Gene expression profiling reveals light regulation on adventitious root formation in lotus (Nelumbo nucifera Gaertn.)

Abstract Background: Lotus is an aquatic horticultural crop, and widely cultivated in most regions of China. Lotus is often used as a kind of an important off-season vegetable with various nutrients. Principle root of lotus is degenerated, and the role of adventitious roots (ARs) is Irreplaceable for plant growth. We found that no ARs could be formed under darkness condition, and high light significantly promote the development of root primordium. Therefore, four libraries with three light intensities were constructed to monitor metabolism changes, especially in IAA and sugar metabolism. Results: We found that ARs formation was significantly affected by light, high light intensity accelerated ARs development. The change of metabolism during ARs formation under different light intensity was evaluated according to gene expression profiling by high-throughput tag-sequencing. It was shown that more than 2.2× 10 4 genes was obtained in each library, and the expression level of most genes were distributed between 1e-01 and 1e+03 (FPKF value). Among these identified genes, 1739, 1683 and 1462 genes were up-regulated, and 1533, 995 and 834 genes were down-regulated in D/CK, E/CK and F/CK libraries respectively. In addition, we also found that 1454 and 478 genes changed expression in D/CK and F/CK libraries when compared D/CK with F/CK libraries. In F/D libraries, the transcriptional level of most differentially expressed genes was between -5~5 fold, and twenty differentially expressed genes were involved in signal transduction pathway. Twenty-eight genes related with IAA response and thirty-five genes involved in sugar metabolism were found to change expression. It was elucidated that IAA content was enhanced after seed germinated, even in darkness condition, which was responsible for ARs formation. Conclusion: The process of ARs formation was very complex, and regulated by multiple factors. The ARs formation was regulated by IAA, even in the dark, induction and developmental process could also be completed. In addition, the genes (36 genes) changed expression level in carbohydrate metabolism showed the third number, so sucrose metabolism was involved in the ARs development (expressed stage) according to genes expression and content change characteristic.