Grapevine genome analysis demonstrates the role of gene copy number variation in the formation of monoterpenes

Abstract

Volatile organic compounds such as terpenes influence the quality parameters of grapevine through their contribution to the flavour and aroma profile of berries. Biosynthesis of volatile organic compounds in grapevine is relatively complex and controlled by multiple genes, the majority of which are unknown or uncharacterised. To identify the genomic regions that associate with modulation of these compounds in grapevine berries, volatile metabolic data generated via GC-MS from a grapevine mapping population was used to identify quantitative trait loci (QTLs). Several significant QTLs were associated with terpenes, and candidate genes were proposed for sesquiterpene and monoterpene biosynthesis. For monoterpenes, loci on chromosomes 12 and 13 were shown to be associated with geraniol and cyclic monoterpene accumulation, respectively. The locus on chromosome 12 was shown to contain a geraniol synthase gene (VvGer), while the locus on chromosome 13 contained an α-terpineol synthase gene (VvTer). Molecular and genomic investigation of VvGer and VvTer revealed that these genes were found in tandemly duplicated clusters, displaying high levels of hemizygosity. Gene copy number analysis further showed that not only did VvTer and VvGer copy numbers vary within the mapping population, but also across recently sequenced Vitis cultivars. Significantly, VvTer copy number correlated with both VvTer gene expression and cyclic monoterpene accumulation in the mapping population. A hypothesis for a hyper-functional VvTer allele linked to increased gene copy number in the mapping population is presented and can potentially lead to selection of cultivars with modulated terpene profiles. The study highlights the impact of VvTPS gene duplication and copy number variation on terpene accumulation in grapevine.

Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes

“…listed in Table 2 . A few studies have uncovered new genes and rare alleles that regulate secondary metabolites associated with color and flavor [ 46 , 49 , 165 ], pathogen resistance [ 43 , 47 , 56 , 79 , 145 , 165 , 166 , 167 ], and abiotic stress tolerance [ 41 , 42 , 55 ]. These findings foster an understanding of the genetic basis of diverse traits in domesticated crops and offer promising prospects for introducing candidate genes (for disease resistance and quality traits) through molecular breeding or precise genome editing into elite cultivars.…”

“…Thus, the availability of plant pan-genomes allows researchers and breeders to explore important candidate genes for improving crop yield, nutritional quality, and adaptability to changing climatic conditions and diseases. For instance, a few comparative genomic studies have revealed that gene amplification plays a vital role in disease resistance, abiotic stress tolerance, and other agronomic traits associated with plant development, architecture, and yield [ 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 ]. In addition, the high-quality pan-genomes also make it possible to study previously inaccessible regions of the eukaryotic genomes, including centromeres, long heterochromatic blocks, rDNA regions, etc., that exhibit low recombination, and provide new insights into crop genome evolution [ 50 ].…”

Multi-omic applications for understanding and enhancing tropical fruit flavour

“…Genomics data may further advance tropical fruit flavour through targeted breeding and genetic selection strategies or gene-editing technology (Mathiazhagan et al 2021 ). Genome-wide association studies (GWAS) and quantitative trait loci (QTL) mapping approaches have previously identified genome regions responsible for the regulation of fruit flavour compounds in tomato (Gai et al 2023 ; Sapkota et al 2023 ), grape (Koyama et al 2022 ; Bosman et al 2023 ) and apple (Yang et al 2023 ).…”

Exploring Pan-Genomes of Crops: Genomic Resources and Tools for Unraveling Gene Evolution, Function, and Adaptation

“…Thus, the availability of plant pan-genomes allows researchers and breeders to explore important candidate genes for improving crop yield, nutritional quality, and adaptability to changing climatic conditions and diseases. For instance, a few comparative genomic studies have revealed that gene amplification plays a vital role in disease resistance, abiotic stress tolerance, and other agronomic traits associated with plant development, architecture, and yield [40][41][42][43][44][45][46][47][48][49]. In addition, the highquality pan-genomes also make it possible to study previously inaccessible regions of the eukaryotic genomes, including centromeres, long heterochromatic blocks, rDNA regions, etc., that exhibit low recombination, and provide new insights into crop genome evolution [50].…”