CAAT Box-derived Polymorphism Research Articles

Genetic diversity analysis using molecular markers and in vitro shoot regeneration of strawberry cultivars in Lam Dong

In the present study, start codon targeted (SCoT) polymorphism and CAAT box-derived polymorphism (CBDP) molecular markers were used to study the genetic diversity of ten strawberry cultivars. In addition, shoot regeneration from in vitro leaf explants of ten commercial cultivars, i.e Aicyberry, Kayonoka, Tochiotome, Penchika, Amauo, Pajado, Selva, Monterey, Camarosa, and Albion, was also investigated. The result showed that a total of 9 SCoT primers and 9 CBDP primers detected genetic polymorphism among ten strawberry cultivars. Comparatively, SCoT markers proved to be more efficient than CBDP markers in terms of percentage polymorphism as the former detected an average of 74.49% and the latter at 71.15%. Meanwhile, the indices of genetic diversity from the aggregated data of two techniques SCoT and CBDP are as follows: expected heterozygosity (He) 0.2480, Shannon index (I) 0.3749, polymorphic band ratio 75.56%. The highest level of genetic similarity among the cultivars was 0.827 (between Aicyberry and Kayonoka varieties), the lowest was 0.586 (between Aicyberry and Selva varieties), and the average was 0.724. In addition, the results of shoot regeneration of strawberry varieties from leaf discs with different sizes were strongly dependent on the genotype and weakly on explant size. Leaf explants (3 mm in size) of Camarosa cultivar cultured on MS medium supplemented with 7 g/l agar, 30 g/l sucrose and 2 mg/l TDZ gave the best shoot regeneration.

Assessing salinity tolerance and genetic variation in mung bean (Vigna radiata) through CAAT box and SCoT marker analysis

Vigna is a genus of approximately 100 wild species found in tropical and sub-tropical region. The three varieties of green gram (Vigna radiata L.) (VBN3, VBN6 & CO8) was widely cultivated in Tamil Nadu. Soil salinity is a significant issue in food production because excessive salt concentrations in soil inhibit plant development, delaying maturity and reducing crop yield or causing wilting. In the present study, we investigate the effective screening of saline tolerance in green gram, carried out the mechanism of physiological, biochemical and genetic variation using molecular markers of salinity stress of green gram under different concentration of NaCl (control, 50, 100, 150 and 200 mM). The result shows that, the salinity stress significantly reduced the physiological, biochemical and plant growth characteristics. Besides, the gene-targeted like Start Codon Targeted (SCoT) and CAAT box derived polymorphism (CBDP) markers were used to examine the genetic variability under saline stress of green gram. Herein, the SCoT and CBDP primers produced 54 and 90 polymorphic bands with an average of 5.7 and 7.8 bands per primer, respectively. The Analysis of Molecular Variance (AMOVA) and Principal Coordinate Analysis (PCoA) revealed genetic diversity within species was greater than between them, indicating that all of the saline-treated samples from the three varieties displayed genetic variation. The present study concludes that the increased concentration of NaCl reduced the plant growth and significantly affects the physiological, biochemical and genetic variation.

Genetic diversity of Artemisia species based on CAAT-box derived polymorphism (CBDP) and start codon targeted (SCoT) markers

Genetic diversity of Artemisia species based on CAAT-box derived polymorphism (CBDP) and start codon targeted (SCoT) markers

Development of highly discriminatory SCoT- and CBDP-based SCAR fingerprint for authentication of Indian senna (Senna alexandrina Mill.) formerly Cassia angustifolia Vahl.).

