Basic leucine zipper gene VvbZIP61 is expressed at a quantitative trait locus for high monoterpene content in grape berries

Abstract

The widely appreciated muscat flavor of grapes and wine is mainly attributable to the monoterpenes that accumulate in ripe grape berries. To identify quantitative trait loci (QTL) for grape berry monoterpene content, an F₁ mapping population was constructed by a cross between two grapevine genotypes, one with neutral aroma berries (cv. ‘Beifeng’) and the other with a pronounced muscat aroma (elite Vitis vinifera line ‘3–34’). A high-density genetic linkage map spanning 1563.7 cM was constructed using 3332 SNP markers that were assigned to 19 linkage groups. Monoterpenes were extracted from the berry of the F₁ progeny, then identified and quantified by gas chromatography–mass spectrometry. Twelve stable QTLs associated with the amounts of 11 monoterpenes in berries were thus identified. In parallel, the levels of RNA in berries from 34 diverse cultivars were estimated by RNA sequencing and compared to the monoterpene content of the berries. The expression of five genes mapping to stable QTLs correlated well with the monoterpene content of berries. These genes, including the basic leucine zipper VvbZIP61 gene on chromosome 12, are therefore considered as potentially being involved in monoterpene metabolism. Overexpression of VvbZIP61 in Vitis amurensis callus through Agrobacterium-mediated transformation significantly increased the accumulation of several monoterpenes in the callus, including nerol, linalool, geranial, geraniol, β-myrcene, and D-limonene. It is hypothesized that VvbZIP61 expression acts to increase muscat flavor in grapes. These results advance our understanding of the genetic control of monoterpene biosynthesis in grapes and provide important information for the marker-assisted selection of aroma compounds in grape breeding.

Acknowledgements

We thank Dr Haohao Zhang and Ms Mingxi He of the Institute of Botany, Chinese Academy of Sciences for GC–MS, Dr Yingzhen Yang of USDA-ARS Grape Genetics Research Unit, Geneva, New York, US for GBS library construction, Dr Yuepeng Han of Wuhan Botanical Garden, Chinese Academy of Sciences for map construction and manuscript revision, Professor Eric Duchêne of Unite Mixte de Recherche 1131, INRAE, University of Strasbourg for his guidance and revision of this manuscript. We also would like to thank Golden (www.goldenenglishediting.com) for editing and proofreading this manuscript. This work was supported by the National Key Research and Development Program (2018YFD1000205), the National Science Foundation of China (31372028), the Agricultural Breeding Project of Ningxia Hui Autonomous Region NXNYYZ202101, the Alliance of International Science Organizations (ANSO-CR-PP-2020-04).

Data availability

The data for this manuscript have been deposited in National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (https://ncbi.nlm.nih.gov/bioproject/PRJNA565689).

Conflict of interest statement

None declared.

Supplementary data

Supplementary data is available at Horticulture Research online.

References

[1] Rapp A . Volatile flavour of wine: correlation between instrumental analysis and sensory perception. Die Nahrung. 1998; 42: 351-63

[2] Sáenz-Navajas M-P, Ballester J, Pêcher C et al. Sensory drivers of intrinsic quality of red wines: effect of culture and level of expertise. Food Res Int. 2013; 54: 1506-18

[3] Lund ST, Bohlmann J . The molecular basis for wine grape quality-a volatile subject. Science. 2006; 311: 804-5

[4] Hellín P, Manso A, Flores P et al. Evolution of aroma and phenolic compounds during ripening of ’Superior Seedless’ grapes. J Agric Food Chem. 2010; 58: 6334-40

[5] Mateo JJ, Jiménez M . Monoterpenes in grape juice and wines. J Chromatogr A. 2000; 881: 557-67

[6] Yang C, Wang Y, Liang Z et al. Volatiles of grape berries evaluated at the germplasm level by headspace-SPME with GC-MS. Food Chem. 2009; 114: 1106-14

[7] Fenoll J, Manso A, Hellín P et al. Changes in the aromatic composition of the Vitis vinifera grape Muscat Hamburg during ripening. Food Chem. 2009; 114: 420-8

