As one of the rare and precious wood species since the ancient times, Gingko is also known as “living fossil”, which is a special plant resource of China. Gingko leaves, containing rich flavonoids, are valued with great medicinal significances. This paper treated Ginkgo seedlings by exogenous Sodium selenite (SS) in two ways: Foliage dressing (FD) and Root application (RA). Then transcriptome sequencing and metabolome test are performed. Results show that external SS has significant influence on the related gene expression level of flavonoids synthesis ways of Gingko, the FD can significantly induce gene expressions as CHS, FLS, FOMT, PAL, MYB1 and MYB2, and RA can significantly induce gene expressions as FOMT, MYB1 and MYB2. Compared with the control group, FA selenium application can help to accumulation of flavonoids, flavonols, flavonoids-C and isoflavones, especially quercetin and kaempferol that had a remarkable increase. This proved that a proper concentration of inorganic SS could promote the synthesis and accumulation of flavonoids in Gingko. qRT-PCR analysis also depicts that leaves treatment of sodium selenite can remarkably enhance the gene expression of CHS, FLS, FOMT and PAL, and RA selenium application can induce the gene expression of FLS and FOMT, but restrain the gene expression of CHS and PAL. Through the ways of FD and RA selenium application, this paper basically studied the regulatory effect of SS on ginkgo flavonoids synthesis and has laid a theoretical basis to improve flavonoids content in Ginkgo leaves through cultivation control means.
 
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 In press - Online First. Article has been peer reviewed, accepted for publication and published online without pagination. It will receive pagination when the issue will be ready for publishing as a complete number (Volume 47, Issue 3, 2019). The article is searchable and citable by Digital Object Identifier (DOI). DOI link will become active after the article will be included in the complete issue.
 
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