Evaluation of Potential DNA Barcoding Loci from Plastid Genome: Intraspecies Discrimination in Rice (Oryza species)

Singh, Jaya; Kakade, Datta P.; Wallalwar, Mayur R.; Raghuvanshi, Rishiraj; Kongbrailatpam, Miranda; Verulkar, Satish; Banerjee, Shubha

doi:10.20546/ijcmas.2017.605.308

Cited by 11 publications

(8 citation statements)

References 31 publications

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“…Interestingly, in plants, DNA barcoding depends mainly on chloroplast genome sequence data. The use of the chloroplast genome has several advantages, ( 1) it has a simple and stable genetic structure, (2) it is haploid and recombination is rare and (3) it is generally uniparentally transferred [103]. Indeed, plastid DNA barcoding was tested to discriminate among Oryza species [103].…”

Section: Dna Barcodingmentioning

confidence: 99%

“…The use of the chloroplast genome has several advantages, ( 1) it has a simple and stable genetic structure, (2) it is haploid and recombination is rare and (3) it is generally uniparentally transferred [103]. Indeed, plastid DNA barcoding was tested to discriminate among Oryza species [103]. The authors concluded that a better standardization of universal primers is needed to improve amplification efficiency and detect polymorphisms [103].…”

Section: Dna Barcodingmentioning

confidence: 99%

“…Indeed, plastid DNA barcoding was tested to discriminate among Oryza species [103]. The authors concluded that a better standardization of universal primers is needed to improve amplification efficiency and detect polymorphisms [103]. Recently Zang et al, 2021 [104] explored DNA barcoding to discriminate 21 species of Oryza.…”

Section: Dna Barcodingmentioning

confidence: 99%

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DNA-Based Tools to Certify Authenticity of Rice Varieties—An Overview

Vieira

Faustino

Lourenço

et al. 2022

Foods

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Rice (Oryza sativa L.) is one of the most cultivated and consumed crops worldwide. It is mainly produced in Asia but, due to its large genetic pool, it has expanded to several ecosystems, latitudes and climatic conditions. Europe is a rice producing region, especially in the Mediterranean countries, that grow mostly typical japonica varieties. The European consumer interest in rice has increased over the last decades towards more exotic types, often more expensive (e.g., aromatic rice) and Europe is a net importer of this commodity. This has increased food fraud opportunities in the rice supply chain, which may deliver mixtures with lower quality rice, a problem that is now global. The development of tools to clearly identify undesirable mixtures thus became urgent. Among the various tools available, DNA-based markers are considered particularly reliable and stable for discrimination of rice varieties. This review covers aspects ranging from rice diversity and fraud issues to the DNA-based methods used to distinguish varieties and detect unwanted mixtures. Although not exhaustive, the review covers the diversity of strategies and ongoing improvements already tested, highlighting important advantages and disadvantages in terms of costs, reliability, labor-effort and potential scalability for routine fraud detection.

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Section: Dna Barcodingmentioning

confidence: 99%

Section: Dna Barcodingmentioning

confidence: 99%

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DNA-Based Tools to Certify Authenticity of Rice Varieties—An Overview

Vieira

Faustino

Lourenço

et al. 2022

Foods

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show abstract

“…Currently, chloroplast DNA (cpDNA), known as DNA barcoding markers can be used to determine the genetic diversity and relationship of germplasm, including orchids (Jheng et al, 2012;Tsai et al, 2012). These markers have advantages over some of the previously mentioned, such as faster and more accurate in determining the genetic diversity of germplasm (Lee et al, 2017;Li et al, 2015;Singh et al, 2017). The Consortium for the Barcode of Life's or CBOL ( 2009) have recommended several DNA barcoding markers, two of these are the rbcL and trnL-F.…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Relationships of Phalaenopsis Based on the rbcL and trnL-F Markers: In Silico Approach

