Efficiency of RAPD, ISSR, iPBS, SCoT and phytochemical markers in the genetic relationship study of five native and economical important bamboos of North-East India

Amom, Thoungamba; Tikendra, Leimapokpam; Apana, Nandeibam; Goutam, Moirangthem; Sonia, Paonam; Koijam, Arunkumar Singh; Potshangbam, Angamba Meetei; Rahaman, Hamidur; Nongdam, Potshangbam

doi:10.1016/j.phytochem.2020.112330

Cited by 64 publications

(24 citation statements)

References 45 publications

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“…This difference is because each marker detects different sequences of the genome (Shahlaei et al, 2014). The SCoT marker produced a higher polymorphism than ISSR, this result confirmed the finding of Pakseresht et al (2013), Shahlaei et al (2014), Etminan et al (2016) and Amom et al (2020). Fig.…”

Section: -Molecular Characterization: A-polymorphism and Diversity Asupporting

confidence: 86%

“…Therefore, the SCoT marker has a higher capacity in the detection of polymorphism. Several results are consistent with this result (Pakseresht et al, 2013, Shahlaei et al, 2014and Amom et al, 2020. On the other hand, the primer resolving power (Rp) was calculated to select the best primer having the highest ability for detection of polymorphism.…”

Section: -Molecular Characterization: A-polymorphism and Diversity Asupporting

confidence: 66%

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Evaluation of Yield, Fruit Quality and Molecular Diversity for Three Grape Cultivars under New Valley Conditions

Bashandy

Kamel

Ferweez

2020

Journal of Agricultural Chemistry and Biotechnology

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The current investigation was performed to evaluate the performance and DNA molecular analysis of three grape cultivars under the New Valley governorate, Egypt conditions. Most of the evaluated traits significantly varied among the cultivars. Superior cultivar had the best performance in cluster trait (weight, length and width), berries trait (number per cluster and 100 berries weight) and the total yield per vine. On the other hand, Flame cultivar overtopped in some quality traits (Total Soluble Solids, reducing and total reducing sugars). Molecular analysis was performed by using start codon targeted (SCoT) and inter-simple sequence repeats (ISSR) markers. The detected polymorphism was 68.38% and 41.84%, respectively. The polymorphism information content (PIC) for SCoT and ISSR markers was 0.29 and 0.19, respectively. Thus, SCoT marker was more informative. In contrast, the obtained dendrogram by ISSR showed a better clustering pattern than the SCoT marker.

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Section: -Molecular Characterization: A-polymorphism and Diversity Asupporting

confidence: 86%

Section: -Molecular Characterization: A-polymorphism and Diversity Asupporting

confidence: 66%

Evaluation of Yield, Fruit Quality and Molecular Diversity for Three Grape Cultivars under New Valley Conditions

Bashandy

Kamel

Ferweez

2020

Journal of Agricultural Chemistry and Biotechnology

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“…The genetic differentiation between the two species may have resulted from the adaptive selection to varied environmental factors, such as C. corifolia preferably occur in habitats with high moisture in evergreen forest whereas C. volubilis mostly found in the edge of mixed forests (Vanijajiva and Kadereit 2008), and geographic isolation. A similar successful phenomenon of iPBS technique was observed in several recent plant genetic studies (Kalendar et al 2019;Amom et al 2020). The information generated by the iPBS marker system suggests that this system can be used effectively for genetic diversity and structure studies in Cissampelopsis species.…”

Section: Evaluation Of Ipbs Markersupporting

confidence: 68%

“…The population genetic variation and structure estimation at the molecular level is available (Minn et al 2015;Grover and Sharma 2016;Allendorf 2017;Amom and Nongdam 2017;Comes et al 2017;Nadeem et al 2018), for several different markers, but only a few dominant markers are most regularly used, such as Randomly Amplified Polymorphic DNA (RAPD), Inter-Simple Sequence Repeats (ISSR), and Amplified Fragment Length Polymorphism (AFLP) (Suratman et al 2015;Grover and Sharma 2016;Al-Naggar et al 2017;Bidyaleima et al 2019;Amom et al 2020). Despite that, retrotransposon marker method is one of excellent sources of efficient genetic markers (Kalendar et al 2019;Ghonaim et al 2020).…”

Section: Introductionmentioning

confidence: 99%

“…Kalendar et al (2010) established inter primer-binding sites (iPBS) retrotransposon indicator systems for eukaryotic organisms, particularly in plants. Due to this, the iPBS technique is an easy-to-use technique that requires no sequence data, cost-effective, not age or tissue-specific, highly informative, and no affected by environmental influences (Nemli et al 2015;Amom et al 2020). Thus, the iPBS retrotransposon technique has been selected as a marker to examine population genetic diversity and structure in many plant genera such as Cicer (Andeden et al 2013), Vitis (Guo et al 2014), Pisum (Baloch et al 2015), Phaseolus (Nemli et al 2015), Psidium (Mehmood et al 2017), Castanea, Fagus and Quercus (Coutinho et al 2018), Chenopodium (Hossein-Pour et al 2019), Laurus (Karık et al 2019), Hordeum (Bonchev et al 2019), Origanum (Karagoz et al 2020).…”

