Population diversity analyses provide insights into key horticultural traits of Chinese native thymes

Abstract

Chinese native thymes (CNTs) in the genus Thymus (family Lamiaceae) are rich in bioactive terpenes, which exert antiviral, anti-inflammatory, antioxidation, immunological, and antimicrobial effects. Plants exhibit morphological variation, including erect-type and creeping-type growth forms; however, the molecular mechanisms underlying important horticultural traits have not been determined. Here, we collected 39 CNTs providing strategic plant resources for studies of lignin, terpenoids, and glandular trichomes of thymes. Using resequencing data as well as phenotypic, metabonomic, phylogenetic, population genetic, and transcriptomic analyses, we identified and characterized key genes involved in lignin biosynthesis, terpenoid biosynthesis, and glandular trichome formation. We found many regulatory genes or transcription factors related to these three important horticultural traits, including genes encoding caffeic acid O-methyltransferase (COMT), terpene synthase (TPS), v-myb avian myeloblastosis viral oncogene homolog (MYB), and homeodomain-leucine zipper (HD-ZIP). Population diversity analyses provided insights into growth form, terpenoid, and glandular trichome evolution in CNTs. Furthermore, our results revealed that T. mongolicus accessions might be wild ancestors, and T. quinquecostatus, T. quinquecostatus var. asiaticus, and T. quinquecostatus var. przewalskii might be transitional accessions that derived from T. mongolicus accessions. Finally, T. nervulosus, T. inaequalis, T. mandschuricus, T. curtus, T. amurensis, T. proximus, T. altaicus, T. roseus, and T. marschallianus showed high divergence. We found evidence for introgression between erect-type European cultivated thymes and CNTs. These findings improve our understanding of the determinants of variation in horticultural traits and provide candidate loci for research and breeding.

Acknowledgements

This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (grant no.XDA23080603). We thank Xiuping Xu and Ronghua Liang from the Plant Science Facility of the Institute of Botany, Chinese Academy of Science, for their excellent technical assistance in scanning electron microscopy and fluorescence microscopy. We thank Yan Zhu from the Plant Science Facility of the Institute of Botany, Chinese Academy of Science, for her excellent technical assistance in MS analysis.

Author contributions

M.Y.S. and Y.N.Z. performed the experiments, analyzed the data, and wrote the manuscript; H.T.B. and G.F.S. collected samples and analyzed the data; J.Z.Z. collected samples and designed the research; L.S. was involved in research design and revising the manuscript. All authors read and approved the manuscript.

Data availability

The raw sequence data for resequencing have been deposited in NCBI under project accession no. PRJNA690675. All supplementary figures and tables are provided in the Supplementary Data files.

Conflict of interest

The authors declare no competing financial interests.

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