et al. 2021

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In silico is the more comprehensive and applicable approach in supporting, both conservation and breeding programs of germplasm. The study aimed to analyze and determine the genetic diversity and relationships of 24 species of Phalaenopsis using two DNA barcoding markers, namely the rbcL and trnL-F, by in silico approach. All sequences of these markers were collected randomly from the NCBI website and analyzed using several softwares and methods, such as ClustalW and MultAlin for multiple sequence alignments and MEGA-X to determine its genetic diversity and relationships. Specifically, the genetic diversity was determined using a nucleotide diversity index and their relationships by the Maximum Likelihood method. The results showed that Phalaenopsis has a low genetic diversity of 0.24, 0.32, and 0.19, respectively. The phylogenetic analysis revealed that this orchid separated into five (for the rbcL), six (trnL-F), and seven clades (a combined one), where the closest relationship is shown by P. amboinensis vs. P. venosa, whereas the farthest by P. gibbosa vs. P. doweryensis, P. stuartiana vs. P. micholitzii, and P. celebensis vs. P. pulchra. The results have novel information on the diversity and relationships of Phalaenopsis on the in silico approach. Thus, our findings might be used in supporting the conservation and breeding program of Phalaenopsis, both locally and globally.

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“…Genetic or molecular markers from chloroplast genome (cpDNA) are widely used in plants, especially in angiosperms, because they are relatively simple and stable with respect to structure in comparison to those of nuclear DNA (Dong et al 2012;Ong et al 2012). Another advantage of using cpDNA markers in plant genetic analysis is the absence of contamination with DNAs of other organisms having no cpDNA such as fungi and bacterial (Singh et al 2017).…”

Section: Introductionmentioning

confidence: 99%

Intergeneric hybrids of Phalaenopsis 2166 x Vanda ‘Saint Valentine’ showing maternal inheritance: Genetic analysis based on ndhE partial gene

2020

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Abstract. Dwiati M, Susanto AH, Prayoga L. 2020. Intergeneric hybrids of Phalaenopsis 2166 x Vanda ‘Saint Valentine’ showing maternal inheritance: Genetic analysis based on ndhE partial gene. Biodiversitas 21: 5138-5145. Genetic characterization in the intergeneric hybridization of orchids employing a particular molecular marker, such as ndhE gene, is needed to avoid phenotypic plasticity. The hybridization between Phalaenopsis 2166 as a female parent and Vanda ‘Saint Valentine'as a male parent has been successfully made to produce various leaf shapes and colors of the hybrid seedlings, which tend to resemble those of the female parent. This study aims to assess whether the maternally phenotypic traits of the hybrids of Phalaenopsis 2166 x Vanda ‘Saint Valentine’ are congruent with the inheritance pattern of ndhE partial sequences. The result reveals that the ndhE partial sequences of the hybrids are seemingly similar to that of Phalaenopsis 2166 as the female parent rather than to that of Vanda ‘Saint Valentine’. It is also found that three hybrids, i.e. F1.9, F1.11, and F1.14 show slightly different ndhE partial sequences from those of the other hybrids in that some base substitutions are observed. In general, the ndhE partial sequences of the hybrids are maternally inherited. This finding provides a fact that maternally phenotypic traits of the hybrids of Phalaenopsis 2166 x Vanda ‘Saint Valentine’ have strong genetic background rather than environmental involvement.

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Evaluation of Potential DNA Barcoding Loci from Plastid Genome: Intraspecies Discrimination in Rice (Oryza species)

Cited by 11 publications

References 31 publications

DNA-Based Tools to Certify Authenticity of Rice Varieties—An Overview

DNA-Based Tools to Certify Authenticity of Rice Varieties—An Overview

Genetic Diversity and Relationships of Phalaenopsis Based on the rbcL and trnL-F Markers: In Silico Approach

Intergeneric hybrids of Phalaenopsis 2166 x Vanda ‘Saint Valentine’ showing maternal inheritance: Genetic analysis based on ndhE partial gene

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