Genetic analysis of stilbenoid profiles in grapevine stems reveals a major mQTL hotspot on chromosome 18 associated with disease-resistance motifs

Abstract

Grapevine (Vitis spp.) contains a wealth of phytochemicals that have received considerable attention due to health-promoting properties and biological activities as phytoalexins. To date, the genetic basis of the quantitative variations for these potentially beneficial compounds has been limited. Here, metabolic quantitative trait locus (mQTL) mapping was conducted using grapevine stems of a segregating F₂ population. Metabolic profiling of grapevine stems was performed using liquid chromatography–high-resolution mass spectrometry (LC-HRMS), resulting in the detection of 1317 ions/features. In total, 19 of these features matched with literature-reported stilbenoid masses and were genetically mapped using a 1449-SNP linkage map and R/qtl software, resulting in the identification of four mQTLs. Two large-effect mQTLs that corresponded to a stilbenoid dimer and a trimer were mapped on chromosome 18, accounting for phenotypic variances of 29.0% and 38.4%. Functional annotations of these large-effect mQTLs on the VitisNet network database revealed a major hotspot of disease-resistance motifs on chromosome 18. This 2.8-Mbp region contains 48 genes with R-gene motifs, including variants of TIR, NBS, and LRR, that might potentially confer resistance to powdery mildew, downy mildew, or other pathogens. The locus also encompasses genes associated with flavonoid and biosynthetic pathways that are likely involved in the production of secondary metabolites, including phytoalexins. In addition, haplotype dosage effects of the five mQTLs further characterized the genomic regions for differential production of stilbenoids that can be applied in resistance breeding through manipulation of stilbenoid production in planta.

References

[1] Lopez, M., Martinez, F., Del Valle, C., Orte, C. & Miro, M. Analysis of phenolic constituents of biological interest in red wines by high-performance liquid chromatography. J. Chromatogr. A 922, 359-363 (2001).

[2] Stervbo, U., Vang, O. & Bonnesen, C. A review of the content of the putative chemopreventive phytoalexin resveratrol in red wine. Food Chem. 101, 449-457 (2007).

[3] Pawlus, A. D., Waffo-Téguo, P., Shaver, J. & Mérillon, J. M. Stilbenoid chemistry from wine and the genus Vitis, a review. J. Int. des. Sci. de. la Vigne et. du Vin. 46, 57-111 (2012).

[4] Adrian, M., Jeandet, P., Veneau, J., Weston, L. A. & Bessis, R. Biological activity of resveratrol, a stilbenic compound from grapevines, against Botrytis cinerea, the causal agent for gray mold. J. Chem. Ecol. 23, 1689-1702 (1997).

[5] Anstey, K. J., Mack, H. A. & Cherbuin, N. Alcohol consumption as a risk factor for dementia and cognitive decline: meta-analysis of prospective studies. Am. J. Geriatr. Psychiatry 17, 542-555 (2009).

[6] Chao, C., Slezak, J. M., Caan, B. J. & Quinn, V. P. Alcoholic beverage intake and risk of lung cancer: the California Men’s Health Study. Cancer Epidemiol. Prev. Biomar. 17, 2692-2699 (2008).

[7] Wang, J. et al. Moderate consumption of Cabernet Sauvignon attenuates Aβ neuropathology in a mouse model of Alzheimer’s disease. FASEB J. 20, 2313-2320 (2006).

[8] Mattivi, F. et al. Profiling of resveratrol oligomers, important stress metabolites, accumulating in the leaves of hybrid Vitis vinifera (Merzling× Teroldego) genotypes infected with Plasmopara viticola. J. Agric. food Chem. 59, 5364-5375 (2011).

[9] Pezet, R., Gindro, K., Viret, O. & Richter, H. Effects of resveratrol, viniferins and pterostilbene on Plasmopara viticola zoospore mobility and disease development. Vitis 43, 145-148 (2004).

[10] Pezet, R., Gindro, K., Viret, O. & Spring, J. L. Glycosylation and oxidative dimerization of resveratrol are respectively associated to sensitivity and resistance of grapevine cultivars to downy mildew. Physiological Mol. Plant Pathol. 65, 297-303 (2004).

[11] Bavaresco, L., & Fregoni, C. Physiological role and molecular aspects of grapevine stilbenic compounds. In Molecular Biology & Biotechnology of the Grapevine (ed. Roubelakis-Angelakis, K. A.) 153-182 (Springer, Dordrecht, 2001).

[12] Bavaresco, L., Fregoni, C., de Macedo Basto, M. V. Z., & Vezzulli, S. Physiology & molecular biology of grapevine stilbenes: an update. In Grapevine Molecular Physiology & Biotechnology (ed. Roubelakis-Angelakis, K. A.) 341-364 (Springer, Dordrecht, 2009).

[13] Dubrovina, A. S. & Kiselev, K. V. Regulation of stilbene biosynthesis in plants. Planta 246, 597-623 (2017).

[14] Dettmer, K., Aronov, P. A. & Hammock, B. D. Mass spectrometry‐based metabolomics. Mass Spectrom. Rev. 26, 51-78 (2007).

[15] Hegeman, A. D. Plant metabolomics-meeting the analytical challenges of comprehensive metabolite analysis. Brief. Funct. genomics 9, 139-148 (2010).

