Start codon targeted (SCoT) polymorphism reveals genetic diversity  of Manilkara in Thailand

Vanijajiva, Ongkarn

doi:10.13057/biodiv/d210232

Cited by 5 publications

(7 citation statements)

References 42 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Each reaction contained 50 ng of template DNA. A standard PCR cycle was used: an initial denaturation step at 94°C for 3 min, followed by 35 cycles of 94°C for 1 min, 50°C for 1 min, and 72°C for 2 min; the final extension at 72°C was held for 5 min (Vanijajiva 2020).…”

Section: Scot-pcr Amplificationmentioning

confidence: 99%

“…However, there was no genetic variation detectable within populations of the same region. As SCoT technology has proved to be a reliable method to find residual genetic characterizations in many studies (Guo et al 2012;Agarwal et al 2019;Vanijajiva 2020), this study may provide that populations within the same regions in the Bang Khun Tien shoreline of Bangkok consist of only one single genotype.…”

Section: Molecular Analysismentioning

confidence: 99%

“…Hence, first-hand information on the genetic characterizations at intra-specific levels helps to formulate effective conservation policies (Hoffmann et al 2015;Frankham et al 2019). The SCoT method is sensitive to low levels of genetic variations and thus provides a very useful tool for analyzing population genetics on a wide range of plants as well as identifying species or populations of the same species (Collard and Mackill 2009;Amom and Nongdam 2017;Vanijajiva 2020). In the present study, the representatives of the S. maritima collected from Bang Khun Tien shoreline, where the plant can still be found in its natural habitat, revealed B I O D I V E R S I T A S 21 (3): 1082-1090, March 2020 1088 that no differentiated by the DNA fingerprinting patterns using SCoT primers.…”

Section: Molecular Analysismentioning

confidence: 99%

“…Molecular markers effectively developed during the last few decades have largely overcome the problems that are associated with the phenotype-based classification. PCRbased start codon targeted (SCoT) marker, based on the short conserved nucleotide sequence that flanks the start codon ATG has been widely used to survey species identification, because their application simple, low cost, highly polymorphic, gene-targeted, and abundant in the genome (Collard and Mackill 2009;Amom and Nongdam 2017;Vanijajiva 2020). Because of the difficulties in the morphological determination of Suaeda maritima (Alghamdi 2012), this preliminary study purposes to examine the morpho-anatomical analysis and molecular investigation of S. maritima and to determine how their morphological and genetic characterizations are related to at Bang Khun Tien shoreline in Bangkok, Thailand.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Anatomical features and SCoT profiles provide new insight into phenotypic plasticity in the halophyte Suaeda maritima in Thailand

2020

Self Cite

View full text Add to dashboard Cite

Abstract. Rittirongsakul K, Srinual A, Vanijajiva O. 2020. Anatomical features and SCoT profiles provide new insight into phenotypic plasticity in the halophyte Suaeda maritima in Thailand. Biodiversitas 21: 1082-1090. Phenotypic plasticity is the variation in phenotypic traits of organisms to survive with fluctuating environments. Halophytes are plants that can naturally tolerate high concentrations of salt in the soil, and their tolerance to salt stress, which reflects the ability of the plants to produce different phenotypic traits in response to changing environmental conditions. Suaeda maritima (L.) Dumort is a polymorphic halophyte and prominent species complex from tropical to temperate regions due to diverse stressful saline habitats. Consequently, the identification of S. maritima based on morphological data is challenging due to high phenotypic plasticity. In Thailand, S. maritima, known as Seablite or Cha Khram, has only been reported for the genus Suaeda which frequently found in coastal salt marshes. The peculiarities of the prevalence of three distinctive color traits, green, green-reddish and reddish, were commonly observed in Thailand. This preliminary study aims to examine the morpho-anatomical characters and molecular analysis of S. maritima and to determine how their morphological and genetic characterizations are related to phenotypic traits, particularly in color variation within the population at Bang Khun Tien shoreline in Bangkok, Thailand. This combined investigation of anatomical characters and start codon targeted (SCoT) fingerprinting profiles provide first evidence of phenotypic variations and genetic characterizations of halophytic S. maritima in Thailand. Anatomical characters of leaf structures confirmed that the species is austrobassioid (C3) types. Meanwhile, molecular investigation of thirty SCoT primers found that only two SCoT primers (SCoT10 and SCoT27) failed to amplify the S. maritima genomic DNA. Thoroughly, twenty-eight SCoT primers produced 162 unambiguous and reproducible banding profiles with 140-1200 bp product size. Despite, there was no genetic variation detectable within the population, SCoT technique was considered a suitable tool to produces adequate characterization for DNA fingerprinting of halophyte S. maritima. However, further studies involving additional samples of S. maritima are needed to obtain a more general view of the conspicuous variation and colonization history in Thailand.

show abstract

Section: Scot-pcr Amplificationmentioning

confidence: 99%

Section: Molecular Analysismentioning

confidence: 99%

Section: Molecular Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Anatomical features and SCoT profiles provide new insight into phenotypic plasticity in the halophyte Suaeda maritima in Thailand

2020

Self Cite

View full text Add to dashboard Cite

show abstract

“…Amplicons are evaluated by standard gel electrophoresis with agarose gels (Collard and Mackill, 2009). (Collard and Mackill, 2009) Similar to other molecular markers, SCoT could be successfully practised for genetic diversity (Vivodík et al, 2019;Vanijajiva et al, 2020;Xiao et al, 2020). In some studies, SCoT markers were combined with other molecular markers.…”

Section: Scot (Start Codon Targeted Polymorphism)mentioning

confidence: 99%