Indian senna (Senna alexandrina Mill.) (formerly Cassia angustifolia Vahl.) is an important medicinal plant of the family Fabaceae. The leaves and pods of Indian senna yield sennosides and rhein-based laxative. Adulteration of Indian senna is a serious issue as with most of the medicinal plants used in the Indian systems of traditional medicine. The bulk of dried leaves and pods of morphologically related species, such as Cassia fistula, Senna occidentalis, Senna sophera, and Senna tora, is usually mixed with those of the Indian senna, and the admixture is used in laxative-based formulations. The present investigation is a modest attempt at developing species-specific start codon targeted (SCoT) polymorphism- and CAAT-box-derived polymorphism (CBDP)-based sequence-characterized amplified region (SCAR) markers for the identification and authentication of Indian senna and four adulterant species (C. fistula, S. occidentalis, S. sophera, and S. tora species). In this study, genomic DNA extracted from 44 accessions of Indian senna and four adulterant species was subjected to SCoT and CBDP PCR. The polymorphic amplicons were identified, eluted, ligated, and transformed into Escherichia coli DH5 α strain. PCR, restriction analysis, and DNA sequencing confirmed the transformed recombinant plasmid clones. Post-sequencing, the sequence of the primary SCoT and CBDP primers was analyzed and extended into the unique signature sequence of the concerned accessions. This resulted in development of one SCoT-44- and two CBDP-25-based SCARs. SCoT-44 SCAR produced a signature amplicon of 287 bp for accession DCA120, and CBDP-25 SCAR yielded signature amplicons of 575 and 345 bp for accessions DCA13 and DCA119, respectively. The developed SCAR markers were validated across 48 samples (44 accessions of Indian senna and 4 adulterant species) and produced distinct amplicons in Indian senna only, while no such amplicon was observed in the other four adulterant species. The information generated using these markers have been faithfully converted to single-locus, unequivocal, highly reproducible, and informative sequence-based SCAR markers. These markers will enable discrimination of individual plants on the basis of unique sequence-specific amplicons, which could be used as diagnostic markers to settle issues pertaining to the true identity of Indian senna.

Exploring the efficacy of targeted fingerprinting marker techniques in genetic studies of the Indian poppy (Papaver somniferum L.): A comparative analysis

Targeted fingerprinting marker techniques have emerged as promising tools in plant sciences, particularly in plant breeding. To initiate an effective breeding program for a licit but industrially potential plant, the opium poppy, a comparative assessment of these markers was conducted. In this study, we compared the Start Codon Targeted polymorphism (SCoT), CAAT box-derived polymorphism (CBDP), and Expressed sequence tag-simple sequence repeats (EST-SSRs) markers for their competence and informativeness in revealing genetic identity, relatedness, and diversity among ten released varieties of the Indian opium poppy. Among the markers studied, EST-SSR markers demonstrated higher discriminating power, attributed to their ability to unveil comparatively higher polymorphic information content, marker index, and effective marker index. While all three marker systems effectively discriminated the poppy varieties, EST-SSR markers showed greater genetic diversity and a more informative ancestral history-based dendrogram topology. Significant correlation coefficients were observed between EST-SSR and CBDP markers, particularly in the combined marker dataset. Furthermore, the co-phenetic correlation was significant for three marker systems, with EST-SSR markers showing maximum correlation. Notably, the dendrograms constructed using EST-SSR markers and combined marker data displayed a significant and positive correlation with phenotypic traits assessed for the ten poppy varieties. Overall, the findings highlight the superiority of EST-SSR markers in deciphering genetic relationships among Indian opium poppy varieties and suggest their potential as valuable tools in breeding and genetic diversity studies.

Genetic diversity, variation, and structure of two populations of bigfin reef squid (Sepioteuthis lessoniana d’Orbigny) in Con Dao and Phu Quoc islands, Vietnam

BackgroundBigfin squid is one of the economically important seafood resources in Vietnam’s fisheries and the waters around Con Dao and Phu Quoc islands are two major fishing grounds where this species has been actively exploited. The start codon targeted polymorphism (SCoT) and CAAT box–derived polymorphism (CBDP) techniques were used to generate DNA fingerprinting data to analyze the genetic diversity, variation, and structure of the two populations in the waters surrounding Phu Quoc and Con Dao islands together with mitochondrial cytochrome C oxidase subunit I (COI) gene sequence data. ResultsCon Dao population possessed a higher diversity [expected heterozygosity (He) = 0.2254, Shannon index (I) = 0.3459, percentage of polymorphic bands (PPB) = 80.14%, nucleotide diversity (π) = 0.0336, haplotype diversity (h) = 0.910 with 16 haplotypes] than Phu Quoc population (He = 0.1854, I = 0.2873, PPB = 70.38%, π = 0.0246, h = 0.838 with 14 haplotypes). The genetic diversity at species level in the investigated region was at level of He = 0.2169, I = 0.3399, PPB = 86.41, π = 0.0289, and h = 0.892 with 24 haplotypes. Based on DNA fingerprinting data, the pairwise genetic similarity coefficients among individuals of the Con Dao population were lower (average of 0.7977) than the Phu Quoc population (average of 0.8316). Based on mitochondrial COI data, the pairwise genetic distances among individuals of the Con Dao population were higher (average of 0.0361) than the Phu Quoc population (average of 0.0263). Gene differentiation (GST) between two investigated populations was 0.0316 and 0.0310 leading to the genetic distance was 0.0573 and 0.0213 and the gene flow between them was Nm = 8.2209 and 11.4700 migrants per generation among populations based on DNA fingerprinting and based on COI gene sequence data, respectively. Genetic variation within individuals of both populations (WP) played the key role in total genetic variation at species level in surveyed region. ConclusionsFor the bigfin reef squid species in the surveyed region, the Con Dao population had the higher genetic diversity than the Phu Quoc population, between them existed a low to moderate genetic differentiation and a genetic exchange via gene flow. The DNA fingerprinting data better revealed the genetic differentiation between the two surveyed populations while the mitochondrial COI gene sequence data could show the phylogenetic relationship among the surveyed individuals and the other from the sea regions in Southeast Asia. Based on the results obtained, fisheries management strategies are suggested toward the conservation and sustainable exploitation of this species.

