the AS genomic group was identified to have the highest GD, while the AAA accessions had the lowest GD indices. The GD parameters identified in the accessions were ranked as AS > AAB > AAAA > AA > ABB > wild diploidy > BB > AB > AAA from high to low based on polymorphic loci of the markers. Total intraspecific GD, interspecific GD, and estimate gene flow identified were 0.433, 0.404, and 7.113, respectively. The coefficient of gene differentiation of 0.066 was obtained, indicating 6.57% among the population and 93.43% within the population. Dendrogram analysis produced nine major groups with subgroups at similarity index of 0.814. These CDDP functional gene-based markers were informative and very efficient in resolving GD, and population indices among the banana and plantain accessions of different genomes. The identified CDDP markers might serve as potential tools for selecting suitable training populations for breeding and conservation of Musa species.

Insights into the heat-responsive transcriptional network of tomato contrasting genotypes

AbstractDuring recent decades, global warming has intensified, altering crop growth, development and survival. To overcome changes in their environment, plants undergo transcriptional reprogramming to activate stress response strategies/pathways. To evaluate the genetic bases of the response to heat stress, Conserved DNA-derived Polymorphism (CDDP) markers were applied across tomato genome of eight cultivars. Despite scattered genotypes, cluster analysis allowed two neighbouring panels to be discriminate. Tomato CDDP-genotypic and visual phenotypic assortment permitted the selection of two contrasting heat-tolerant and heat-sensitive cultivars. Further analysis explored differential expression in transcript levels of genes, encoding heat shock transcription factors (HSFs, HsfA1, HsfA2, HsfB1), members of the heat shock protein (HSP) family (HSP101, HSP17, HSP90) and ascorbate peroxidase (APX) enzymes (APX1, APX2). Based on discriminating CDDP-markers, a protein functional network was built allowing prediction of candidate genes and their regulating miRNA. Expression patterns analysis revealed that miR156d and miR397 were heat-responsive showing a typical inverse relation with the abundance of their target gene transcripts. Heat stress is inducing a set of candidate genes, whose expression seems to be modulated through a complex regulatory network. Integrating genetic resource data is required for identifying valuable tomato genotypes that can be considered in marker-assisted breeding programmes to improve tomato heat tolerance.

Gene-targeted molecular phylogeny, phytochemical analysis, antibacterial and antifungal activities of some medicinal plant species cultivated in Egypt.

Medicinal plants have been used in healthcare since time immemorial, as have their therapeutic activities and the production of plant-based medicines. This study aims to use gene-targeted molecular markers for genetic diversity analysis of 16 medicinal plants. Besides, phytochemical analysis antibacterial and antifungal activities of some medicinal plant extracts commonly used in Egypt are compared to major compounds. DNA-based classification of 16 medicinal species using Conserved DNA-Derived Polymorphism (CDDP) and Start Codon Targeted (SCoT) primers. Three species representing three orders (Pelargonium graveolens, Matricaria chamomilla, and Hyoscyamus muticus were analysed [high-performance liquid chromatography (HPLC), gas chromatography-mass spectrometry (GC-MS)] and evaluated for their antibacterial and antifungal activities against (Escherichia coli O157: H7 ATCC 93111, Salmonella typhimurium ATCC 14028, Methicillin-resistant Staphylococcus aureus (MRSA) ATCC 43300, Bacillus ceruse ATCC 33018, and Sclerotinia sclerotiorum in comparison with some of their antimicrobial components. Our results revealed 309 and 349 polymorphic bands with 100% polymorphism. Among them, 51 and 57 were unique loci for CDDP and SCoT, respectively. The 16 species were categorised into three groups depending on the similarity matrix. The results of antibacterial and antifungal activities revealed that Pelargonium oil showed significant antifungal and antibacterial activities against the tested pathogens. Gallic acid severely reduced all tested bacteria's growth, but atropine severely reduced the growth of the B. ceruse only. Molecular modelling revealed their activity against sclerotium development. The gene-targeted marker techniques were highly useful tools for the classification of the 16 medicinal plant species, despite displaying high similarities at morphological and phytochemical analyses but, have antifungal and antibacterial activities.