[8] Fenoll J, Martínez M-C, Hellín P et al. Changes of free and glycosidically bound monoterpenes and aromatic alcohols in Moscatuel and ruby seedless table grapes during development. OENO One. 2016; 46: 41

[9] Belancic A, Agosin E, Ibacache A et al. Influence of sun exposure on the aromatic composition of Chilean Muscat grape cultivars Moscatel de Alejandría and Moscatel rosada. Am J Enol Vitic. 1997; 48: 181-6

[10] Zhang H, Fan P, Liu C et al. Sunlight exclusion from Muscat grape alters volatile profiles during berry development. Food Chem. 2014; 164: 242-50

[11] Dirninger N, Duc DS, Schneider C et al. Wine quality and terroirs: Influence of environmental characteristics on the Gewurztraminer favor profile. Sciences des Aliments. 1998; 18: 193-209

[12] Reynolds A, Wardle D, Hall J et al. Fruit maturation of four Vitis vinifera cultivars in response to vineyard location and basal leaf removal . Am J Enol Vitic. 1995; 46: 542-58

[13] Reynolds A, Wardle D, Dever M . Vine performance, fruit composition, and wine sensory attributes of Gewürztraminer in response to vineyard location and canopy manipulation. Am J Enol Vitic. 1996; 47: 77-92

[14] Bueno JE, Peinado R, Moreno J et al. Selection of volatile aroma compounds by statistical and enological criteria for analytical differentiation of musts and wines of two grape varieties. J Food Sci. 2003; 68: 158-63

[15] Duchene E, Butterlin G, Claudel P et al. A grapevine (Vitis vinifera L.) deoxy-D:-xylulose synthase gene colocates with a major quantitative trait loci for terpenol content . Theor Appl Genet. 2009; 118: 541-52

[16] EbangOke JP, Billerbeck GM, Ambid C . Temporal expression of the Lis gene from Vitis vinifera L., cv. Muscat de Frontignan . In: Flavour Research at the Dawn of the Twenty first Century Proceedings of the 2003 10th Weurman Flavour Research Symposium. Beaune, France, 25-28 June 2002, 321-5

[17] Lin H, Guo Y, Yang X et al. QTL identification and candidate gene identification for monoterpene content in grape (Vitis vinifera L.) berries . Vitis-Geilweilerhof. 2020; 59: 19-28

[18] Doligez A, Audiot E, Baumes R et al. QTLs for Muscat flavor and monoterpenic odorant content in grapevine (Vitis vinifera L.). Mol Breed. 2006; 18: 109-25

[19] Battilana J, Costantini L, Emanuelli F et al. The 1-deoxy-D:-xylulose 5-phosphate synthase gene co-localizes with a major QTL affecting monoterpene content in grapevine. Theor Appl Genet. 2009; 118: 653-69

[20] Lodhi MA, Daly MJ, Ye GN et al. A molecular marker based linkage map of Vitis. Genome. 1995; 38: 786-94

[21] Dalbó MA, Ye GN, Weeden NF et al. A gene controlling sex in grapevines placed on a molecular marker-based genetic map. Genome. 2000; 43: 333-40

[22] Doligez A, Bouquet A, Danglot Y et al. Genetic mapping of grapevine (Vitis vinifera L.) applied to the detection of QTLs for seedlessness and berry weight . Theor Appl Genet. 2002; 105: 780-95

[23] Welter LJ, Göktürk-Baydar N, Akkurt M et al. Genetic mapping and localization of quantitative trait loci affecting fungal disease resistance and leaf morphology in grapevine (Vitis vinifera L). Mol Breed. 2007; 20: 359-74

[24] Goulão L, Oliveira CM . Molecular characterisation of cultivars of apple (malus × domestica Borkh.) using microsatellite (SSR and ISSR) markers. Euphytica. 2001; 122: 81-9

[25] Schwander F, Eibach R, Fechter I et al. Rpv10: a new locus from the Asian Vitis gene pool for pyramiding downy mildew resistance loci in grapevine. Theor Appl Genet. 2012; 124: 163-76