Genetic diversity in Tamarix aphylla (L.) H. Karst. using CAAT box-derived polymorphism (CBDP) and start codon targeted (SCoT) polymorphism markers

Tamarix aphylla (L.) H. Karst. is an evergreen, haloxeric, ecologically and economically important tree species of the Indian Thar desert. Genetic diversity analysis of this tree species is vital as it survives in extreme climatic conditions. In this study, we employed first time two gene-targeted CAAT box-derived polymorphism (CBDP) and start codon-targeted (SCoT) polymorphism markers for the analysis of the genetic diversity in Tamarix aphylla. A total of 47 wild genotypes of T. aphylla from eight populations of the Indian Thar Desert were analyzed using 12 primers, six from each CBDP and SCoT markers. The percent polymorphism was higher for CBDP (94.84%) than for the SCoT (76.57%) markers. The average PIC value for CBDP and SCoT marker was 0.601 and 0.409, respectively. Both CBDP and SCoT markers demonstrated high levels of genetic differentiation, low gene flow, and high fixation index. Using both marker systems, AMOVA revealed the percent molecular variation was higher in the case of within population than among population. The clustering pattern based on UPGMA and PCoA plots clearly showed that the grouping of genotypes is associated with their geographical origin and habitat. However, few genotypes were significantly diverse from their respective population and grouped in separate clusters with the genotypes of other populations. The findings observed in the present study can be further exploited in the breeding and conservation programs of T. aphylla.

Deciphering the level of genetic diversity in some aegilops species using CAAT box-derived polymorphism (CBDP) and start codon target polymorphism (SCoT) markers.

Maintaining genetic diversity is of the most essential principle for a long-term conservation of plant genetic resources and could play a crucial role in their management. The genus Aegilops is one important member of wheat germplasm, and there are evidences that novel genes of this genus' species can be studied/utilized as ideal sources for the wheat cultivar improvement. The objective of this study was to dissect the genetic diversity and population structure among a set of Iranian Aegilops using two gene-based molecular markers. This study investigated the level of genetic diversity among 157 Aegilops accessions consisting of Ae. tauschii Coss. (DD genome), Ae. crassa Boiss. (DDMM genome), and Ae. cylindrica Host. (CCDD genome) belonging to NPGBI using two sets of CBDP and SCoT markers. The SCoT and CBDP primers yielded 171 and 174 fragments, out of which 145 (90.23%) and 167 (97.66%) fragments were polymorphic, respectively. The average of polymorphism information content (PIC)/ marker index (MI)/resolving power (Rp) for SCoT and CBDP markers were 0.32/3.59/16.03 and 0.29/3.01/16.26, respectively. Results of AMOVA revealed the genetic variability within species was greater than the variation observed among them (SCoT: 88% vs. 12%; CBDP: 72% vs. 28%; SCoT + CBDP: 80% vs. 20%). Based on the information obtained from both markers, the higher level of genetic diversity was found in Ae. tauschii as compared to other species. The grouping patterns obtained by Neighbor-joining algorithms, principal coordinate analysis (PCoA), and Bayesian-model-based structure were consistent with each other and resulted in grouping all studied accessions according to their genomic constitutions. The results of this study revealed a high level of genetic diversity among Iranian Aegilops germplasm. Moreover, SCoT and CBDP marker systems were efficient in deciphering DNA polymorphism and classification of Aegilops germplasm.