Genome diversity and population structure analysis of Iranian landrace and improved barley (Hordeum vulgare L.) genotypes using arbitrary functional gene-based molecular markers

Barley (Hordeum vulgare L. subsp. vulgare) is one of the earliest domesticated crop plants, which originated in Fertile Crescent. Genetic diversity analysis in primary gene pool and landraces is an effective strategy for germplasm conservation and utilization in breeding programs. In this study, Eighty-two barley genotypes comprised 22 Iranian improved cultivars and 60 landrace accessions collected from different zones of Iran were assumed for genetic diversity analysis using three gene targeted markers, start codon targeted (SCoT) polymorphism, conserved DNA-derived polymorphism (CDDP) and CAAT box-derived polymorphism (CBDP) in comparison with sequence-related amplified polymorphism (SRAP) markers. A total of 40 primers (10 primers from each marker) detected genetic polymorphism among barley genotypes. Four different marker types showed high level of polymorphism and SRAP markers produced higher number of polymorphic bands (67) in comparisons with SCoT, CDDP and CBDP. Average PIC values for SCoT, CDDP, CBDP and SRAP were 0.33, 0.37, 0.37 and 0.31, respectively. Marker index (MI) in SRAP and CBDP markers was higher than SCoT and CDDP markers. Cluster analysis using CDDP, CBDP and SRAP markers grouped barley genotypes in three distinct groups, while SCoT markers divided genotypes in four clusters. There were positive correlations between similarity matrixes obtained by each marker types. The results from cluster analysis and STRUCTURE analysis using combined data grouped barley genotypes in three clusters and the grouping of genotypes was strongly in agreement with their origins. Results showed that genotypes from west and north-west of Iran grouped in distinct clusters from those originated from north-east and center of Iran. To our knowledge, this is the first detailed report of using gene targeted molecular marker for genetic diversity analysis in barley. Our results showed the efficiency of these markers for genetic diversity analysis in barley and their potential for genome diversity and germplasm conservation.

Molecular Assessment of Genetic Stability Using CDDP and DNA-barcoding Assays in Long-term Micropropagated Rose Plant.

Roses are the world's best-known garden plants, established as ornamental plants cultivated for their blooms. Taif rose (Rosa damascena trigintipetala) refers to the Damascus Rose species and is regarded one of Taif Governorate's most significant financial goods, which produces an extremely fragrant commercially precious essential oil. The objective of current study was to assess the genetic stability of micropropagated Taif rose and to assess the usefulness of Conserved DNA Derived Polymorphism (CDDP) and DNA-barcoding genes such as; rpoC1 (chloroplast gene RNA polymerase1) in the detection of somaclonal variation. Ten combinations of CDDP PCR primers were employed and the rpoC1 gene region was sequenced for mother plant (control) and micropropagated plantlets of Taif rose plant. Based on CDDP data, phylogenetic divergence indicated that the distinct specimens of Taif rose micro-propagated plantlets and control were genetically differentiated by a difference of 1% of genetic dissimilarity. Phylogenetic tree which developed using rpoC1 DNA showed that rpoC1 DNA sequencing discovered a genetic difference between the control and micro-propagated plantlets of Taif rose. Furthermore, CDDP and DNA barcoding using rpoC1 gene have demonstrated their usefulness in investigating the genetic history of Rosa species and their ability to explore genetic mutation.

Gene-targeted molecular phylogeny, phytochemical profiling, and antioxidant activity of nine species belonging to family Cactaceae

Cactaceae plant family comprises over 130 genera and 2000 species of succulent flowering plants. The genera Mammillaria and Notocactus (Parodia), which have medicinal and nutritional applications as well as aesthetic appeal, are considered to be among the major genera of the family. Several species of both genera show morphological and chemical similarities and diversities according to environmental conditions and genotypes. Here, we assessed the genetic relationships of nine species belonging to two major genera Mammillaria and Notocactus under the family Cactaceae, using two modern gene-targeting marker techniques, the Start Codon Targeted (SCoT) Polymorphism and the Conserved DNA-Derived Polymorphism (CDDP). Besides, we screened the various phytochemicals and evaluated the antioxidant activities of the nine species of cacti. Five out of the 10 SCoT and eight CDDP primers used to screen genetic variations within the nine species yielded species-specific reproducible bands. The entire 156 loci were detected, of which 107 were polymorphic, 26 were monomorphic, and 23 were unique loci. The nine species were categorized into two groups based on the dendrogram and similarity matrix. Phytochemical profiling revealed that sterols, triterpenes, flavonoids, and tannins were found in all the tested species. Additionally, two Notocactus species (N. shlosserii and N. roseoluteus) and one Mammillaria species (M. spinosissima) revealed a considerable antioxidant activity. Our results demonstrated that gene-targeting marker techniques were highly powerful tools for the classification and characterization of the nine investigated species, despite displaying high similarities at both morphological and phytochemical levels.