[26] Vezzulli S, Malacarne G, Masuero D et al. The Rpv3-3 haplotype and Stilbenoid induction mediate downy mildew resistance in a grapevine interspecific population. Frontiers Plant Science. 2019; 10: 234

[27] Emanuelli F, Battilana J, Costantini L et al. A candidate gene association study on Muscat flavor in grapevine (Vitis vinifera L.). BMC Plant Biol. 2010; 10: 241

[28] Battilana J, Emanuelli F, Gambino G et al. Functional effect of grapevine 1-deoxy-D-xylulose 5-phosphate synthase substitution K284N on Muscat flavour formation. J Exp Bot. 2011; 62: 5497-508

[29] Dalla Costa L, Emanuelli F, Trenti M et al. Induction of terpene biosynthesis in berries of microvine transformed with VvDXS1 alleles. Frontiers Plant Science. 2017; 8: 2244

[30] Yu Y, Zhang X, Yuan J et al. Genome survey and high-density genetic map construction provide genomic and genetic resources for the Pacific white shrimp Litopenaeus vannamei. Sci Rep. 2015; 5: 15612

[31] Elshire RJ, Glaubitz JC, Sun Q et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One. 2011; 6: e19379

[32] Poland JA, Brown PJ, Sorrells ME et al. Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One. 2012; 7: e32253

[33] Byrne S, Czaban A, Studer B et al. Genome wide allele frequency fingerprints (GWAFFs) of populations via genotyping by sequencing. PLoS One. 2013; 8: e57438

[34] Sonah H, Bastien M, Iquira E et al. An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS One. 2013; 8: e54603

[35] Smith HM, Clarke CW, Smith BP et al. Genetic identification of SNP markers linked to a new grape phylloxera resistant locus in Vitis cinerea for marker-assisted selection . BMC Plant Biol. 2018; 18: 360

[36] Fu P, Tian Q, Lai G et al. Cgr1, a ripe rot resistance QTL in Vitis amurensis ’Shuang Hong’ grapevine. Hortic Res. 2019; 6: 67

[37] Tello J, Roux C, Chouiki H et al. A novel high-density grapevine (Vitis vinifera L.) integrated linkage map using GBS in a half-diallel population . Theor Appl Genet. 2019; 132: 2237-52

[38] Possamai T, Wiedemann-Merdinoglu S, Merdinoglu D et al. Construction of a high-density genetic map and detection of a major QTL of resistance to powdery mildew (Erysiphe necator Sch.) in Caucasian grapes (Vitis vinifera L.). BMC Plant Biol. 2021; 21: 528

[39] Alahakoon D, Fennell A, Helget Z et al. Berry anthocyanin, acid, and volatile trait analyses in a grapevine-interspecific F2 population using an integrated GBS and rhAmpSeq genetic map. Plants (Basel). 2022; 11: 696

[40] Lytkin K, Nosulchak V, Agakhanov M et al. Development of a high-density genetic map for Muscadine grape using a mapping population from selfing of the perfect-flowered vine ’Dixie’. Plants (Basel). 2022; 11: 3231

[41] Sapkota S, Chen LL, Yang S et al. Construction of a high-density linkage map and QTL detection of downy mildew resistance in Vitis aestivalis-derived ’Norton’ . Theor Appl Genet. 2019; 132: 137-47

[42] Wang Z, Gerstein M, Snyder M . RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009; 10: 57-63

[43] Fan Y, Wang Q, Kang L et al. Transcriptome-wide characterization of candidate genes for improving the water use efficiency of energy crops grown on semiarid land. J Exp Bot. 2015; 66: 6415-29

[44] Xiao Y, Ji Q, Gao S et al. Combined transcriptome and metabolite profiling reveals that IiPLR1 plays an important role in lariciresinol accumulation in Isatis indigotica. J Exp Bot. 2015; 66: 6259-71

[45] Yendrek CR, Koester RP, Ainsworth EA . A comparative analysis of transcriptomic, biochemical, and physiological responses to elevated ozone identifies species-specific mechanisms of resilience in legume crops. J Exp Bot. 2015; 66: 7101-12

[46] Zhang H, Wang H, Yi H et al. Transcriptome profiling of Cucumis melo fruit development and ripening. Hortic Res. 2016; 3: 16014

[47] Shapiro SS, Wilk MB . An analysis of variance test for normality. Biometrika. 1965; 52: 591-611

[48] R Core Team . R: a language and environment for statistical computing. 2011; 1: 12-21

[49] Canaguier A, Grimplet J, Di Gaspero G et al. A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3). Genomics Data. 2017; 14: 56-62

[50] Ooijen JW . JoinMap® 4, Software for the calculation of genetic linkage maps in experimental populations. 2006.