Phytochemical and genetic marker (SCoT and CBDP) based study of genetic diversity and population structure in natural populations of Cannabis sativa L.: A high-value sustainable biodiversity of North-Indian Himalaya

Cannabis sativa is a versatile, sustainable cash crop grown in vast agro-climatic zones of India. The present study used comprehensive datasets involving phytochemical and molecular genotyping to characterize forty-two wild cannabis accessions collected from fourteen geographical locations of the North Indian Himalayas. Two gene-targeted dominant molecular markers, i.e., start codon targeted (SCoT) polymorphism and CAAT-box derived polymorphism (CBDP), were used for molecular genotyping to evaluate genetic assortment and interrelatedness among and within wild inhabitants of C.sativa. Multiple t-tests indicated significant differences among the studied cannabis populations for the phytochemical traits. Five major cannabinoids were identified in Indian Cannabis sativa germplasm, and most of the populations were of drug/marijuana types. The considerable diversity in drug types was observed at the chemical and genetic levels. Twenty-six SCoT and twenty-one CBDP markers generated a sum of 134, and 80 alleles averaged with 3.08 and 6.65 alleles per primer, respectively. The average polymorphic information content (PIC) and resolving power per primer indicated both SCoT and CBDP as ideal markers system for genetic diversity study in Cannabis sativa. The population diversity analysis based on SCoT, CBDP, and cumulative marker dataset revealed a high genetic differentiation (Gst>0.15), and a low estimated gene flow (Nm<1.0) between the studied populations. The highest gene diversity (H) and Shannon diversity Index (I) were observed for the population of Matiyal location (Pop3) using SCoT and cumulative marker dataset. However, Population 7 (Pop7) of location Kanatal was found to be highly diverse using the CBDP marker dataset. The multivariate analyses, i.e., Neighbour-joining tree based phenetic analysis, Principal Coordinate Analysis (PCoA), and Structure, revealed that there was no individual geographical location based grouping among the cannabis populations using both markers data set individually and their cumulative datasets. However, the allocation of accessions in common groups corresponding to their geographical locations was maximum in the case of Analysis with a cumulative marker data set. Analysis of molecular variance (AMOVA) also demonstrated a maximum percentage of molecular variation at the intra-population level (77–86%) rather than the inter-population level (14–23%). Altogether, our data suggest that both SCoT and CBDP markers are the ideal markers to study the genetic relationship among geographically different populations of C.sativa, and populations identified as highly diverse can be utilized as parents in Indian cannabis breeding programs.

Investigation of molecular variability in some Aegilops species using Start Codon Targeted Polymorphism (SCoT) and CAAT-Box Derived Polymorphism (CBDP) markers

Among wild relatives of wheat, Aegilops species are ideal genetic resources for the discovery of new characteristics such as resistance to environmental stresses and even grain quality for wheat improvement. Hence, knowledge of the population structure and genetic diversity of this germplasm is very important for their conservation and further utilization. In the present study, 80 accessions of the Aegilops including Ae. tauschii, Ae. cylindrica and Ae. triuncialis were investigated for genetic diversity using SCoT and CBDP markers. Eight SCOT and twelve CBDP primers amplified a total of 84 and 94 fragments with a mean of 10.50 and 7.83 fragments per primer, respectively. Resolving power (Rp) for SCoT and CBDP primers varied between 6.04 and 11.65, and 13.08 and 28.02, with the polymorphic information content (PIC) from 0.40 to 0.49 and 0.35 to 0.48, respectively. The results of analysis of molecular variance (AMOVA) indicated that the highest proportion of genetic variance referred to between species. SCoT primers indicated high values for all informativeness parameter (except resolving power) than CBDP primers across all tested accessions. However, CBDP primers indicated higher values of the genetic parameters than using SCoT primers. As a result, the maximum values for genetic parameters such as number of effective alleles (Ne), Nei?s gene diversity (H) and Shannon?s information index (I) were detected in Ae. cylindrica and Ae. triuncialis using SCoT and CBDP markers, respectively. Cluster analysis based on those molecular system grouped all accessions into three main clusters. The grouping pattern observed by CBDP primers indicated more clear phylogenetic relationship among some Aegilops species, so that PCoA?s results confirmed the grouping pattern. In conclusion, it was observed that SCoT and CBDP displayed good efficiency in depicting polymorphism among the tested accessions, however, CBDP markers provided a clear grouping pattern of evaluated accessions. Hence, the use of CBDP markers in determining population structure and estimating genetic diversity in other plant species is recommended.

