Genetic diversity and relationships of medicinal Chrysanthemum morifolium revealed by start codon targeted (SCoT) markers

2016 ◽  
Vol 201 ◽  
pp. 118-123 ◽  
Author(s):  
Shang-Guo Feng ◽  
Ren-Feng He ◽  
Meng-Ying Jiang ◽  
Jiang-Jie Lu ◽  
Xiao-Xia Shen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Chrysanthemum Morifolium ◽  
Start Codon

scholarly journals Molecular diversity analysis in hexaploid wheat (Triticum aestivum L.) and two Aegilops species (Aegilops crassa and Aegilops cylindrica) using CBDP and SCoT markers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Ghazal Ghobadi ◽  
Alireza Etminan ◽  
Ali Mehras Mehrabi ◽  
Lia Shooshtari
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Crop Improvement ◽  
Wild Relatives ◽  
Resolving Power ◽  
Start Codon ◽  
Aegilops Cylindrica ◽  
Aegilops Crassa

Abstract Background Evaluation of genetic diversity and relationships among crop wild relatives is an important task in crop improvement. The main objective of the current study was to estimate molecular variability within the set of 91 samples from Triticum aestivum, Aegilops cylindrica, and Aegilops crassa species using 30 CAAT box–derived polymorphism (CBDP) and start codon targeted (SCoT) markers. Results Fifteen SCoT and Fifteen CBDP primers produced 262 and 298 fragments which all of them were polymorphic, respectively. The number of polymorphic bands (NPB), polymorphic information content (PIC), resolving power (Rp), and marker index (MI) for SCoT primers ranged from 14 to 23, 0.31 to 0.39, 2.55 to 7.49, and 7.56 to 14.46 with an average of 17.47, 0.34, 10.44, and 5.69, respectively, whereas these values for CBDP primers were 15 to 26, 0.28 to 0.36, 3.82 to 6.94, and 4.74 to 7.96 with a mean of 19.87, 0.31, 5.35, and 6.24, respectively. Based on both marker systems, analysis of molecular variance (AMOVA) indicated that the portion of genetic diversity within species was more than among them. In both analyses, the highest values of the number of observed (Na) and effective alleles (Ne), Nei’s gene diversity (He), and Shannon’s information index (I) were estimated for Ae. cylindrica species. Conclusion The results of cluster analysis and population structure showed that SCoT and CBDP markers grouped all samples based on their genomic constitutions. In conclusion, the used markers are very effective techniques for the evaluation of the genetic diversity in wild relatives of wheat.

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

2018 ◽  
Vol 28 (2) ◽  
pp. 171-182 ◽  
Author(s):  
Abbas Saidi ◽  
Zahra Daneshvar ◽  
Zohreh Hajibarat
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variation ◽  
Molecular Markers ◽  
Rapd Markers ◽  
Start Codon ◽  
Similarity Matrix ◽  
Random Amplification ◽  
Anthurium Andraeanum ◽  
Rapd Polymorphism

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 variation between and within two populations of Rhabdocline pseudotsugae in Germany

2016 ◽  
Vol 46 (5) ◽  
pp. 716-724 ◽  
Author(s):  
Kristin Morgenstern ◽  
Jens-Ulrich Polster ◽  
Doris Krabel
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Spatial Distribution ◽  
Pseudotsuga Menziesii ◽  
Early Stage ◽  
Start Codon ◽  
Fruiting Bodies ◽  
Clear Differentiation ◽  
High Degree ◽  
Two Populations

Knowledge of the ecology and biology of Rhabdocline pseudotsugae Sydow is still at a very early stage. Recent results indicate the existence of an endophytic stage of the fungus in the form of symptomless infections in various Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) tissue types. This study represents the first description of genetic variation between and within two populations of R. pseudotsugae. Needles featuring fruiting bodies of R. pseudotsugae were collected from sample areas in Saxony and North Rhine-Westphalia (in Germany), with different fungal genotypes distinguished using the start codon targeted polymorphism (SCoT) and branch point signal sequences (BPS) techniques. Five of the 20 primers tested could be selected for further investigation. A total of 349 fragments were amplified at an average of 69.8 fragments per primer. Results showed the two sample areas to exhibit a high degree of both genetic variability and genetic diversity. A clear differentiation between the sample areas was not observed. There was nevertheless a clear connection between the genetic distance and spatial distribution of the fruiting bodies of R. pseudotsugae within the sample areas themselves.

Genetic diversity analysis of Iranian Nigella sativa L. landraces using SCoT markers and evaluation of adjusted polymorphism information content

2015 ◽  
Vol 15 (1) ◽  
pp. 64-71 ◽  
Author(s):  
Khaled Mirzaei ◽  
Ghader Mirzaghaderi
Keyword(s):  
Genetic Diversity ◽  
Information Content ◽  
Polymorphism Information Content ◽  
Nigella Sativa ◽  
Genetic Relationships ◽  
Start Codon ◽  
Discrimination Power ◽  
Black Cumin ◽  
Scot Marker ◽  
Mediterranean Regions