Conserved DNA-derived polymorphism, new markers for genetic diversity analysis of Tunisian Pistacia vera L.

Pistachio trees (Pistacia vera L.) have been cultivated in Tunisia for decades and the plantation was extended mostly in the center of the country contributing to the economic growth of marginalized areas. Herein we used conserved DNA derived polymorphism (CDDP) technique, which target specifically conserved sequences of plant functional genes, to assess the genetic diversity and construct genetic relationships among 65 Tunisian pistachio trees. A set of nine primers were used and 157 CDDP markers were revealed with an average of 17.44 showing a high degree of polymorphism (99.37%). The average of polymorphism information content of CDDP markers was of 0.86, which indicates the efficiency of CDDP primers in the estimation of genetic diversity between pistachios. UPGMA dendrogram and the principal component analysis showed four clusters of analyzed pistachios trees. Our results showed that the genetic structure depends on: (1) the gene exchanges between groups, (2) the geographical origin and (3) the sex of the tree. The same result was revealed by the Bayesian analysis implemented in STRUCTURE at K = 4, in which the pistachio genotypes of El Guettar, Kasserine and Sfax were assigned with more than 80% of probability. Our results prove polymorphism and efficiency of CDDP markers in the characterization and genetic diversity analysis of P. vera L. genotypes to define conservation strategy.

Comparison of Genetic Variation of Anthurium (Anthurium andraeanum) Cultivars Using SCoT, CDDP and RAPD Markers

To evaluate the genetic diversity among 10 cultivars of anthurium were performed using three molecular markers such as Start Codon Targeted (SCoT) and Conserved DNA-derived Polymorphism (CDDP), and Random Amplification of Polymorphic DNA (RAPD). Polymorphism index content (PIC) was calculated 0.39, 0.42 and 0.37 for RAPD, SCoT and CDDP, respectively. This result showed all the three molecular markers had almost an identical potential in estimating genetic diversity. Cluster analysis using SCoT, CDDP and RAPD divided the cultivars to three distinct clusters. The similarity matrix obtained through SCoT and CDDP was positively significantly correlated (r = 0.76, p < 0.01). This is the first report in which the efficiency of two targeted DNA region molecular markers (SCoT and CDDP) together with RAPD technique have been compared with each other in a set of anthurium cultivras. Results suggested that SCOT, CDDP and RAPD fingerprinting techniques are of sufficient ability to detect polymorphism in anthurium cultivars.
 Plant Tissue Cult. & Biotech. 28(2): 171-182, 2018 (December)

Genetic diversity and population structure analysis of landrace and improved safflower (Cartamus tinctorious L.) germplasm using arbitrary functional gene-based molecular markers

The genetic diversity and relationships among 48 landrace and improved safflower (Carthamus tinctorius L.) genotypes were analyzed using three gene-targeted markers, start codon-targeted (SCoT) polymorphism, conserved DNA-derived polymorphism (CDDP) and CAAT box-derived polymorphism (CBDP). A total of 30 primers (10 primers from each marker) detected genetic polymorphism among the safflower genotypes. Three different marker types showed high level of polymorphism and the CDDP markers produced a higher number of polymorphic bands (74) in comparisons with SCoT and CBDP. The average PIC values for SCoT, CDDP, and CBDP were 0.39, 0.43, and 0.41, respectively. The marker index (MI) in CDDP markers was higher than that in SCoT and CBDP markers. Cluster analysis using SCoT and CDDP markers grouped the safflower genotypes into three distinct groups, whereas the CBDP markers divided the genotypes into two clusters. There were positive correlations between the similarity matrices obtained by each marker type. The results from the cluster analysis and STRUCTURE analysis using combined data grouped the genotypes into two clusters, generally in agreement with their origins. To our knowledge, this is the first detailed report of using gene-targeted molecular markers for genetic diversity analysis in safflower. Our results showed the efficiency of these markers for genetic diversity analysis in safflower and their potential for genome diversity and germplasm conservation.