[16] Allwood, J. W., Ellis, D. I. & Goodacre, R. Metabolomic technologies and their application to the study of plants and plant-host interactions. Physiologia Plant. 132, 117-135 (2008).

[17] Young, N. D. QTL mapping and quantitative disease resistance in plants. Annu. Rev. Phytopathol. 34, 479-501 (1996).

[18] Chambers, A. H. et al. Identification of a strawberry flavor gene candidate using an integrated genetic-genomic-analytical chemistry approach. BMC genomics 15, 217 (2014).

[19] Eduardo, I. et al. Genetic dissection of aroma volatile compounds from the essential oil of peach fruit: QTL analysis and identification of candidate genes using dense SNP maps. Tree Genet. Genomes 9, 189-204 (2013).

[20] Liu, Z. et al. Identification of a Solanum pennellii chromosome 4 fruit flavor and nutritional quality-associated metabolite QTL. Front. plant Sci. 7, 1671 (2016).

[21] Tieman, D. M. et al. Identification of loci affecting flavour volatile emissions in tomato fruits. J. Exp. Bot. 57, 887-896 (2006).

[22] Toubiana, D. et al. Combined correlation‐based network and mQTL analyses efficiently identified loci for branched‐chain amino acid, serine to threonine, and proline metabolism in tomato seeds. Plant J. 81, 121-133 (2015).

[23] McCallum, S. et al. Genetic and environmental effects influencing fruit colour and QTL analysis in raspberry. Theor. Appl. Genet. 121, 611-627 (2010).

[24] Riedelsheimer, C. et al. Genome-wide association mapping of leaf metabolic profiles for dissecting complex traits in maize. Proc. Natil Acad. Sci. USA 109, 8872-8877 (2012).

[25] Vosman, B. et al. QTL mapping of insect resistance components of Solanum galapagense. Theor. Appl. Genet. 132, 531-541 (2019).

[26] Yang, S. et al. Next generation mapping of enological traits in an F2 interspecific grapevine hybrid family. PLoS ONE 11, e0149560 (2016).

[27] Pawlus, A. D. et al. Stilbenoid profiles of canes from Vitis and Muscadinia species. J. Agric. Food Chem. 61, 501-511 (2013).

[28] Schnee, S., Viret, O. & Gindro, K. Role of stilbenes in the resistance of grapevine to powdery mildew. Physiological Mol. Plant Pathol. 72, 128-133 (2008).

[29] Vezzulli, S. et al. The Rpv3-3 haplotype and stilbenoid induction mediate downy mildew resistance in a grapevine interspecific population. Front. Plant Sci. 10, 234 (2019).

[30] Di Gaspero, G. et al. Selective sweep at the Rpv3 locus during grapevine breeding for downy mildew resistance. Theor. Appl. Genet. 124, 277-286 (2012).

[31] Zyprian, E. et al. Quantitative trait loci affecting pathogen resistance and ripening of grapevines. Mol. Genet. Genomics 291, 1573-1594 (2016).

[32] Riaz, S., Tenscher, A. C., Ramming, D. W. & Walker, M. A. Using a limited mapping strategy to identify major QTLs for resistance to grapevine powdery mildew (Erysiphe necator) and their use in marker-assisted breeding. Theor. Appl. Genet. 122, 1059-1073 (2011).

[33] Singh, B. & Sharma, R. A. Plant terpenes: defense responses, phylogenetic analysis, regulation and clinical applications. 3 Biotech 5, 129-151 (2015).

[34] Treutter, D. Significance of flavonoids in plant resistance and enhancement of their biosynthesis. Plant Biol. 7, 581-591 (2005).

[35] Berger, S., Sinha, A. K. & Roitsch, T. Plant physiology meets phytopathology: plant primary metabolism and plant-pathogen interactions. J. Exp. Bot. 58, 4019-4026 (2007).

[36] Bolton, M. D. Primary metabolism and plant defense-fuel for the fire. Mol. plant-microbe Interact. 22, 487-497 (2009).

[37] Schwachtje, J. & Baldwin, I. T. Why does herbivore attack reconfigure primary metabolism?. Plant Physiol. 146, 845-851 (2008).

[38] Grimplet, J. et al. Comparative analysis of grapevine whole-genome gene predictions, functional annotation, categorization and integration of the predicted gene sequences. BMC Res. Notes 5, 213 (2012).

[39] Fennell, A., Mathiason, K. & Luby, J. Genetic segregation for indicators of photoperiod control of dormancy induction in Vitis species. Acta Horticulturae 689, 533-540 (2005).

[40] Fennell, A., Alahakoon, D., Luby, J. & Clark, M. Mapping the genetic architecture of grapevine bud growth cycling quantitative traits. XII Int. Conf. Grapevine Breed. Genet. 1248, 337-344 (2018).

[41] Smith, C. A., Want, E. J., O’Maille, G., Abagyan, R. & Siuzdak, G. XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal. Chem. 78, 779-787 (2006).

[42] Broman, K. W., Wu, H., Sen, Ś. & Churchill, G. A. R/qtl: QTL mapping in experimental crosses. Bioinformatics 19, 889-890 (2003).

[43] Grimplet, J. et al. VitisNet: “Omics” integration through grapevine molecular networks. PLoS ONE 4, e8365 (2009).

[44] Osier, M. V. VitisPathways: gene pathway analysis for “V. vinifera”. Vitis: J. Grapevine Res. 55, 129-133 (2016).