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

Table 3 Pathways enriched in differentially expressed genes in the transgenic line DXT, MAB breeding line DXB and a rice variety MH86 with respect to recipient line D62B

Pathways	DXT	DXB	MH86
Ribosome	√	√	√
Flavonoid biosynthesis	√	√	√
Vitamin B6 metabolism	√	√	√
Biosynthesis of phenylpropanoids	√	√
Benzoxazinoid biosynthesis	√	√
Flavone and flavonol biosynthesis	√	√
Oxidative phosphorylation	√	√
Carotenoid biosynthesis	√
Regulation of autophagy	√
Arachidonic acid metabolism	√
Anthocyanin biosynthesis	√
Zeatin biosynthesis		√	√
ABC transporters		√	√
Inositol phosphate metabolism		√	√
Phenylalanine metabolism		√
Glycine, serine and threonine metabolism		√
Phagosome		√
Biosynthesis of secondary metabolites		√
Circadian rhythm - plant		√
Sulfur metabolism		√
Metabolism of xenobiotics by cytochrome P450			√
Spliceosome			√
Endocytosis			√
Biosynthesis of plant hormones			√
Biosynthesis of unsaturated fatty acids			√
Glutathione metabolism			√
Linoleic acid metabolism			√
Biosynthesis of terpenoids and steroids			√
alpha-Linolenic acid metabolism			√
Phosphatidylinositol signaling system			√
Limonene and pinene degradation			√
Non-homologous end-joining			√
Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid			√
Glycosylphosphatidylinositol(GPI)-anchor biosynthesis			√

Listed are significantly enriched KEGG terms with cutoff of p ≤ 0.05. “√” means significantly affected pathway. Note that the four pathways enriched in DXT but not listed under DXB in the table were also enriched in DXB at a less significant level (with p-values from 0.06 to 0.88).

ISSN: 1471-2164