Evaluation of Genetic Diversity by DNA Barcoding of Local Tomato Populations from North-Western Romania

Căprar, M.; Copaci, C. M.; Chende, Diana M.; Sicora, Oana; Şumălan, R.; Sicora, Cosmin

doi:10.15835/nbha45110601

Cited by 5 publications

(5 citation statements)

References 13 publications

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“…Sequences of rpoC1 identified the tomato germplasm as Solanum violaceimarmoratum with 99 or 100% identity. Caprari et al (2017) did barcode sequence of local tomato plant from north-western Romania. They used four barcode genes trnH-psbA, rbcL, rpoB and rpoC1 and got 100% success in PCR for all the loci.…”

Section: Resultsmentioning

confidence: 99%

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Barcoding of ToLCV Resistant Tomato Germplasm in Bangladesh

Jannat

Eva

Sarker

et al. 2020

Plant Tissue Cult. & Biotech.

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The current study was carried out to confirm the existence of the ToLCV resistant genes (Ty-1 to Ty-5) in the germplasm using molecular markers and to identify at the genomic level following phylogenetic relationships analysis among some local tomato germplasm using DNA barcoding. Most of the tomato germplasm (Ten out of 14) contain the dominant Ty-genes as revealed by PCR analysis. “Barcoding” of the non-coding plastid trnH-psbA intergenic spacer region, three plastidal regions: rbcL, rpoB, rpoC1, spacer region of nuclear genome ITS and a mitochondrial region matK were employed following PCR and sequence analysis of the germplasm. Among all the barcode genes, rpoB, rbcL, trnH-psbA and ITS were leading candidates for successful amplification and used for the identification of the germplasm as S. lycopersicum in multi-locus identification based on their sequences. Neighbor-Joining phylogenetic tree was constructed in which the germplasm were clustered into five main clades. The current study was successful to establish an efficient barcoding protocol for the correct identification of tomatoes and was capable of establishing elite gene source(s) for biotic stress resistance tomato varieties which would serve as potential donor plants in modern breeding programs. Plant Tissue Cult. & Biotech. 30(1): 107-117, 2020 (June)

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Section: Resultsmentioning

confidence: 99%

“…PCR amplification was performed on a Thermal Cycler (Applied Biosystem). PCR condition were used following condition reported by Caprari et al (2017). The success of PCR amplification was verified by subjecting 10 μl of the PCR product to 1% agarose gel electrophoresis in TAE buffer and visualized under an UV trans-illuminator.…”

Section: Methodsmentioning

confidence: 99%

Barcoding of ToLCV Resistant Tomato Germplasm in Bangladesh

Jannat

Eva

Sarker

et al. 2020

Plant Tissue Cult. & Biotech.

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“…Some previous reports have suggested successful amplification and use of the matK region to investigate phylogeny in both monocots and dicots such as Zingiberaceae [11], Erythronium [24], Myristica fragrans [25], local tomato [26], and oil-bearing roses [27].…”

Section: Discussionmentioning

confidence: 99%

“…This could broaden the interspecific variation if the two loci are considered as two-gene approach and thus they reported interspecific variation (p-distance 0.002-0.003) but no intraspecific variation (p-distance 0.00). Another work reported having three variable sites in trnH-psbA sequences among seven tomato varieties with genetic distance ranging from 0 to 0.004 [26].…”

Section: Discussionmentioning

confidence: 99%

Evolution of matK Gene among the Elite Tea Clones (Camellia sinensis) Revealed by Nucleotide Substitution within the Consensus Region

