Identification of SNP loci and candidate genes genetically controlling norisoprenoids in grape berry based on genome-wide association study

Qi Sun; Lei He; Lei Sun; Hai-Ying Xu; Ya-Qun Fu; Zheng-Yang Sun; Bao-Qing Zhu; Chang-Qing Duan; Qiu-Hong Pan

doi:10.3389/fpls.2023.1142139

Identification of SNP loci and candidate genes genetically controlling norisoprenoids in grape berry based on genome-wide association study

Front Plant Sci. 2023 Mar 1:14:1142139. doi: 10.3389/fpls.2023.1142139. eCollection 2023.

Authors

Qi Sun^{1

2}, Lei He^{1

2}, Lei Sun³, Hai-Ying Xu³, Ya-Qun Fu^{1

2}, Zheng-Yang Sun^{1

2}, Bao-Qing Zhu⁴, Chang-Qing Duan^{1

2}, Qiu-Hong Pan^{1

2}

Affiliations

¹ Center for Viticulture & Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.
² Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, China.
³ Beijing Academy of Forestry and Pomology Sciences, Beijing, China.
⁴ College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.

Abstract

Obtaining new grapevine varieties with unique aromas has been a long-standing goal of breeders. Norisoprenoids are of particular interest to wine producers and researchers, as these compounds are responsible for the important varietal aromas in wine, characterized by a complex floral and fruity smell, and are likely present in all grape varieties. However, the single-nucleotide polymorphism (SNP) loci and candidate genes genetically controlling the norisoprenoid content in grape berry remain unknown. To this end, in this study, we investigated 13 norisoprenoid traits across two years in an F₁ population consisting of 149 individuals from a hybrid of Vitis vinifera L. cv. Muscat Alexandria and V. vinifera L. cv. Christmas Rose. Based on 568,953 SNP markers, genome-wide association analysis revealed that 27 candidate SNP loci belonging to 18 genes were significantly associated with the concentrations of norisoprenoid components in grape berry. Among them, 13 SNPs were confirmed in a grapevine germplasm population comprising 97 varieties, including two non-synonymous mutations SNPs within the VvDXS1 and VvGGPPS genes, respectively in the isoprenoid metabolic pathway. Genotype analysis showed that the grapevine individuals with the heterozygous genotype C/T at chr5:2987350 of VvGGPPS accumulated higher average levels of 6-methyl-5-hepten-2-one and β-cyclocitral than those with the homozygous genotype C/C. Furthermore, VvGGPPS was highly expressed in individuals with high norisoprenoids concentrations. Transient overexpression of VvGGPPS in the leaves of Vitis quinquangularis and tobacco resulted in an increase in norisoprenoid concentrations. These findings indicate the importance of VvGGPPS in the genetic control of norisoprenoids in grape berries, serving as a potential molecular breeding target for aroma.

Keywords: genetic regulation; genome-wide association study; grape berry; norisoprenoids; single nucleotide polymorphism.

Grants and funding

This research was funded by the National Natural Science Foundation of China (grant number: 32072513 to Q-HP) and the Earmarked Fund for China Agriculture Research System (CARS-29 to C-QD)