The genetic diversity of 39 Iranian black cumin (Nigella sativa L.) landraces was analysed using 14 polymorphic Start Codon Targeted (SCoT) markers. A total of 106 bands ranging from 3 (for SCoT70) to 13 (for SCoT23) were observed. Of them, 33 (31%) bands were polymorphic with a mean of 1.65 bands per primer. Polymorphism information content (PIC) per primer ranged from 0.035 (for SCoT12) to 0.133 (for SCoT70), with an average of 0.078. Besides PIC, Simpson's diversity (D) index was also calculated for each SCoT marker as an indication of discrimination power across population. The D index was used to adjust the PIC of the SCoT markers. As the adjusted PIC (PICD= PIC × D) was calculated based on both the PIC and the rate of band dispersion, this reflected the informativeness of a dominant marker more precisely than PIC. Genetic relationships were estimated using Jaccard's similarity coefficient-generated values between different pairs of genotypes that varied from 80 to 97% with an average of 88%. These coefficients were applied to construct a dendrogram using the UPGMA algorithm. A high genetic similarity was observed that might be due to the fact that N. sativa is a self-pollinated plant not originated from Iran and might have been imported from the Mediterranean regions.

scholarly journals Analysis of genetic diversity in Prunus sibirica L. in inner Mongolia using SCoT molecular markers

2022 ◽  
Author(s):  
Ha Buer ◽  
Sa Rula ◽  
Zi Yuan Wang ◽  
Shu Fang ◽  
Yu´e Bai
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Genetic Differentiation ◽  
Inner Mongolia ◽  
Start Codon ◽  
Group Method ◽  
Pair Group ◽  
Protection And Utilization ◽  
Minimum Number ◽  
Polymorphic Bands

AbstractPopulation genetic diversity contributes to the protection and utilization of germplasm resources, especially via genetic breeding. In the present study, start codon targeted polymorphism (SCoT) molecular markers were used to study the genetic diversity of 278 individuals from 10 Prunus sibirica L. populations in Inner Mongolia. A total of 289 polymorphic bands were amplified with 23 SCoT primers, showing a polymorphism percentage of 98.87% and an average of 12.6 polymorphic bands per primer. The SCoT21, SCoT32, and SCoT53 primers amplified up to 17 bands, and the polymorphism percentage was 100%. The minimum number of bands amplified by SCoT25 was 9, and the polymorphism percentage was 90%. Therefore, SCoT molecular markers were shown to be highly polymorphic and suitable for genetic diversity studies of P. sibirica in Inner Mongolia. The analysis of molecular variance showed that 39% of the observed genetic differentiation occurred among populations and 61% occurred within populations, indicating that the genetic differentiation within populations was greater than that among populations. The results of the unweighted pair-group method with an arithmetic cluster analysis, principal coordinate analysis and STRUCTURE analysis were basically the same and divided the 278 individuals from the 10 populations into 2 groups. The results indicated that the efficient SCoT molecular marker-based genetic diversity analysis of P. sibirica in Inner Mongolia can provide a reference for P. sibirica variety breeding and resource development.

scholarly journals Universal Rice Primer (URP) and Start Codon Target (SCoT) Markers in Studying Population Structures and Genetic Variation in Ferula AssafoetidaL. Accessions

2021 ◽  
Author(s):  
Reyhane Sadeghi ◽  
Mansour Omidi ◽  
Reza Azizinezhad ◽  
Alireza Etminan ◽  
Hassanali Naghdi Badi
Keyword(s):  
Genetic Diversity ◽  
Economic Value ◽  
Diversity Indices ◽  
High Rate ◽  
Start Codon ◽  
Good Efficiency ◽  
Information Index ◽  
Rich Diversity ◽  
Ferula Assafoetida ◽  
Combined Data

Abstract Ferula assafoetidais an herbaceous, annual and monocarpic genus of the Apiaceae family. So far, there has been common usage of Ferula oleo resinous gum in food and herbal medicines.The origin of F.assafoetidais can be traced back into the steppes of Iran and some reigns of Afghanistan with an extended distribution. Despite the economic value and therapeutic importance of F.assafoetida, only a few studies have reported on the genetic capacity of this herb.The present study was carried out on a set of 90 individual plants belonging to different populations of Ferula assafoetida L. via the start codon target marker (SCoT) and the universal rice primer (URP) markers. Twelve SCoT and twelve URP primers generated 192 and 149 polymorphic fragments, while having 16 and 12.41 fragments respectively on average per primer. The Polymorphism information content (PIC) for URP primers and ScoT ranged from 0.31 to 0.43 and 0.34 to 0.44 respectively, which indicated a good efficiency forboth markers. The diversity indices including heterozygosity (He), percentage of polymorphic bands (PPB), Shannon’s information index (I) and marker index (MI) were calculated based on the SCoT and URP data.The results revealed that SCoT primers were more efficient than URP primers in identifying genetic diversity within populations. Neighbor joining (Nj), as a base for clustering, classified 90 accessions into 5 and 6 groups using SCoT and URP data respectively. Moreover, the combined data (SCoT+URP) succeeded in classifying all accessions into 6 groups, although this did not correspond with the geographical distribution of accessions. Structure analysis divided 90 genotypesinto 5 subpopulations using SCoT and URP markers, whereas the combined data (SCoT+URP) divided the accessions into 6 subpopulations, which confirmed the classification achieved by the Nj method. Principal coordinate analysis (PCoA) corroborated these conclusions. According to the analysis of molecular variance) AMOVA(, a high percentage of genetic diversity was found within the species, suggesting a rich diversity of germplasm for breeding plans. The assessment of population structure demonstrated a high rate of gene flow and the mixture of populations. Taken together, our findings suggest SCoT markers are more efficient than URP markers in assessing genetic diversity among F.assafoetida genotypes. All in all, genetic diversity could help the selection of appropriate markers and special genotypes for breeding plans.

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