[51] Liu J, Chen N, Chen F et al. Genome-wide analysis and expression profile of the bZIP transcription factor gene family in grapevine (Vitis vinifera). BMC Genomics. 2014; 15: 281

[52] Zou C, Karn A, Reisch B et al. Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus. Nat Commun. 2020; 11: 413

[53] Riaz T, Shehzad W, Viari A et al. ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Res. 2011; 39: e145

[54] Blanc S, Wiedemann-Merdinoglu S, Dumas V et al. A reference genetic map of Muscadinia rotundifolia and identification of Ren5, a new major locus for resistance to grapevine powdery mildew. Theor Appl Genet. 2012; 125: 1663-75

[55] Venuti S, Copetti D, Foria S et al. Historical introgression of the downy mildew resistance gene Rpv12 from the Asian species Vitis amurensis into grapevine varieties . PLoS One. 2013; 8: e61228

[56] Barba P, Cadle-Davidson L, Harriman J et al. Grapevine powdery mildew resistance and susceptibility loci identified on a high-resolution SNP map. Theor Appl Genet. 2014; 127: 73-84

[57] Chen J, Wang N, Fang L-C et al. Construction of a high-density genetic map and QTLs mapping for sugars and acids in grape berries. BMC Plant Biol. 2015; 15: 28

[58] Houel C, Chatbanyong R, Doligez A et al. Identification of stable QTLs for vegetative and reproductive traits in the microvine (Vitis vinifera L.) using the 18 K Infinium chip . BMC Plant Biol. 2015; 15: 205

[59] Zyprian E, Šimon S, Schwander F et al. Efficiency of single nucleotide polymorphisms to improve a genetic map of complex pedigree grapevines. Vitis-Geilweilerhof. 2015; 54: 29-32

[60] Teh SL, Fresnedo-Ramírez J, Clark MD et al. Genetic dissection of powdery mildew resistance in interspecific half-sib grapevine families using SNP-based maps. Mol Breed. 2017; 37: 1

[61] Barba P, Loughner R, Wentworth K et al. A QTL associated with leaf trichome traits has a major influence on the abundance of the predatory mite Typhlodromus pyri in a hybrid grapevine population. Hort Res. 2019; 6: 6

[62] Royo C, Rodriguez-Lorenzo M, Carbonell-Bejerano P et al. Characterization of deletions causing berry-color variation in Garnacha and Tempranillo. Acta Hortic. 2019; 463-70

[63] Crespan M, Migliaro D, Larger S et al. Unraveling the genetic origin of ‘Glera’, ‘Ribolla Gialla’ and other autochthonous grapevine varieties from Friuli Venezia Giulia (northeastern Italy). Sci Rep. 2020; 10: 7206

[64] Duchêne É, Dumas V, Butterlin G et al. Genetic variations of acidity in grape berries are controlled by the interplay between organic acids and potassium. Theor Appl Genet. 2020; 133: 993-1008

[65] Fu P, Wu W, Lai G et al. Identifying Plasmopara viticola resistance loci in grapevine (Vitis amurensis) via genotyping-by-sequencing-based QTL mapping . Plant Physiol Biochem. 2020; 154: 75-84

[66] Sun L, Li S, Jiang J et al. New quantitative trait locus (QTLs) and candidate genes associated with the grape berry color trait identified based on a high-density genetic map. BMC Plant Biol. 2020; 20: 302

[67] Wang H, Yan A, Sun L et al. Novel stable QTLs identification for berry quality traits based on high-density genetic linkage map construction in table grape. BMC Plant Biol. 2020; 20: 411

