Comparative transcriptome profiling of different tissues from beta-carotene-enhanced transgenic soybean and its non-transgenic counterpart

Abstract

Beta-carotene-enhanced transgenic soybeans, harboring genes encoding phytoene synthase and carotene desaturase under the control of a seed-specific promoter, were developed to alleviate vitamin A deficiency in populations, the diet of which was deficient in this vitamin. However, metabolic engineering of carotenoid biosynthetic pathways often has unintended effects, leading to major metabolic changes in plants that harbor endogenous beta-carotene biosynthesis pathways. In the present study, we performed transcriptome profiling analysis using RNA-seq to investigate the changes in the transcriptome and some unintended pleiotropic effects on the leaves, stems, roots, and seeds of beta-carotene-enhanced transgenic soybean lines, and compared them to those of their non-transgenic counterpart donor variety Kwangan. We observed that transgenic soybeans showed significant changes in secondary metabolic biosynthesis in leaves and down-regulated galactose metabolism in roots. Differentially expressed genes in the transgenic group, which were significantly up-regulated, included those encoding glycine-aspartic acid-serine-leucine-motif esterase/lipase, known as cutin synthase and cutinase. These results suggested enhanced beta-carotene biosynthesis may affect related enzymes to carbohydrate metabolism and fatty acid metabolism. Hence, we speculated that upregulation of cutin polymerization resulted in thickened seed coat and delayed seed germination of transgenic soybeans. Furthermore, downregulation of raffinose family oligosaccharide biosynthesis may cause redundancy of myo-inositol, a substrate of phytin formation. This could lead to phytic globoids accumulation in transgenic soybean seeds. The present imformation would be important for transgenic plant development via carotenoid metabolic engineering, with focus on beta-carotene over-production.