Section: Introductionmentioning

confidence: 99%

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Inter-primer binding site (iPBS) markers reveal the population genetic diversity and structure of tropical climbing Cissampelopsis (Asteraceae) in Thailand

Vanijajiva

Pornpongrungrueng

2020

Biodiversitas

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Abstract. Vanijajiva O, Pornpongrungrueng P. 2020. Inter-primer binding site (iPBS) markers reveal the population genetic diversity and structure of tropical climbing Cissampelopsis (Asteraceae) in Thailand. Biodiversitas 21: 3919-3928. Cissampelopsis is a small climbing tropical Asian genus of Asteraceae-Senecioneae. In Thailand, the genus is represented by two species, C. corifolia and C. Volubilis, distributed through the mountain evergreen forest. Study on the genetic diversity and structure of populations of both Cissampelopsis species provide better understanding of the biology and pattern of species diversification in the genus. To identify the genetic diversity, we used the inter-primer binding site (iPBS) retrotransposon system, in 96 accessions of Cissampelopsis species collected from different regions in Thailand. A total of 120 iPBS bands were scored as presence⁄ absence characters. Results from UPGMA and PCoA analyses indicated that C. corifolia and C. volubilis are different species. Genetic diversity and genetic differentiation among and within populations of C. volubilis is higher than C. corifolia. Molecular Variance (AMOVA) analysis of both species indicated that the genetic variance value within populations is higher than among populations of each species. Bayesian model-based STRUCTURE analysis detected two gene pools for both Cissampelopsis and showed admixture within individuals. Differences among the two Cissampelopsis species, in total diversities and levels of population differentiation, indicated that the genetic structure of Cissampelopsis populations are congruent with long-lived perennial habit with regional distribution, even for congeneric species, may vary considerably. This study suggests the effectiveness of the iPBS marker system to estimate the population genetic diversity and structure of Cissampelopsis genotypes.

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Genetic diversity, population structure, and gene flow analysis of lowland bamboo [Oxytenanthera abyssinica (A. Rich.) Munro] in Ethiopia

Oumer

Dagne

Feyissa

et al. 2020

Ecology and Evolution

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Bamboo, a member of subfamily Bambusoideae in the grass family (Poaceae), is one of the most important nontimber forest resources and a potential alternative to wood and wood products. Ethiopian lowland bamboo ( Oxytenanthera abyssinica ) is an economically and ecologically important species which accounts about 85% of total bamboo coverage in the country. This species is experiencing population decline due to a number of anthropogenic factors. As a foundation step, genetic diversity, population structure, and gene flow analysis of various O. abyssinica populations found in Ethiopia are studied using inter‐simple sequence repeat markers. One hundred and thirty isolates of bamboo belonging to 13 geographically diverse populations were collected for DNA extraction and analysis. Heterozygosity, level of polymorphism, marker efficiency, Nei's gene diversity ( H ), and Shannon's information index ( I ) analysis, analysis of molecular variance (AMOVA), analysis for cluster, principal coordinates (PCoA), and admixture analyses were performed based on the markers banding pattern. The results indicated high genetic variation (84.48%) at species level. The H , I , observed and effective number of alleles at the species level were 0.2702, 0.4061, 1.8448, and 1.4744, respectively, suggesting a relatively high level of genetic diversity. However, genetic differentiation at the population level was relatively low. Using grouped populations, AMOVA revealed that most (61.05%) of the diversity was distributed within the populations with F ST = 0.38949, F SC = 0.10486, and F CT = 0.31797. Cluster analysis grouped the populations into markedly distinct clusters, suggesting confined propagation in distinct geographic regions. STRUCTURE analyses showed K = 2 for all populations and K = 11 excluding Gambella population. Using these markers, we found strong evidence that the genetic diversity of the lowland bamboo is associated with distinct geographic regions and that isolates of Gambella Region, with their unique genetic origin, are quite different from other bamboos found in the country.

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Efficiency of RAPD, ISSR, iPBS, SCoT and phytochemical markers in the genetic relationship study of five native and economical important bamboos of North-East India

Cited by 64 publications

References 45 publications

Evaluation of Yield, Fruit Quality and Molecular Diversity for Three Grape Cultivars under New Valley Conditions

Evaluation of Yield, Fruit Quality and Molecular Diversity for Three Grape Cultivars under New Valley Conditions

Inter-primer binding site (iPBS) markers reveal the population genetic diversity and structure of tropical climbing Cissampelopsis (Asteraceae) in Thailand

Genetic diversity, population structure, and gene flow analysis of lowland bamboo [Oxytenanthera abyssinica (A. Rich.) Munro] in Ethiopia

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