[68] Hugalde IP, Paolinelli M, Agüero CB et al. Prioritization of vigor QTL-associated genes for future genome-directed Vitis breeding. Revista de la Facultad de Ciencias Agrarias UNCuyo. 2021; 53: 27-35

[69] Mamani M, Lopez ME, Correa J et al. Identification of stable quantitative trait loci and candidate genes for sweetness and acidity in tablegrape using a highly saturated single-nucleotide polymorphism-based linkage map. Grape Wine Res. 2021; 27: 308-24

[70] Negus KL, Chen L-L, Fresnedo-Ramírez J et al. Identification of QTLs for berry acid and tannin in a Vitis aestivalis-derived ’Norton’-based population. Fruit Res. 2021; 1: 1-11

[71] Su K, Guo Y, Zhong W et al. High-density genetic linkage map construction and white rot resistance quantitative trait loci mapping for genus Vitis based on restriction site-associated DNA sequencing. Phytopathology. 2021; 111: 659-70

[72] Alahakoon D, Fennell A, Helget Z et al. Berry anthocyanin, acid, and volatile trait analyses in a grapevine-interspecific F2 population using an integrated GBS and rhAmpSeq genetic map. Plan Theory. 2022; 11: 696

[73] Rist F, Schwander F, Richter R et al. Relieving the phenotyping bottleneck for grape bunch architecture in grapevine breeding research: implementation of a 3D-based phenotyping approach for quantitative trait locus mapping. Horticulturae. 2022; 8: 907

[74] Hugalde I, Riaz S, Agüero C et al. Studying growth and vigor as quantitative traits in grapevine populations. In: Maia RT, Campos MA Integrated View of Population Genetics. London: IntechOpen, 2019, 9-24

[75] Guillaumie S, Decroocq S, Ollat N et al. Dissecting the control of shoot development in grapevine: genetics and genomics identify potential regulators. BMC Plant Biol. 2020; 20: 43

[76] Wang Y, Zhang R, Liang Z et al. Grape-RNA: a database for the collection, evaluation, treatment, and data sharing of grape RNA-Seq datasets. Genes (Basel). 2020; 11: 315

[77] Crespan M, Migliaro D, Vezzulli S et al. A major QTL is associated with berry grape texture characteristics. OENO One. 2021; 55: 183-206

[78] Karn A, Zou C, Brooks S et al. Discovery of the REN11 locus from Vitis aestivalis for stable resistance to grapevine powdery mildew in a family segregating for several unstable and tissue-specific quantitative resistance loci . Front Plant Sci. 2021; 12: 733899

[79] Wen YQ, Zhong GY, Gao Y et al. Using the combined analysis of transcripts and metabolites to propose key genes for differential terpene accumulation across two regions. BMC Plant Biol. 2015; 15: 240

[80] Wu Y, Zhang W, Yu W et al. Study on the volatile composition of table grapes of three aroma types. LWT. 2019; 115: 108450

[81] Liu X, Fan P, Jiang J et al. Evolution of volatile compounds composition during grape berry development at the germplasm level. Sci Hortic. 2022; 293: 110669

[82] Liu C, Fan P, He M et al. Inheritance of Muscat berry volatiles in grape interspecific cross population. Euphytica. 2016; 208: 73-89

[83] Kosambi DD . The estimation of map distances from recombination values. Ann Eugenics. 1943; 12: 172-5

[84] Voorrips RE . MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered. 2002; 93: 77-8

[85] Bolger AM, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30: 2114-20

[86] Kim D, Pertea G, Trapnell C et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013; 14: R36

[87] Trapnell C, Roberts A, Goff L et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and cufflinks. Nat Protoc. 2012; 7: 562-78

[88] Shannon P, Markiel A, Ozier O et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13: 2498-504

[89] Livak KJ, Schmittgen TD . Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods. 2001; 25: 402-8

[90] Zhao T, Wang Z, Su L et al. An efficient method for transgenic callus induction from Vitis amurensis petiole. PLoS One. 2017; 12: e0179730