Molecular Identification of Malaysian Pineapple Cultivar based on Internal Transcribed Spacer Region

Hidayat, Topik; Abdullah, Farah Izana; Kuppusamy, Chandrika; Samad, Azman Abdul; Wagiran, Alina

doi:10.1016/j.apcbee.2012.11.025

Cited by 16 publications

(12 citation statements)

References 13 publications

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“…Among 103 sequences, 31 species where taken as representative for the comparative analysis for cultivar and wild samples from the laboratory source with subspecies and hybrids from the GenBank (Fig 3). The phylogenetic tree (Fig 3) [43], grapevine [44], pineapple [45]. In this study, ITS2 possess sufficient variable region between the cultivar species for determination of genetic divergence with high discriminatory ability.…”

Section: Phylogenetic Analysismentioning

confidence: 88%

Molecular identification and evolutionary relationships between the subspecies of Musa by DNA barcodes

Selvaraj

Ashutosh

Gowtham

et al. 2020

Preprint

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Background: The banana ( Musa sp., AAA ) genome is constantly increasing due to high frequency somaclonal variations. Due to its large diversity, a conventional numerical and morphological based taxonomic identification of banana cultivars is laborious, difficult, and often is a subject of disagreements. Results: In study, we used ITS2 region to identify and determine the genetic relationship between the cultivars and varieties of banana. Herein, a total of 16 banana cultivars were PCR amplified using ITS2 region. In addition, 321 sequences were retrieved from GenBank, USA, and used for the study. The sequences were aligned using Clustal W and genetic distances computed using MEGA V5.1. The significant divergence between the intra- and -specific genetic distances of ITS2 region was observed and the presence of a DNA barcoding gap was obvious. Based on BLAST1 and Distance methods, the results proved that ITS2 region can be successfully identified and distinguished for the cultivar and varieties of banana. Secondly, in this study, ITS2 revealed the relations between the cultivar and varieties of banana. Conclusion: Thus, from this study, it is clear that ITS2 is not only an efficient DNA barcode to identify the banana species but also a potential candidate to study phylogenetic relationships between subspecies and cultivars. This is the first comprehensive study to categorically distinguish the economically important banana sub-species and varieties using DNA barcodes and to understand its evolutionary relationship

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Section: Phylogenetic Analysismentioning

confidence: 88%

Molecular identification and evolutionary relationships between the subspecies of Musa by DNA barcodes

Selvaraj

Ashutosh

Gowtham

et al. 2020

Preprint

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show abstract

“…To our knowledge, this is the first report wherein DNA barcoding has been employed in the identification of different species and cultivars of Musa using a large sample size. An ideal DNA barcode should include higher inter-specific but low intra-specific divergence to discriminate different species [ 24 ] which has been shown in many earlier studies for various species and cultivars of Colletotrichum isolates [ 41 ], fig [ 42 ], grapevine [ 43 ], and pineapple [ 44 ]. In the present study, ITS2 was found to possess a sufficient variable region between the different species and cultivars for the determination of genetic divergence with high discriminatory ability.…”

Section: Discussionmentioning

confidence: 99%

Molecular identification and evolutionary relationships between the subspecies of Musa by DNA barcodes

Dhivya

Ashutosh²,

Gowtham

et al. 2020

BMC Genomics

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Background The banana (Musa sp., AAA) genome is constantly increasing due to high-frequency of somaclonal variations. Due to its large diversity, a conventional numerical and morphological based taxonomic identification of banana cultivars is laborious, difficult and often leads to subject of disagreements. Results Hence, in the present study, we used universal DNA barcode ITS2 region to identify and to find the genetic relationship between the cultivars and varieties of banana. Herein, a total of 16 banana cultivars were PCR amplified using ITS2 primer pair. In addition, 321 sequences which were retrieved from GenBank, USA, were used in this study. The sequences were then aligned using Clustal W and genetic distances were computed using MEGA V5.1. The study showed significant divergence between the intra- and inter-specific genetic distances in ITS2 region. BLAST1 and Distance methods proved that ITS2 DNA barcode region successfully identified and distinguished the cultivar and varieties of banana. Conclusion Thus, from the results of the present study, it is clear that ITS2 is not only an efficient DNA barcode to identify the banana species but also a potential candidate for enumerating the phylogenetic relationships between the subspecies and cultivars. This is the first comprehensive study to categorically distinguish the economically important banana subspecies and varieties using DNA barcodes and to understand its evolutionary relationship.

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“…Fruit Mango (Hidayat, Kusumawaty, & Pancoro, 2013) Citrus species (Yu, Yan, Lu, & Zhou, 2011) Goji (Xin et al, 2013) Berries (Jaakola et al, 2010) Pineapple (Hidayat, Abdullah, Kuppusamy, Samad & Wagiran, 2012) Olives and Olive oil (Agrimonti, Vietina, Pafundo, & Marmiroli, 2011;Ganopoulos et al, 2013 …”

Section: Foodstuff Category Raw Materials / Food Product Referencesmentioning

confidence: 99%

Emerging DNA-based technologies to characterize food ecosystems

Galimberti

Bruno

Mezzasalma

et al. 2015

Food Research International

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Molecular Identification of Malaysian Pineapple Cultivar based on Internal Transcribed Spacer Region

Cited by 16 publications

References 13 publications

Molecular identification and evolutionary relationships between the subspecies of Musa by DNA barcodes

Molecular identification and evolutionary relationships between the subspecies of Musa by DNA barcodes

Molecular identification and evolutionary relationships between the subspecies of Musa by DNA barcodes

Emerging DNA-based technologies to characterize food ecosystems

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