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Do transgenesis and marker-assisted backcross breeding produce substantially equivalent plants? - A comparative study of transgenic and backcross rice carrying bacterial blight resistant gene Xa21

Lifen Gao12, Yinghao Cao13, Zhihui Xia1, Guanghuai Jiang1, Guozhen Liu3, Weixiong Zhang24* and Wenxue Zhai1*

Author Affiliations

1 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

2 Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China

3 College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China

4 Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA

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BMC Genomics 2013, 14:738  doi:10.1186/1471-2164-14-738

Published: 29 October 2013



The potential impact of genetically modified (GM) plants on human health has attracted much attention worldwide, and the issue remains controversial. This is in sharp contrast to the broad acceptance of plants produced by breeding through Marker Assisted Backcrossing (MAB).


Focusing on transcriptome variation and perturbation to signaling pathways, we assessed the molecular and biological aspects of substantial equivalence, a general principle for food safety endorsed by the Food and Agricultural Organization and the World Health Organization, between a transgenic crop and a plant from MAB breeding. We compared a transgenic rice line (DXT) and a MAB rice line (DXB), both of which contain the gene Xa21 providing resistance to bacterial leaf blight. By using Next-Generation sequencing data of DXT, DXB and their parental line (D62B), we compared the transcriptome variation of DXT and DXB. Remarkably, DXT had 43% fewer differentially expressed genes (DEGs) than DXB. The genes exclusively expressed in DXT and in DXB have pathogen and stress defense functions. Functional categories of DEGs in DXT were comparable to that in DXB, and seven of the eleven pathways significantly affected by transgenesis were also perturbed by MAB breeding.


These results indicated that the transgenic rice and rice from MAB breeding are substantial equivalent at the transcriptome level, and paved a way for further study of transgenic rice, e.g., understanding the chemical and nutritional properties of the DEGs identified in the current study.

Transgenesis; Marker-assisted backcrossing; Substantial equivalence; Transcriptome profile; Xa21