Start Codon Targeted (SCoT) marker reveals genetic diversity of Dendrobium nobile Lindl., an endangered medicinal orchid species

Bhattacharyya, Paromik; Kumaria, Suman; Kumar, Suresh; Tandon, Pramod

doi:10.1016/j.gene.2013.07.096

Cited by 128 publications

(65 citation statements)

References 29 publications

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“…SCoT is similar to random amplified polymorphic DNA or intersimple sequence repeat, but has some advantages such as being closely linked with the target gene, provides more information correlated with biological traits, and universality in plants compared with random DNA markers. These advantages have been verified in rice (Oryza sativa) (Collard and Mackill, 2009), mango (Mangifera indica) (Luo et al, 2011), peanut (Arachis hypogaea) (Xiong et al, 2011), grape (Vitis vinifera) (Guo et al, 2012), dendrobe (Dendrobium nobile) (Bhattacharyya et al, 2013), and limpograss (Hemarthria altissima) (Huang et al, 2013) for cultivar identification and genetic diversity analysis.…”

Section: Introductionmentioning

confidence: 95%

Optimization of SCoT-PCR reaction system in Dactylis glomerata by orthogonal design

Zeng¹,

Huang²,

Huang³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. The effects of 5 factors (template DNA, Mg 2+ , dNTPs, Taq DNA polymerase, and primer) on the polymerase chain reaction (PCR) were investigated to optimize the start codon targeted polymorphism (SCoT)-PCR system of Dactylis glomerata L., using an orthogonal design L 16 (4 5 ). A suitable SCoT-PCR system for D. glomerata was established; the 20 µL reaction volume contained 3.0 mM Mg 2+ , 0.2 mM dNTPs, 1.0 U Taq DNA polymerase, 0.2 µM primer, 20 ng template DNA, and 2 µL 10X buffer. Each factor had a different effect on the amplification reaction, and the concentration of dNTPs had the largest effect on the SCoT-PCR system. We tested 10 orchardgrass samples to determine and verify the stability of the reaction system. The results showed that amplified bands from diverse materials were clear, stable, 3052-3061 (2015) and rich in polymorphisms, indicating that the optimized system was very stable.

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Section: Introductionmentioning

confidence: 95%

Optimization of SCoT-PCR reaction system in Dactylis glomerata by orthogonal design

Zeng¹,

Huang²,

Huang³

et al. 2015

Genet. Mol. Res.

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“…Using RAPD markers, the average value of PIC recorded in castor genotypes was 0.88 (Gajera et al, 2010), 2.47 in Indian bitter gourd accessions ( Behera et al, 2008), 0.243in rice landraces (Muthusamy et al, 2008) and 0.241 in Vanilla genus ( Verma et al,2009). In addition, the average number of PIC for SCoT was 0.142 using 10 primers on 10 tomato cultivars (Shahlaei et al, 2014) , 0.78 as detected 36 primers on 60 medicinal plants (Bhattacharyya et al, 2013) and 0.82 using 36 primers on 64 grapes varieties (Guo et al, 2015). Furthermore, by employing two SAMPL primer combinations on 55 bread wheat genotypes, the PIC average was 0.221 and the PIC values ranged from 0.035 to 0.499 with an average of 0.264 (Roy et al, 2002).…”

Section: Polymorphism Among the Olive Varieties As Detected By The DImentioning

confidence: 99%

Selective Amplification of Start codon Polymorphic Loci (SASPL): a new PCR-based molecular marker in olive

Alsamman¹,

Adawy²,

Ibrahim³

et al. 2017

Plant Omics

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The Selective Amplification of Start Codon Polymorphic Loci (SASPL) has been developed as a new PCR-based molecular marker. SASPL was validated for the analysis of varietal diversity on ten olive varieties. Validation included in vitro comparison against RAPD, SCoT and SAMPL markers. Assessment of these techniques included primer selectivity, genome coverage and the ability to target genic regions through in silico PCR analysis. Candidate PCR fragments were further sequenced to annotate non-identified genes in olive. Eight SASPL primers were compared to 24 RAPD, 39 SCoT and 12 SAMPL primers. The TA produced by the RAPD, SCoT, SAMPL and the eight SASPL primers were 359, 642, 571 and 269 amplicons, respectively. The highest average number of TA was revealed by SAMPL (47.6), average of PA (18.1) and genetic similarity (GS) (96%) among the olive varieties. On the other hand, SASPL analysis provided higher average number of TA (33.6), average of PA (16.2) and GS (93%) than SCoT and RAPD. The highest average of (PIC) (0.2909) was exhibited by SASPL analysis and the lowest average (0.2038) was revealed by SCoT. The highest number of UB (111) was revealed by SCoT and the lowest UB (43) was obtained by SASPL. Across the four marker types, variety Maraki was characterized by the highest number of unique markers (74). Meanwhile, the variety Manzanillo was characterized by the lowest number of unique markers (8). In addition, in the in silico analysis SASPL exhibited the highest chromosomal coverage (0.59%) and targeted genes (1090) using the lowest number of primers. Additionally, the average area covered by the SASPL primers (354kb) was larger than SCoT and SAMPL. RAPD analysis provided the lowest potential, chromosomal coverage (0.04%) and number of targeted genes (17) compared to SASPL, SCoT and SAMPL analysis. The total coverage of the genome, revealed by combined data was higher (1.21%) than that of each technique separately. Meanwhile, the difference between the actual and the total genomic regions covered by the combined data was about 652kb. Our results suggested that the newly developed SASPL marker is the most adequately and each of the studied marker target different genomic areas, while some areas are shared. Two SCoT and one RAPD fragment were sequenced and showed a high similarity to genes of high physiological functions; such as cyclic plant-specific DNA-binding transcription factor, SANT domain and Copia-type retrotransposon.

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“…Shortly, the SCoT polymorphism method is similar to RAPD and ISSR, because of the use of a single forward and reverse primer (Bhattacharyya et al, 2013). There are several advantages of SCoT technique, including low cost, simple operation, simple primer design, highly effective polymorphism, good reproducibility and good universality (Hu et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Using Start Codon Targeted (SCoT) polymorphism for Genetic Diversity Analysis of three Red Sea fishes (Family: Carangidae)

Marie¹,

Allam²

2017

IOSRJPBS

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Start Codon Targeted (SCoT) marker reveals genetic diversity of Dendrobium nobile Lindl., an endangered medicinal orchid species

Cited by 128 publications

References 29 publications

Optimization of SCoT-PCR reaction system in Dactylis glomerata by orthogonal design

Optimization of SCoT-PCR reaction system in Dactylis glomerata by orthogonal design

Selective Amplification of Start codon Polymorphic Loci (SASPL): a new PCR-based molecular marker in olive

Using Start Codon Targeted (SCoT) polymorphism for Genetic Diversity Analysis of three Red Sea fishes (Family: Carangidae)

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