Start Codon Targeted (SCoT) Polymorphism: A Simple, Novel DNA Marker Technique for Generating Gene-Targeted Markers in Plants

Collard, B. C. Y.; Mackill, David J.

doi:10.1007/s11105-008-0060-5

Cited by 713 publications

(559 citation statements)

References 43 publications

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“…Ten ScoT primers deveoped by Collard and Mackill (2009b) were used for genetic diversity analysis in durum genotypes (Table 2). For optimization, PCR amplification was performed in a 20 μL reaction mixture containing 1× PCR buffer, 30 ng sample DNA, 0.2 mM dNTPS, 0.3 μM of primer and 1 U of Taq polymerase (Cinnagene, Iran).…”

Section: Scot Analysismentioning

confidence: 99%

“…In recent years, different molecular markers that generate polymorphism in conserved gene regions of the plant genome have been used, such as start codon targeted polymorphism (SCoT; Collard, Mackill 2009b) and Environmental and Experimental Biology ISSN 2255-9582 conserved DNA derived polymorphism (CDDP; Collard, Mackill 2009a). The SCoT primers are based on conserved regions flanking the initiation codon sequences of genes and CDDPs are short primers to generate useful genetic markers across functional domains of well-characterised plant genes (Collard, Mackill 2009a;Collard, Mackill 2009b).…”

Section: Introductionmentioning

confidence: 99%

“…The SCoT primers are based on conserved regions flanking the initiation codon sequences of genes and CDDPs are short primers to generate useful genetic markers across functional domains of well-characterised plant genes (Collard, Mackill 2009a;Collard, Mackill 2009b). These marker techniques has been successfully employed in genetic diversity analysis of several plants, such as chickpea (Pakseresht et al 2013), wheat (Hamidi et al 2014), ramie (Satya et al 2015) and jojoba (Heikrujam et al 2015).…”

Section: Introductionmentioning

confidence: 99%

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Geographical diversity pattern in Iranian landrace durum wheat (Triticum turgidum) accessions using start codon targeted polymorphism and conserved DNA-derived polymorphism markers

Seyedimoradi¹,

Talebi²,

Fayaz³

2016

EEB

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Genetic diversity and relationships among 38 Iranian durum wheat accessions were analysed using conserved DNA-derived polymorphism (CDDP) and start codon targeted (SCoT) markers. A total of 10 CDDP and 10 SCoT primers were used to estimate genetic polymorphism among 38 durum wheat accessions. Comparatively, both CDDP and SCoT markers proved to be more effective and in terms of percentage of polymorphisms and polymorphic information content value were relatively similar. The average polymorphic information content value of CDDP was 0.39 which was relatively higher than those of SCoT where the respective values of polymorphic information content was 0.35. Using the neighbor joining clustering method, CDDP and SCoT markers were used to generate dendrograms, which revealed that the durum accessions were clustered into three and two major groups, respectively. According to the present results, CDDP markers proved more informative in studying genetic diversity among durum accessions. In both marker types, low correlation between genetic distances and geographical origin in examined durum landrace accessions was found. However, accessions from the same geographical regions mostly showed more genetic similarity than those with origins far apart. The results demostrated that CDDP and SCoT markers are useful for genetic diversity analysis of durum accessions. This information is useful for future germplasm collection and efficient utilization of landrace durum germplasm in plant breeding.

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Section: Scot Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Geographical diversity pattern in Iranian landrace durum wheat (Triticum turgidum) accessions using start codon targeted polymorphism and conserved DNA-derived polymorphism markers

Seyedimoradi¹,

Talebi²,

Fayaz³

2016

EEB

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“…This has been validated through study on genetic diversity among rice varieties and marker segregation in rice backcross population [8]. There is an urgent need to develop more suitable and tightly linked markers for improved traits (molecular signature) and its further utilization in plant improvement and breeding programmes for exploitation of genetic resources for the sake of commercial and academic needs.…”

Section: Introductionmentioning

confidence: 99%

Efficiency of Triple-SCoT Primer in Characterization of Genetic Diversity and Genotype-Specific Markers against SSR Fingerprint in Some Egyptian Barley Genotypes