Elucidating genetic diversity and population structure in jamun [Syzygium cumini (L.) Skeels] using morpho-physiological traits and CAAT box-derived polymorphism

• Assessment of morpho-physiological and molecular diversity in Syzygium cumini . • Population structure analysis using CBDP markers. • CBDP markers were highly informative in detecting the polymorphism. • Evidence for high levels of gene flow and less genetic differentiation. The use of molecular markers has received little attention in jamun [ Syzygium cumini (L.) Skeels], an underutilized fruit crop highly valued for its medicinal and nutraceutical properties. In this study, 50 jamun accessions from four different populations were analyzed using 21 morpho-physiological traits and 22 polymorphic gene-targeted CAAT box-derived polymorphism (CBDP) markers. The morpho-physiological variability was fairly high among the jamun accessions. The UPGMA analysis based on morpho-physiological traits produced three clusters with a cophenetic correlation of 0.75, reflecting a good fit between the original matrix and the clustering algorithm. The average polymorphism of 91.17% and the wide-ranging heterozygosity values (0.282-0.499) for the CBDP markers revealed considerable genetic variation among jamun genotypes. The average PIC of 0.352 evinced a high discriminatory power of the CBDP markers in distinguishing the accessions. CDBP data-based UPGMA clustering and population structure analysis identified four distinct populations; albeit with overlaps among them. This, together with the existence of admixed types in all four populations, indicated a fairly high degree of gene flow within jamun populations sampled in this study. It is therefore likely that despite widely differing geographic origins, some accessions in all the populations have a shared ancestral origin. Analysis of Molecular Variance also supports this assumption, as an exceedingly higher within-population variance (84%) than among-population variance (16%) reflected a high degree of gene flow and low genetic differentiation for the Jamun populations examined. Our findings improve the existing understanding vis-à-vis genetic diversity and population structure in jamun, and are expected to increase the use of CBDP and similar marker techniques in cultivar development programs.

An Analysis of Genetic Variability and Population Structure in Wheat Germplasm Using Microsatellite and Gene-Based Markers.

Knowledge of the natural patterns of genetic variation and their evolutionary basis is required for sustainable management and conservation of wheat germplasm. In the current study, the genetic diversity and population structure of 100 individuals from four Triticum and Aegilops species (including T. aestivum, Ae. tauschii, Ae. cylindrica, and Ae. crassa) were investigated using two gene-based markers (start codon targeted (SCoT) polymorphism and CAAT-box derived polymorphism (CBDP)) and simple-sequence repeats (SSRs). The SCoT, CBDP, and SSR markers yielded 76, 116, and 48 polymorphism fragments, respectively. The CBDP marker had greater efficiency than the SCoT and SSR markers due to its higher polymorphism content information (PIC), resolving power (Rp), and marker index (MI). Based on an analysis of molecular variance (AMOVA) performed using all marker systems and combined data, there was a higher distribution of genetic variation within species than among them. Ae. cylindrica and Ae. tauschii had the highest values for all genetic variation parameters. A cluster analysis using each marker system and combined data showed that the SSR marker had greater efficiency in grouping of tested accessions, such that the results of principal coordinate analysis (PCoA) and population structure confirmed the obtained clustering patterns. Hence, combining the SCoT and CBDP markers with polymorphic SSR markers may be useful in genetic fingerprinting and fine mapping and for association analysis in wheat and its germplasm for various agronomic traits or tolerance mechanisms to environmental stresses.

Genetic diversity and relationship analyses of mango (Mangifera indica L.) germplasm resources with ISSR, SRAP, CBDP and CEAP markers

