Start codon targeted (SCoT) polymorphism marker in plant genome analysis: current status and prospects

Manoj, K.

doi:10.1007/s00425-023-04067-6

Cited by 46 publications

(21 citation statements)

References 173 publications

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“…Furthermore, lengthy primers and high annealing temperatures improve the reproducibility of SCoT primer [ 43 , 46 ]. SCoT markers appear frequently in the genome and give considerable genetic information since they are associated with initiation codons [ 47 , 48 ].…”

Section: Resultsmentioning

confidence: 99%

Assessment of genetic homogeneity of in-vitro propagated apple root stock MM 104 using ISSR and SCoT primers

Bisht,

Rawat,

Gaira

et al. 2024

BMC Plant Biol

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Apple is an important fruit crop that is always in demand due to its commercial and nutraceutical value. Also, the requirement for quality planting material for this fruit crop for new plantations is increasing continuously. In-vitro propagation is an alternative approach, which may help to produce genetically identical high grade planting material. In this study, for the first time, an efficient and reproducible propagation protocol has been established for apple root stock MM 104 via axillary bud. Culturing axillary buds on Murashige and Skoog apple rootstock (MM 104) resulted in better in-vitro propagation. (MS) basal medium supplemented with 3.0% (w/v) sucrose and 0.8% (w/v) agar. The axillary buds were established in MS basal medium with BA (5.0 µM), NAA (1.0 µM) and further used to establish invitro propagation protocol. Plant Growth Regulators (PGRs), BA (1.0 µM) in combination with NAA (1.0 µM) was found most efficient for shoot multiplication (100%) and produced 9.8 shoots/explants with an average shoot length of (2.4 ± cm). All the shoots produced roots in 0.1 µM IBA with a 5-day dark period. Acclimatization of in-vitro raised plantlets was obtained with vermiculite: perlite: sand: soil (2:2:1:1) resulting in 76% survival under field conditions. The study showed that the use of axillary bud is efficient for multiple-shoot production of apple rootstock (MM 104). This is the first comprehensive report on in-vitro growth of apple root stock MM 104 with an assessment of genetic stability using DNA fingerprinting profiles based on Inter Simple Sequence Repeats (ISSR) and Start Codon Targeted (SCoT). The genetic stability of in-vitro-produced plants, as determined by SCoT and ISSR primers, demonstrated genetic closeness to the mother plant.

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Section: Resultsmentioning

confidence: 99%

Assessment of genetic homogeneity of in-vitro propagated apple root stock MM 104 using ISSR and SCoT primers

Bisht,

Rawat,

Gaira

et al. 2024

BMC Plant Biol

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“…Due to their simplicity, relatively low cost requirements, high reproducibility, and considerable association with phenotypic data, SCoT markers has been applied to many genetic studies, including analysis of genetic diversity, detecting intra-and inter-genetic variation in different plant species, stability of in vitro derived plants, phylogenetic relationships, taxonomy, species/cultivar identification, quantitative trait loci (QTL) mapping and DNA fingerprinting in various plants (e.g. Zhang et al 2015;Etminan et al 2018;Jalilian et al 2018;Jedrzejczyk 2020;Zarei and Erfani-Moghadam 2021;Rai 2023).…”

Section: Scot-pcr Amplificationsmentioning

confidence: 99%

Taxonomy and distribution of Taraxacum sect. Erythrosperma (Asteraceae) in Poland

Wolanin¹,

Klichowska²,

Jędrzejczyk³

et al. 2023

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The dandelions from Taraxacum sect. Erythrosperma are taxonomically well distinguished and ecologically restricted to warm and sunlit habitats of steppes, dry and sandy grasslands, and distributed in temperate regions of Europe and Central Asia, with some being introduced to North America. Despite the long tradition of botanical research, the taxonomy and distribution of dandelions of T. sect. Erythrosperma is still underexplored in central Europe. In this paper, by combining traditional taxonomic studies supported by micromorphological, molecular and flow cytometry analyses as well as potential distribution modelling we shed light on taxonomical and phylogenetical relationships between members of T. sect. Erythrosperma in Poland. We also provide an identification key, species-checklist, detailed descriptions of morphology and occupated habitats as well as distribution maps for 14 Polish erythrosperms (T. bellicum, T. brachyglossum, T. cristatum, T. danubium, T. disseminatum, T. dissimile, T. lacistophyllum, T. parnassicum, T. plumbeum, T. proximum, T. sandomiriense, T. scanicum, T. tenuilobum, T. tortilobum). Finally, conservation assessments performed using the IUCN method and threat categories for all the examined species are proposed.