Aboulila¹,

Mansour²

2017

AJMB

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Ten Egyptian barley genotypes (2 commercial varieties and 8 breeding lines) were cultivated under normal condition at the Experimental Farm of Sakha Agricultural Research station and exposed to salinity stress condition at the Experimental Farm of El-hosainia plain Agricultural Research station, Elsharkia Governorate, Egypt, in an attempt to identify the relative salinity tolerant genotypes. A susceptibility index (SI) was used to estimate the relative stress loss because it accounted for variation in yield potential and stress intensity. Giza 123, Line-1, Line-5, Line-6 and Line-8 genotypes were considered as saline tolerant genotypes on the basis of their highly tolerance indices values. Barley genotypes were characterized by seven SSR markers and three SCoT primers in different combinations to discern the extent of genetic variation and develop a fingerprinting key. Normal SCoT reactions amplify single segments of DNA which are 15-to 19-mer long. A new strategy was used to increase SCoT potential in genetic diversity studies by using two and three different primer combinations per reaction. Amplification products scored a polymorphism percentage of 94.44% for Triple-SCoT and 90.91% for SSR, while the average no. of polymorphic fragments/primer was 17 and 7.14 in the two marker systems, respectively. On the other side, Triple-SCoT exhibited the highest average number of positive and negative genotype-specific markers. The cluster analysis of the studied genotypes using these different marker systems revealed four dendrograms varied in their topology. The dendrogram based on Triple-SCoT data exhibited the closest relationships to those illustrated by SSR dendrogram.

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“…Similar to RAPD, the SCoT marker involves a single oligonucleotide primer and is based on polymerase chain reaction (PCR) analysis (Collard and Mackill, 2009). As a new molecular marker method, the SCoT marker with high polymorphism and efficiency was successfully used in rice (Collard and Mackill, 2009), peanuts (Xiong et al, 2011), mangos (Luo et al, 2012), potatoes (Gorji et al, 2011), grapes (Guo et al, 2012), sugarcane (Que et al, 2014), and orchids (Feng et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Assessment of Genetic Relationship and Diversity among Chinese Sugarcane Parental Clones using SCoT and ISSR Markers

Chen¹,

Shen²,

Xu³

et al. 2017

IJAB

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Sugarcane is an allopolyploid crop with ≥120 or more chromosomes, of which~5.0-10% are Saccharum spontaneum and 90-95% are S. officinarum. The genetic characteristics of sugarcane provides a complex genetic background. The objective of this study was to use two molecular marker systems, start codon targeted (SCoT) and inter-simple sequence repeat (ISSR), to assess the genetic relationship and diversity of 75 sugarcane parental clones from Chinese sugarcane breeding program. Twenty-four SCoT primers produced 227 loci, of which 200 (88.11%) were polymorphic, whereas 15 ISSR primers resulted in a total of 146 loci, with 123 (84.25%) being polymorphic. Mean polymorphism information content values of 0.8152 and 0.8361 were detected using SCoT and ISSR primers, respectively. The genetic similarity coefficients ranged from 0.542 between ROC22 and HoCP95-988 to 0.831 between ROC25 and ROC20, with a mean value of 0.687 based on SCoT+ISSR data set. The unweighted pair group method of arithmetic averages (UPGMA) clusters and principal coordinate analysis (PCA) gave similar results. The 75 Chinese sugarcane parental clones were clustered into two main groups (A and B). Group A was primarily comprised of 42 clones from all Q-series, all CP-, HoCP-, or LCP-series, all YT-series and three Erianthus arundinaceus F4 innovative parental clones, etc., while 33 parental clones of Group B contained all TT-series, all GT-series, three Saccharum officinarum species, etc. The genetic similarity was high among the Q-series, CP-series, HoCP-series and YT-series. The genetic relationship was close among TT-series, GT-series and three S. officinarum species, while the genetic similarity between YT-series and TT-series or GT-series was low. There was an abundant genetic diversity among these sugarcane parental clones however the parental clones bred by the same breeding organization have a narrow genetic basis. This information was useful for selecting crossing parents and combinations. Correlation detection between SCoT and ISSR was not significant, but highly complementary, indicating that the combination of the two marker systems could avoid biases based on a single marker.

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Start Codon Targeted (SCoT) Polymorphism: A Simple, Novel DNA Marker Technique for Generating Gene-Targeted Markers in Plants

Cited by 713 publications

References 43 publications

Geographical diversity pattern in Iranian landrace durum wheat (Triticum turgidum) accessions using start codon targeted polymorphism and conserved DNA-derived polymorphism markers

Geographical diversity pattern in Iranian landrace durum wheat (Triticum turgidum) accessions using start codon targeted polymorphism and conserved DNA-derived polymorphism markers

Efficiency of Triple-SCoT Primer in Characterization of Genetic Diversity and Genotype-Specific Markers against SSR Fingerprint in Some Egyptian Barley Genotypes

Assessment of Genetic Relationship and Diversity among Chinese Sugarcane Parental Clones using SCoT and ISSR Markers

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