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Rapid discrimination of CMS cybrid lines between Brassica oleracea var. capitata and Raphanus sativus L. using Fourier transform infrared (FT-IR) spectroscopy of genomic DNA

Jie, EunYee, Ahn, MyungSuk, Lee, YoungPyo, Sung, SoonKee, Min, ByungWhan, Liu, JangRyol, Kim, SukWeon
Plant biotechnology reports 2018 v.12 no.3 pp. 217-228
Brassica oleracea var. capitata, DNA, DNA fingerprinting, Fourier transform infrared spectroscopy, Raphanus sativus, callus, cell lines, cybrids, discriminant analysis, least squares, moieties, principal component analysis, progeny, rapid methods, screening, seed industry
The purpose of this study is to establish the rapid discrimination system of cybrid callus lines by Fourier transform infrared (FT-IR) spectroscopy without genetic fingerprinting analysis. Genomic DNA isolated from two parental lines (Brassica oleracea var. capitata and Raphanus sativus L.) and their cybrid callus lines were analyzed by FT-IR spectroscopy in the spectral region from 4000 to 400 cm⁻¹. Several spectral differences between the two parental lines were detected in the frequency regions of N–H stretching (amide I), C=O stretching vibrations (amide II), and PO₂⁻ ionized asymmetric and symmetric stretching. Principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were used to discriminate cybrid cell lines from the two parental species at the genomic DNA level. PLS-DA analysis provided more clear discrimination between the two parental lines and their progeny cybrid lines in the score plot. PCA loading values also showed that obvious spectral differences played a significant role in discrimination between the two parental lines and their cybrid lines. These spectral differences might be directly related to subtle changes in the base functional groups and backbone structures of genomic DNA. Considering these results, this technique could provide a research foundation for the FT-IR spectral-based diagnosis, selection, and discrimination of parental lines and their cybrids. Furthermore, this technique could be applied in the hybrid seed industry for rapid screening with high heterogeneity.