Forty-eight mango accessions were compared for genetic diversity and relationships based on four molecular marker assays, namely, inter-simple sequence repeat (ISSR), sequence-related amplified polymorphism (SRAP), CAAT-box derived polymorphism (CBDP), and cis-element amplified polymorphism (CEAP). Comparative analyses of the marker assays based on Nei's genetic diversity (H), Shannon's information index (I), polymorphism information content (PIC), the marker index (MI), and resolving power (Rp) revealed that (i) the CEAP markers provided the most information according to the PIC, MI and Rp values; (ii) the CBDP and ISSR markers exhibited valuable information according to the H and I values. The correlation values (r) of the Mantel test ranged from 0.334 (ISSR and CEAP) to 0.819 (CEAP and the combination of the four marker assays). The unweighted pair group method with arithmetic mean (UPGMA) cluster results showed that a single-marker assay can accurately reflect the genetic relationships of some mango samples but cannot accurately reflect the genetic relationships of all mango samples and that when multiple markers are used to evaluate the genetic relationships of mango germplasm resources, the results are more accurate than those of a single-marker assay. The combined cluster analysis of the molecular marker types shows higher discrimination according to genetic relationships. Nine mango accessions were suggested to be likely parental or sister lines based on the combination of the ISSR, SRAP, CBDP, and CEAP marker assays.

Effects of low energy (160 keV) X-ray on microbial inactivation, sprouting inhibition and genetic variation in potato

The effects of low energy X-ray irradiation on microbial inactivation, sprouting inhibition and genetic variation were surveyed. There was an inverse correlation between the exposure dose in range of 0 Gy–5000 Gy and the survival rate of microorganisms. The dose of 1000 Gy seemed to be suitable for inactivation of microorganisms because the respective survival rate is relatively low (0.59%). Dose rate of 13.87 Gy/min was the most appropriate to inactivate the microorganisms, with the survival rate of 0.37%. Applying the irradiation dose of 1000 Gy and dose rate of 13.87 Gy/min, there was a significant sprouting inhibition of irradiated potatoes compared to the control for six months storage. The effect of irradiation dose (100–1200 Gy) and dose rate (8.63–19.62 Gy/min) on genetic variation of the irradiated samples was assessed by DNA fingerprints induced from using three molecular techniques including Random Amplified Polymorphic DNA (RAPD), Start Codon Targeted Polymorphism (SCoT) and CAAT box – derived polymorphism (CBDP). At the irradiation dose of 1000 Gy and dose rate of 13.87 Gy/min, the level of genetic variation was relatively low (4.85%). Thus, this treatment is a suitable condition of irradiation for potato treatment with the purpose of preservation.

Genetic diversity and population structure of Clerodendrum serratum (L.) Moon using CBDP, iPBS and SCoT markers

An investigation into the level of genetic diversity and population structure of medicinally important endangered Clerodendrum serratum was conducted for the first time in Manipur, a North-Eastern state of India, using CAAT box-derived polymorphism (CBDP), inter primer binding site (iPBS), and start codon targeted (SCoT) markers. The comparative analysis of the three marker systems revealed SCoT to be the most effective among other markers in detecting polymorphism and genotype differentiation. Mantel test revealed a positive correlation between CBDP and iPBS (r = 0.22), SCoT and CBDP (r = 0.48), and iPBS and SCoT (r = 0.62), indicating the effectiveness of each marker system and reliability of using them in conjunction with one another to generate accurate and consistent results. Marker analysis disclosed a moderately high estimate of moderately high gene flow (Nm = 1.133) between the populations which resulted in low genetic differentiation (Gst = 0.310) among populations. Mantel test disclosed a non-significant correlation between the geographic and genetic distances between the 8 different populations of C. serratum. Analysis of molecular variance (AMOVA) showed the existence of genetic variation (66 %) within the population and the remaining variation (34 %) among the populations. Unweighted pair group arithmetic mean method (UPGMA) dendrograms constructed based on pooled CBDP, iPBS, SCoT marker data produced clusters similar to the pattern generated by the two-dimensional principal coordinate analysis (PCoA). Bayesian model STRUCTURE analysis of C. serratum populations based on CBDP, iPBS, and SCoT markers gave three genetic clusters (K = 3), but the pooled marker data generated 5 different genetic groups with high admixture. GENELAND further assigned the 8 populations comprising 97 individual genotypes into two main genetic pools. The genetic information obtained from the present investigation will contribute to offering proper recommendations for the effective management and conservation of endangered C. serratum plants in the region.

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

BackgroundEvaluation 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. ResultsFifteen 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. ConclusionThe 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.

