Combining paired analytical metabolomics and common garden trial to study the metabolism and gene variation of Ginkgo biloba L. cultivated varieties

Secondary metabolites play a pivotal role in plant physiology and medicinal function. Much work has been carried out to uncover the genetic basis of plant secondary metabolite variation, but direct screening of gene variation in the whole genome is extremely time- and labor-consuming. The prediction of a candidate locus of a single nucleotide polymorphism (SNP) will save much time and resource. In this work, we combined a paired analytical metabolomics and a common garden trial to bridge the association of plant metabolism and related gene variation of Ginkgo cultivated varieties. Firstly, the leaves of 30 cultivated varieties of Ginkgo biloba L. grown in the same garden since 1990 were analyzed by UHPLC-QQQ MS/MS. Thirty-six metabolites in the flavonoid biosynthetic pathway were quantified. The biosynthetic rate of flavonoids in different cultivated varieties could reflect the related enzyme gene variation, since the environmental influence was minimized. Thus, the role of SNPs in possible varied genes was further associated with flavonoid synthesis. Results showed that after long term environment and artificial influence, different accessions of G. biloba showed a varied ability in flavonoid aglycone synthesis due to some gene polymorphism; this difference may be heritable but not obvious. Compared with previous methods, this strategy is advantageous in accuracy, low sample requirement and easier operation, providing effective information in phenotype–genotype association, and it can also be used in the heritability study of artificial breeding before large-area introduction.