GWAS identifies a molecular marker cluster associated with monoterpenoids in grapes

Abstract

Monoterpenoids are vital compounds that impart a distinctive floral flavor. They exist in both glycosidic and free forms in grapes. The breeding of improved monoterpenoid varieties has consistently been a topic of interest, yet only a limited number of molecular markers have been documented. This study employed a genome-wide association study (GWAS) on an F₁ population crossed between a typical muscat variety (‘Muscat of Alexandria’) and a non-aromatic variety (‘Christmas Rose’), conducted over two consecutive years. A total of 4089 significant single nucleotide polymorphism sites (sigSNPs) and 892 candidate genes associated with monoterpenoids were identified. The sigSNPs corresponding to the glycosidic and total (glycosidic plus free) concentrations of various monoterpenoid compounds exhibited a high similarity. The majority of sigSNPs were located on chromosome 5, indicating the existence of a monoterpenoid-related marker cluster. Sixty-one lead SNPs located within the gene region and stably appearing in 2 years were selected and verified using a germplasm population. The alleles of the 25 lead SNPs were confirmed to be highly associated with monoterpenoid levels. The genes containing these lead SNPs were mainly glycoside hydrolase, ABC transporter, as well as the previously reported 1-deoxy-D-xylulose-5-phosphate synthase (VvDXS1) and geranylgeranyl pyrophosphate synthase large subunit (VvGGPPS-LSU). The function of VvGGPPS-LSU in regulating monoterpenoid levels was elucidated through in vivo overexpression, demonstrating the reliability of the marker cluster. The present study proposes a molecular marker set for the breeding with the objective of improving aroma, and a candidate gene network for the regulation of monoterpenoid synthesis in grapevine.

Acknowledgements

All authors thank Prof. Bao-Qing Zhu and Prof. Wen-Hao Bo from Beijing Forestry University for their assistance in GWAS analysis. We also sincerely thank scientist Xiao-Ping Tang and Zhi-Gang Dong from Shanxi Academy of Agricultural Sciences Pomology Institute for providing grapevine germplasm population. This work was funded by the Key R&D projects in Ningxia Hui Autonomous Region (grant numbers: 2024BBF01002 to Q.H.P.) and the National Natural Science Foundation of China (grant no. U20A2042 to C.Q.D. and 32072513 to Q.H.P.).

Author contributions

Q.H.P and C.Q.D conceived the project and supervised this study. H.M.Z performed data analysis, original draft preparation, and main experiments. X.J.L contributed to the transgenic calli experiments and measurement of aromas. Z.Y.S and Q.S. detected the aroma of F₁ population. Y.C.W participated in the collection of the germplasm population. L.S. and H.Y.X provided the F₁ population. L.H helped the bioinformatics analysis. All authors contributed to the article and approved the submitted version.

Data availability

The genome resequencing data of this article can be found in the China National Center for Bioinformation National Genomics Data Center (https://ngdc.cncb.ac.cn/) under accession number CRA009145. Other data are provided in the article and supplementary data files.

Conflict of interest

The authors declare no conflicts of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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