Fourier transform infrared (FT-IR) spectroscopy of genomic DNA to discriminate F1 progenies from their paternal lineage of Chinese cabbage (Brassica rapa subsp. pekinensis)

Song, Seung Yeub; Jie, Eun Yee; Ahn, Myung Suk; Nou, Ill–Sup; Min, Byung Whan; Kim, Suk Weon

doi:10.1007/s11032-013-9963-4

Cited by 17 publications

(8 citation statements)

References 36 publications

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“…However, the two marked groups overlap as a result of their input data similarities in terms of band relative intensity, corresponding wavenumbers, and spectral profile. Our results are in accordance with the results derived from a previous research carried out by Song et al (2014) [24], who stated that discrimination of F1 progenies based on FT-IR spectral similarity can be explained by their genomic similarity. This result was expected as the two groups of samples originated from the same parent (P1).…”

Section: Discussionsupporting

confidence: 93%

“…The differences among spectral bands might be directly related to subtle changes in the base structural groups and backbone structures of genomic DNA from different plant samples, such as hybrids and their parents [24]. Thus, considering these results, it can be stated that FT-IR spectral analysis could be applied as a useful tool to distinguish F1 hybrids from their parents based on structural variability of plant genomic DNA.…”

Section: Introductionmentioning

confidence: 99%

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Assessment of Genetic Relationships between Streptocarpus x hybridus V. Parents and F1 Progenies Using SRAP Markers and FT-IR Spectroscopy

Hârța

Borsai

Muntean

et al. 2020

Plants

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The genetic relationship among three Streptocarpus parents and twelve F1 hybrids was assessed using sequence-related amplified polymorphism (SRAP) molecular markers and Fourier-transform infrared (FT-IR) spectroscopy. Both methods were able to discriminate F1 hybrids and parents as revealed by cluster analysis. For hybrid identification, the type III SRAP marker was the most effective due to the presence of male-specific bands in the hybrids. Different behaviors in the biochemical variability of DNA samples have been observed by FT-IR spectral analysis, which might be attributed to the inherent nature of the genomic DNA from parents and their F1 progenies. Mantel test was also carried out to compare morphological, SRAP, and FT-IR results based on genetic distances. The highest correlation coefficient was found between morphological and SRAP marker distances (R = 0.607; p ≤ 0.022). A lower correlation was observed between the morphological and FT-IR distance matrix (R = 0.231; p ≤0.008). Moreover, a positive correlation was found between the distances generated with SRAP and FT-IR analyses (R = 0.026) but was not statistically significant. These findings show that both SRAP and FT-IR techniques combined with morphological descriptions can be used effectively for nonconventional breeding programs for Streptocarpus to obtain new and valuable varieties.

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Section: Discussionsupporting

confidence: 93%

Section: Introductionmentioning

confidence: 99%

Assessment of Genetic Relationships between Streptocarpus x hybridus V. Parents and F1 Progenies Using SRAP Markers and FT-IR Spectroscopy

Hârța

Borsai

Muntean

et al. 2020

Plants

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“…27 Meanwhile, the appearance of peaks at 1103 cm −1 and 1236 cm -1 was ascribed to the presence of -PO 2 stretching vibration of phosphodiester bond 28,29 and the peak observed at 1710 cm -1 can be attributed to carbonyl group in nucleotides. 30 To further verify the modification process and explore the light adsorption properties, UV-Vis analysis was performed ( Figure 3B).…”

Section: Accepted Manuscriptmentioning

confidence: 99%

Designer SiO2@Au nanoshells towards sensitive and selective detection of small molecules in laser desorption ionization mass spectrometry

Gan

Wei

et al. 2015

Nanomedicine: Nanotechnology, Biology and Medicine

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“…The FT-IR spectroscopy analysis was performed as described by Song et al (2014). Briefly, 4 lg of prepared genomic DNA was transferred into 384-well silicon plates on a hot stand prewarmed to 37°C.…”

Section: Ft-ir Spectroscopymentioning

confidence: 99%

“…Previously FT-IR spectroscopy has been successfully applied as sensitive and effective assay for plant genomic DNA to discriminate F1 progenies from their potential lineage of Chinese cabbage (Song et al 2014). Application of FT-IR spectroscopy to bacterial genomic DNA, which does not change even when the growth conditions change, for identifying microbial strains has not been examined.…”

Section: Introductionmentioning

confidence: 99%

Rapid tool for identification of bacterial strains using Fourier transform infrared spectroscopy on genomic DNA

et al. 2019

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Aims We developed a new rapid and reliable method for identifying bacteria using a combination of Fourier transform infrared (FT‐IR) spectroscopy of bacterial genomic DNA and multivariate analysis. Methods and Results FT‐IR spectra of genomic DNA from four type strains of Pseudomonas spp., three type strains of Escherichia spp. and two type strains of Bacillus spp. were analysed in the 4000–400 cm−1 region. Spectral differences were found in the frequency regions of N–H stretching (amide I), C=O stretching vibrations (amide II) and PO2− ionized asymmetric and symmetric stretching. Partial least squares discriminant analysis of the FT‐IR spectra showed that the microbial strains could be discriminated by hierarchical clustering analysis. Conclusions FT‐IR spectral analysis of bacterial genomic DNA has potential for the rapid identification of bacteria at the genus and species levels. Significance and Impact of the Study This study reports a new bacterial identification method using multivariate analysis of FT‐IR spectra of bacterial genomic DNA.

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Fourier transform infrared (FT-IR) spectroscopy of genomic DNA to discriminate F1 progenies from their paternal lineage of Chinese cabbage (Brassica rapa subsp. pekinensis)

Cited by 17 publications

References 36 publications

Assessment of Genetic Relationships between Streptocarpus x hybridus V. Parents and F1 Progenies Using SRAP Markers and FT-IR Spectroscopy

Assessment of Genetic Relationships between Streptocarpus x hybridus V. Parents and F1 Progenies Using SRAP Markers and FT-IR Spectroscopy

Designer SiO2@Au nanoshells towards sensitive and selective detection of small molecules in laser desorption ionization mass spectrometry

Rapid tool for identification of bacterial strains using Fourier transform infrared spectroscopy on genomic DNA

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