Labar¹,

Pallab²,

Prosenjit³

et al. 2021

J App Biol Biotech

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The medicinally and economically important tea plant of India lacks a report on barcode study. Thus, we aimed to establish the DNA barcode of some elite tea clones of Darjeeling and Dooars along with the study of variation within the chloroplast region. A thorough investigation of 29 tea clones based on the matK (maturase K) gene has been carried out in our study. The laid objectives were fulfilled following DNA isolation, purification, amplification of the matK region, and sequencing. The sequences were further analyzed using BLAST analysis and phylogenetic tree construction along with the study of the aligned consensus region among all the clones. A BLAST search of NCBI revealed 24 clones to share 100% identity with Camellia sinensis. The remaining 5 clones showed 99.29-99.89% identity with Camellia sinensis. However, clones such as 11125 and 11126 showed a higher percentage of similarity, that is, 99.87% and 99.57% with other species of Camellia when compared, respectively, to 99.61% and 99.29% with Camellia sinensis. The relatedness to other Camellia species was also evident from the distinct cluster in the phylogenetic tree. This study reports a total of 14 variable sites within the matK region where the high consensus region revealed a total of nine variable sites and the low consensus region revealed a total of five variable sites. Therefore, this study is the first report of barcode analysis of Indian tea clones, wherein we successfully utilized the single locus matK gene to study variation within the chloroplast region and also conclude that the matK region is not 100% conserved with the same species of Camellia.

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“…PCR amplification was performed on a Thermal Cycler (Applied Biosystem). The PCR amplified conditions were as follows: Initial denaturation at 95 °C for 3min, 30 cycles of 95 °C for 30s, annealing temperature 50°C for 30s and 72°C for 90s followed by a final extension at 72 °C for 2min reported by Caprari et al (2017). The success of PCR amplification was verified by subjecting 10μl of the PCR product to 1% agarose gel electrophoresis in TAE buffer at 90W for 30 min and visualized under Gel Documentation System (CSL-MDOCUV254/365 1D, Cleaver Scientific LTD, USA).…”

Section: Methodsmentioning

confidence: 99%

Morphological and Genotypic Characterization Of Different Lotus (Nelumbo Nucifera Gaertn.) Samples Available in Bangladesh

Roy

Jannat

Tabassum

et al. 2022

Bangladesh J. Plant Taxon

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Asian lotus (Nelumbo nucifera Gaertn.), commonly known as sacred lotus is a basal eudicot. It has been grown and cultivated as food, medicine and for cultural, and religious activities. In the current study, samples were collected from six different locations to evaluate the variation among different lotus germplasm based on external morphological characteristics, as well as, to study the genetic variation and the molecular characterization. Analysis of variance showed a higher level of variations among the germplasm for all the morphological features. Based on the morphological features, a dendrogram was constructed to assess the linkage among the germplasm. The yellow lotus of Cumilla was considered superior among the germplasm studied. To assess the genetic diversity and the correct identification of lotus germplasm, molecular method “Barcoding” was performed. To achieve the goal, two plastidial regions: rpoB and rpoC1 were employed. The germplasm showing successful PCR were subjected to sequence analysis of their barcode genes. All the selected barcode genes showed successful identification of all the germplasm as N. nucifera in multilocus identification based on their sequences except for the germplasm of Rajshahi and also confirmed the yellowish lotus of Cumilla considered as a new cultivar N. nucifera ‘Gomoti’, newly found in Bangladesh. Genetic sequences obtained in the context of DNA barcoding had also been used to create a phylogenetic tree in which the germplasm were clustered into five main clades. The current study was successful in establishing an efficient protocol for the correct identification of lotus germplasm and was capable of establishing an elite gene source. Moreover, future studies are warranted to see the identifying capability and diverging power of the barcodes. Bangladesh J. Plant Taxon. 29(1): 85-95, 2022 (June)

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Evaluation of Genetic Diversity by DNA Barcoding of Local Tomato Populations from North-Western Romania

Cited by 5 publications

References 13 publications

Barcoding of ToLCV Resistant Tomato Germplasm in Bangladesh

Barcoding of ToLCV Resistant Tomato Germplasm in Bangladesh

Evolution of matK Gene among the Elite Tea Clones (Camellia sinensis) Revealed by Nucleotide Substitution within the Consensus Region

Morphological and Genotypic Characterization Of Different Lotus (Nelumbo Nucifera Gaertn.) Samples Available in Bangladesh

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