Assessment of genetic diversity among Iranian Aegilops triuncialis accessions using ISSR, SCoT, and CBDP markers

BackgroundCrop wild relatives (CWRs) are commonly used as a suitable genetic reservoir for plant breeding. They can be used for enhancing the tolerance of plant varieties to biotic and abiotic stresses. Studying the genetic diversity of related wheat species in Iran could be useful to improve different traits of bread wheat, since the country is one of the major centers of genetic diversity and distribution of Aegilops species. Therefore, the aim of the present study was to determine the relationship among 48 Aegilops triuncialis accessions using three DNA marker systems, including start codon targeted (SCoT), CAAT box-derived polymorphism (CBDP), and inter-simple sequence repeat (ISSR) markers. ResultsA total of 359 amplified DNA fragments were generated using 13 CBDP, 14 SCoT, and 16 ISSR primers that produced 96, 147, and 152 bands, respectively. The discriminating power of the three markers was assessed using polymorphism information content (PIC), marker index (MI), and resolving power (Rp). The mean values of PIC for ISSR, SCoT, and CBDP markers were 0.3, 0.26, and 0.34, respectively, indicating the efficiency of the three markers in detecting polymorphism among the studied accessions. ISSR markers had the highest values of MI, Rp, and polymorphism percentage as compared to SCoT and CBDP markers. Based on the Shannon index and heterozygosity values, genetic diversity in the Alborz population was more than in other populations. The accessions were classified into six, five, and five groups based on ISSR, SCoT, and CBDP using the UPGMA method. According to the results of cluster and PCoA analyses, the variation patterns corresponded with the geographical distribution of the Ae. triuncialis accessions. ConclusionsThe three markers provided a comprehensive pattern of the genetic diversity among the Iranian Ae. triuncialis accessions. This information could allow for a future insight into wheat breeding programs.

Evaluation of genetic variability and relatedness among eight Centaurea species through CAAT-box derived polymorphism (CBDP) and start codon targeted polymorphism (SCoT) markers

Centaurea is a value-ultimate genus of medicinal plants showing high diversification levels, especially within the Mediterranean basin, and is still traditionally recognized as a complicated taxon. So far, few studies utilizing molecular markers have been done on Centaurea spp. towards a better dissection of its phylogeny and accurate assessment of genetic diversity. Here, two functional marker systems, start codon targeted (SCoT) polymorphism and CAAT box-derived polymorphism (CBDP), were implemented to assess the genetic diversity between eight wild Centaurea species in Egypt. Seventeen SCoT and 19 CBDP primers generated 197 and 179 bands, respectively. These primers generated 158 (80.2%) and 131 (73.18%) polymorphic amplicons with an average of 9.29 and 6.89 amplicons per primer, respectively. SCoT primers exhibited higher levels in % of polymorphism, % of heterozygosity, effective multiplex ratio, discriminating power, resolving power parameters compared to the CBDP. In contrast, no significant differences were observed between SCoT and CBDP in polymorphism information content, marker index and mean heterozygosity parameters. The UPGMA (unweighted pair group method with arithmetic mean) dendrogram of the combined data classified the Centaurea species under two major clades; the first comprised two species, whereas the second grouped five species. C. pallescens was kept separated as the most diverged among the eight Centaurea species. Principal component analysis (PCA) topology revealed highly similar results to those obtained from the cluster analysis. Ultimately, our results represent the first report utilising two gene-targeting marker systems as powerful techniques for assessing the genetic variability and relatedness among these eight valuable Centaurea species.

Genetic Diversity and Population Structure Analysis of Landrace and Wild Relatives of Lentil Germplasm Using CBDP Marker

Assessment of genetic diversity and population structure of germplasm collections provides an opportunity for plant breeders to develop new and improved cultivars. In this study, genotypic variation of 90 lentil genotypes was evaluated using 10 CAAT Box Derived Polymorphism (CBDP) markers. The polymorphism percentage was 100% with an average of 100% indicating a high polymorphism level. A total of 117 alleles were identified for different genetic locations and with an average of 13 alleles per primer. Among CBDP markers used, the highest allele amplified belonged to CBDP22 marker with 21 bands and the lowest allele amplified corresponded to CBDP3, CBDP6 and CBDP13 markers with 11 bands. The Polymorphic information content (PIC) ranged from 0.413 to 0.471 with an average of 0.448. Marker Index (MI) ranged from 4.85 to 9.90. The highest index for genetic diversity (PIC and MI) belonged to the CBDP22 indicating a high resolution for this marker as compared to other markers. Based on neighbor joining clustering for molecular data, genotypes were grouped into five distinct groups. Population structure analysis showed that the highest peak was at K = 3, indicating the presence of three major clusters. The results of this study showed that CBDP markers can be used as a useful tool for studying the genetic diversity of lentil germplasm.

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.