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“…The amplicons that were created are possibly disseminated within gene regions that comprise genes on both the plus and minus DNA strands. As a result, it can identify genetic variations in a speci c gene that are linked to a speci c trait (Rai 2023).…”

Section: )mentioning

confidence: 99%

“…SCoT marker studies have been widely used to investigate genetic population structure and to guide conservation efforts and these markers are usually polymorphic which are depend on shorter conserved sequences which ank the ATG start codon. In this method, a single primer is used as both forward and reverse primers, similar to how RAPD or ISSR markers are used to create DNA markers through the use of polymerase chain reaction (PCR) (Collard and Mackill 2009;Hajibarat et al 2015;Rai 2023). Li and Quiros (2001) established SRAP as a marker technology for amplifying ORFs (open reading frames).…”

Section: Introductionmentioning

confidence: 99%

Evaluation of genetic diversity and population structure of reticulate iris genotypes in the Iraqi Kurdistan region using SCoT and SRAP markers

Majeed,

Faraj,

Rasul

et al. 2023

Preprint

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The reticulate iris is one of the most attractive wild ornamentals, bulbous irises, widely distributed throughout the mountains of the Iraqi Kurdistan region. Due to a lack of information available about the genetic variability and population structure of this group of plants in Iraq. Thus, ten start codon targeted (SCoT) polymorphic and ten sequence-related amplified polymorphisms (SRAP) markers were used in the present study to evaluate genetic diversity and population structure in 50 wild reticulate iris genotypes from five different sites in Iraqi Kurdistan region. Over all, SCoT and SRAP markers produced 135 and 87 polymorphic bands, respectively. The average of number of polymorphic bands (TPB), number of observed alleles (Na), Shannon’s information index (I), effective number of alleles (Ne), expected heterozygosity or gene diversity (He), polymorphic information content (PIC), and unbiased expected heterozygosity (uHe), of SCoT primers were (13.7, 1.54, 0.35, 1.40, 0.23, 0.31, and 0.25) and of SRAP primers were 8.7, 1.54, 0.36, 1.40, 0.24, 0.32, and 0.25, respectively. According to the UPGMA dendrogram and structure analysis, SCoT markers grouped 50 reticulate iris genotypes into two main clades with some sub-clades, while SRAP markers separated these genotypes into four main clades. The analysis of molecular variance revealed 80 and 76% variability among populations with SCoT and SRAP markers, respectively, which indicated gene exchange between populations. Except for the number of private bands index in SCoT and SRAP markers, populations 3 and 1 had the highest diversity indices (Na, Ne, I, H uHe, and percentage of polymorphic loci (PPL)). The highest distance between populations was revealed by SCoT markers between population 1 and both population 2 and population 4, with 13% dissimilarity, while the maximum dissimilarity was observed by SRAP markers between population 1 and population 4, with 17% dissimilarity. The study's findings revealed the efficacy of these markers for genetic variation in iris genotypes, in addition to their ability for germplasm conservation and genome diversity.

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Start codon targeted (SCoT) polymorphism marker in plant genome analysis: current status and prospects

Cited by 46 publications

References 173 publications

Assessment of genetic homogeneity of in-vitro propagated apple root stock MM 104 using ISSR and SCoT primers

Assessment of genetic homogeneity of in-vitro propagated apple root stock MM 104 using ISSR and SCoT primers

Taxonomy and distribution of Taraxacum sect. Erythrosperma (Asteraceae) in Poland

Evaluation of genetic diversity and population structure of reticulate iris genotypes in the Iraqi Kurdistan region using SCoT and SRAP markers

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Start codon targeted (SCoT) polymorphism marker in plant genome analysis: current status and prospects

Cited by 46 publications

References 173 publications

Assessment of genetic homogeneity of in-vitro propagated apple root stock MM 104 using ISSR and SCoT primers

Assessment of genetic homogeneity of in-vitro propagated apple root stock MM 104 using ISSR and SCoT primers

﻿Taxonomy and distribution of Taraxacum sect. Erythrosperma (Asteraceae) in Poland

Evaluation of genetic diversity and population structure of reticulate iris genotypes in the Iraqi Kurdistan region using SCoT and SRAP markers

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Taxonomy and distribution of Taraxacum sect. Erythrosperma (Asteraceae) in Poland