Evaluation of genetic diversity of carnation cultivars using CDDP and DAMD markers and morphological traits

This study was aimed to evaluate genetic diversity using molecular markers and morphological traits in carnation, Dianthus caryophyllus (fam: Cryophyllaceae) widely grown as an ornamental. Fifteen cultivars were examined employing seven Conserved DNA-derived Polymorphism (CDDP) and seven Directed Amplification of Minisatellite DNA (DAMD) markers. These varieties were planted in a randomized complete block design in three replicates at the experimental farm of the National Institute of Ornamental Plants, Mahallat, Iran. Analysis of variance for morphological traits showed significant differences among the examined cultivars. Morphological traits such as flower longevity, flower diameter and number of branches were statistically significant at 1 percent probability level. CDDP and DAMD markers produced an average polymorphic index content of 0.38 and 0.29 for CDDP and DAMD markers, respectively. Genetic distance matrix ranged from 0.02 to 0.84 in CDDP and from 0.09 to 0.78 in DAMD marker analysis. Cluster analysis for the two markers revealed that cultivars were grouped in three clusters. Results of molecular evaluation showed that CDDP and DAMD markers have high ability to differentiate carnation cultivars through assessment of the genetic diversity.

Analysis of genetic relationships in Rosa rugosa using conserved DNA-derived polymorphism markers

ABSTRACTThe genetic diversity and relationships among populations of Chinese-endemic rugged rose (Rosa rugosa) were studied at the molecular level, to provide theoretical guidance and technical support for the scientific evaluation, preservation and development of the germplasm resources of this endangered species. DNA samples of 120 specimens of R. rugosa, originating from six different Chinese source populations were amplified with CDDP (conserved DNA-derived polymorphism) primers. A total of 121 polymorphic loci out of the 128 total bands (94.53%) were recovered using 13 informative and reliable primers. The average number of amplified bands per primer was about 9.84. The number of specific bands was 8, accounting for 6.25%. Nei's gene diversity (H), Shannon's information index (I) and the effective number of alleles (Ne) were 0.3057, 0.4646 and 1.5131, respectively. A UPGMA (unweighted pair group method with arithmetic mean) cluster analysis suggested that these populations of rugged rose could be divided into six major groups, with a similarity coefficient of 0.81. Here we show that the CDDP marker technique can effectively reveal the genetic diversity among Chinese-endemic populations of the rugged rose. Based on the results from the cluster analysis, we suggest that although the population genetic structure mirrors the geographic structure to some extent, it is clear that other factors besides geographic distance contribute to the generation of genetic variation.

Genetic Diversity Analysis among Fennel Genotypes Employing Gene Targeted Molecular Markers, CAAT-Box Derived Polymorphism (CBDP) and Conserved DNA Derived Polymorphism (CDDP) Markers

Genetic diversity analysis was carried out in 14 varieties of Foeniculum vulgare by using CAAT-box derived polymorphism (CBDP) and conserved DNA derived polymorphism (CDDP) markers. DNA was isolated from young leaves followed by a standard CTAB method. A total of 25 CBDP primers were screened to study the diversity and with all 25 primers were amplifying reproducible bands, and 21 CDDP primers were screened, out of which 20 primers could show amplification. A part of that CDDP 17 primer could not amplify reproducible bands. Which produced a total of 222 bands (8.0 bands per primer), of which 151 were polymorphic. The analysis revealed 66.14% polymorphism for CBDP.CDDP analysis produced a total of 258 bands (12.0 bands per primer), of which 148 were polymorphic. The analysis revealed 56.18% polymorphism. The polymorphism was the maximum (100%) with primer CBDP 24 and the lowest (12.5%) with primer CBDP-11. Similarly, the polymorphism was the maximum (92.30%) with primer CDDP 08 and the lowest (0%) with primers CDDP 10 and CDDP 13. All the CBDP and CDDP primers generated polymorphic markers in fennel cultivars, and an UPGMA dendrogram based on Jaccard's similarity grouped. Interestingly, they could potentially be exploited in other species as well for assessing genetic diversity, cultivar identification, construction of linkage map, and markerassisted selection.

Development of Sex-Specific PCR-Based Markers in Date Palm.

Molecular markers are used efficiently in the development and identification of gender-specific PCR-based markers in date palm. There is mounting evidence that different marker systems vary in their mechanisms of detecting polymorphism and genome coverage. Therefore, they could complement each other to generate accurate sex-specific markers in date palm. This chapter describes the uses of PCR-based molecular markers to develop and identify the gender in different date palm genotypes; these are amplified fragment length polymorphism (AFLP), start codon targeted polymorphism (SCoT), conserved DNA-derived polymorphism (CDDP), intron-targeted amplified polymorphism (ITAP), and random amplified polymorphic DNA (RAPD). Also described is how to characterize the identified markers by Sanger sequencing and to explore their functions through alignment of their sequences with the Genbank databases.