This five-year collaborative project examined how root systems of long-lived (perennial) plants impact aboveground structures (shoot systems- stems, leaves, flowers, fruits). Clonally propagated, grafted crops provide the optimal system for understanding root system (rootstock) effects on shoot system (scion) phenotypes across variable climates. This project focused on the most economically important berry crop in the world, grapevine (Vitis spp). We used the ancient horticultural and modern commercial practice of grafting, mechanical joining of a clonally propagated rootstock with a genetically distinct, clonally propagated scion, to experimentally manipulate which rootstocks and scions were growing together. In three tightly integrated aims, we investigated how plant performance and other traits expressed in the scion are affected by rootstock genotype through examining: 1) A single grapevine cultivar (‘Chambourcin’) grafted to three commercial rootstocks in one single environment; 2) how local environmental conditions impact root-shoot communication in ‘Cabernet Sauvignon’ and ‘Chardonnay’ in four rootstock-scion combinations in multiple commercial vineyards in California; and 3) genetic variation in rootstocks in awild grapevine genetic mapping population grown as intact vines and as rootstocks grafted with a single scion (‘Marquette’), replicated in four climatic zones. A fourth aim leveraged our strong partnership with an industry partner, a large California winery, where together we carried out research in commercial vineyards and conducted outreach and industry-relevant training. 

Major outcomes of the work include:

Development of extensive genomic resources for hybrid grapevines. Our group sequenced and annotated hybrid grapevine cultivars ‘Chambourcin’ and ‘Marquette’, both of are important for viticulture in the Eastern half of the United States.  Combined with publicly available genome resources for other cultivars (e.g., ‘Chardonnay,’ ‘Cabernet Sauvignon’) our project demonstrated foliar gene expression changes daily, seasonally, and annually, and is modulated by rootstock and local climate. We demonstrated that changes in the epigenome correlated with differences in vine water availability, suggesting that grafting, irrigation, and their interaction shape phenotypic plasticity. 

Deep understanding of the range in phenotypic plasticity present in grapevines. The framework of our study of phenotypic plasticity (the range of different traits expressed by clonal replicates of a single genetic individual) included foliar traits observed across seasons, years, rootstocks, and environments. We showed that rootstock genotype is a strong modulator of elemental composition in scion leaves, and that there is a genetic basis in the root to variable ion concentrations in grapevines leaves. We also used carbon isotope analysis to investigate how rootstock and environment interact and impact vine water use efficiency, demonstrating that currently available commercial rootstocks have limited potential for adapting to shifting water availability when compared with the rootstock mapping population developed for this study. Finally, using metabolite analysis, we demonstrated that differences in berry chemistry and wine volatiles in cultivated grapevine is greatly influenced by the interaction between rootstock and environment, with persistent rootstock effects observed year after year.

Identification of genetic loci associated with grapevine physiological plasticity. Using a wild grapevine based rootstock mapping population, we developed a globally unique experimental vineyard replicated across diverse climatic viticultural regions (NY, SD, MO) that we are using to investigate the role of root systems on shoot system plasticity. Each vineyard holds one copy of 165 genetically distinct rootstocks, derived from a cross between two wild grape species, V. rupestris and V. riparia.  Using two different genetic marker platforms, we developed genetic maps for this population, enabling our team to examine the genetic architecture of phenotypic traits including leaf elemental concentration, nitrogen metabolism, water use efficiency, leaf shape, disease resistance, and vine vigor.  In addition, these vineyards hold a second copy of 140 of these vines which are grafted with the grapevine scion cultivar ‘Marquette’.  This design enabled our team to not only genetically map QTL in the own-rooted population, but also genetically map QTL for shoot system traits conferred by the root system in each climate.  

Broader Impacts: In the course of these studies we published 37 peer reviewed  journal articles, reviews, software packages and commentaries with topics ranging from sequenced grapevine genomes, to wine metabolite analysis, to the use of hyperspectral drones for evaluating plant growth and productivity. Team members gave ~150 presentations on this work to academic, industry, and stakeholder groups, as well as to the general public. The broader impacts of this study resulted in the training of 9 postdoctoral scholars, 29 graduate, 49 undergraduate and 2 high school students. The project featured direct collaboration of project participants with industry collaborators as part of the Grant Opportunities for Academic Liaisons with Industry (GOALI) program, which placed approximately 20 project participants in commercial vineyards in California, where they participated in research and training activities.  Placement for all project trainees is high: seven postdocs in faculty or industry positions, 14 graduate students in postdoc, industry, faculty, museum, or university positions; and 32 undergraduates are in graduate school, museum, or industry positions. 

Last Modified: 12/20/2024
Modified by: Jason P Londo