Identification and Validation of Genetic Variations in Transgenic Chinese Cabbage Plants (<i>Brassica rapa</i> ssp. <i>pekinensis</i>) by Next-Generation Sequencing
Transgenic plants are usually produced through tissue culture, which is an essential step in <i>Agrobacterium</i>-mediated plant transformation. However, genomic variations, termed somaclonal variations, have been detected in transgenic plants cultured in vitro. The occurrence of these v...
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doaj-22542dfd34ff42bfac30d427098685082021-04-22T23:01:42ZengMDPI AGGenes2073-44252021-04-011262162110.3390/genes12050621Identification and Validation of Genetic Variations in Transgenic Chinese Cabbage Plants (<i>Brassica rapa</i> ssp. <i>pekinensis</i>) by Next-Generation SequencingSo-Jeong Kim0Jee-Soo Park1Yun-Hee Shin2Young-Doo Park3Department of Horticultural Biotechnology, Kyung Hee University, 1732 Deogyoung-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, KoreaDepartment of Horticultural Biotechnology, Kyung Hee University, 1732 Deogyoung-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, KoreaDepartment of Horticultural Biotechnology, Kyung Hee University, 1732 Deogyoung-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, KoreaDepartment of Horticultural Biotechnology, Kyung Hee University, 1732 Deogyoung-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, KoreaTransgenic plants are usually produced through tissue culture, which is an essential step in <i>Agrobacterium</i>-mediated plant transformation. However, genomic variations, termed somaclonal variations, have been detected in transgenic plants cultured in vitro. The occurrence of these variations should be as low as possible to secure the stability of transgenic crops. Determining the cause and mechanism of somaclonal variations in tissue culture-derived plants will help reduce the rate of variation and promote the stable expression of genes in transgenic plants. In order to determine the genetic variability in transgenic Chinese cabbage plants, we performed whole-genome resequencing and compared the sequencing data with the ‘CT001’ reference genome. The variation candidates that were expected to consistently occur in the transgenic lines were selected and validated. The single nucleotide polymorphism (SNP) and insertion and deletion (InDel) candidates were identified using the resequencing data and validated by reverse transcription (RT)-PCR analysis. The deduced amino acid sequences were used to determine whether the variations caused changes in the resulting polypeptide, and the annotations of the mutated genes were analyzed to predict the possible effects of the SNPs on gene function. In conclusion, we selected and validated the genetic variations identified in transgenic Chinese cabbage plants. Their genomes were expected to be affected by the process of <i>Agrobacterium</i>-mediated transformation. The findings of our study will provide a genetic basis for transgenic plant research.https://www.mdpi.com/2073-4425/12/5/621<i>Brassica rapa</i>in vitro cultureresequencingsingle nucleotide polymorphismstransgenic plants |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
So-Jeong Kim Jee-Soo Park Yun-Hee Shin Young-Doo Park |
spellingShingle |
So-Jeong Kim Jee-Soo Park Yun-Hee Shin Young-Doo Park Identification and Validation of Genetic Variations in Transgenic Chinese Cabbage Plants (<i>Brassica rapa</i> ssp. <i>pekinensis</i>) by Next-Generation Sequencing Genes <i>Brassica rapa</i> in vitro culture resequencing single nucleotide polymorphisms transgenic plants |
author_facet |
So-Jeong Kim Jee-Soo Park Yun-Hee Shin Young-Doo Park |
author_sort |
So-Jeong Kim |
title |
Identification and Validation of Genetic Variations in Transgenic Chinese Cabbage Plants (<i>Brassica rapa</i> ssp. <i>pekinensis</i>) by Next-Generation Sequencing |
title_short |
Identification and Validation of Genetic Variations in Transgenic Chinese Cabbage Plants (<i>Brassica rapa</i> ssp. <i>pekinensis</i>) by Next-Generation Sequencing |
title_full |
Identification and Validation of Genetic Variations in Transgenic Chinese Cabbage Plants (<i>Brassica rapa</i> ssp. <i>pekinensis</i>) by Next-Generation Sequencing |
title_fullStr |
Identification and Validation of Genetic Variations in Transgenic Chinese Cabbage Plants (<i>Brassica rapa</i> ssp. <i>pekinensis</i>) by Next-Generation Sequencing |
title_full_unstemmed |
Identification and Validation of Genetic Variations in Transgenic Chinese Cabbage Plants (<i>Brassica rapa</i> ssp. <i>pekinensis</i>) by Next-Generation Sequencing |
title_sort |
identification and validation of genetic variations in transgenic chinese cabbage plants (<i>brassica rapa</i> ssp. <i>pekinensis</i>) by next-generation sequencing |
publisher |
MDPI AG |
series |
Genes |
issn |
2073-4425 |
publishDate |
2021-04-01 |
description |
Transgenic plants are usually produced through tissue culture, which is an essential step in <i>Agrobacterium</i>-mediated plant transformation. However, genomic variations, termed somaclonal variations, have been detected in transgenic plants cultured in vitro. The occurrence of these variations should be as low as possible to secure the stability of transgenic crops. Determining the cause and mechanism of somaclonal variations in tissue culture-derived plants will help reduce the rate of variation and promote the stable expression of genes in transgenic plants. In order to determine the genetic variability in transgenic Chinese cabbage plants, we performed whole-genome resequencing and compared the sequencing data with the ‘CT001’ reference genome. The variation candidates that were expected to consistently occur in the transgenic lines were selected and validated. The single nucleotide polymorphism (SNP) and insertion and deletion (InDel) candidates were identified using the resequencing data and validated by reverse transcription (RT)-PCR analysis. The deduced amino acid sequences were used to determine whether the variations caused changes in the resulting polypeptide, and the annotations of the mutated genes were analyzed to predict the possible effects of the SNPs on gene function. In conclusion, we selected and validated the genetic variations identified in transgenic Chinese cabbage plants. Their genomes were expected to be affected by the process of <i>Agrobacterium</i>-mediated transformation. The findings of our study will provide a genetic basis for transgenic plant research. |
topic |
<i>Brassica rapa</i> in vitro culture resequencing single nucleotide polymorphisms transgenic plants |
url |
https://www.mdpi.com/2073-4425/12/5/621 |
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