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Grapevine rootstocks are gaining importance in viticulture as a strategy to combat abiotic challenges, as well as enhance scion physiology. Direct leaf-level physiological parameters like net assimilation rate, stomatal conductance to water vapor, quantum yield of PSII, and transpiration can illuminate the rootstock effect on scion physiology. However, these measures are time-consuming and limited to leaf-level analysis. This study used different rootstocks to investigate the potential application of aerial hyperspectral imagery in the estimation of canopy level measurements. A statistical framework was developed as an ensemble stacked regression (REGST) that aggregated five different individual machine learning algorithms: Least absolute shrinkage and selection operator (Lasso), Partial least squares regression (PLSR), Ridge regression (RR), Elastic net (ENET), and Principal component regression (PCR) to optimize high-throughput assessment of vine physiology. In addition, a Convolutional Neural Network (CNN) algorithm was integrated into an existing REGST, forming a hybrid CNN-REGST model with the aim of capturing patterns from the hyperspectral signal. Based on the findings, the performance of individual base models exhibited variable prediction accuracies. In most cases, Ridge Regression (RR) demonstrated the lowest test Root Mean Squared Error (RMSE). The ensemble stacked regression model (REGST) outperformed the individual machine learning algorithms with an increase in R2 by (0.03 to 0.1). The performances of CNN-REGST and REGST were similar in estimating the four different traits. Overall, these models were able to explain approximately 55–67% of the variation in the actual ground-truth data. This study suggests that hyperspectral features integrated with powerful AI approaches show great potential in tracing functional traits in grapevines. 

Societal Impact StatementThe innumerable effects of terroir—including climate, soil, microbial environment, biotic interactions, and cultivation practice—collectively alter plant performance and production. A more direct agricultural intervention is grafting, in which genetically distinct shoot and root genotypes are surgically combined to create a chimera that alters shoot performance at a distance. Selection of location and rootstock are intentional decisions in viticulture to positively alter production outcomes. Here, we show that terroir and rootstock alter the shapes of grapevine leaves in commercial vineyards throughout the California Central Valley, documenting the profound effects of these agricultural interventions that alter plant morphology. SummaryEmbedded in a single leaf shape are the latent signatures of genetic, developmental, and environmental effects. In viticulture, choice of location and rootstock are important decisions that affect the performance and production of the shoot. We hypothesize that these effects influence plant morphology, as reflected in leaf shape.We sample 1879 leaves arising from scion and rootstock combinations from commercial vineyards in the Central Valley of California. Our design tests 20 pairwise contrasts between Cabernet Sauvignon and Chardonnay scions from San Joaquin, Merced, and Madera counties from vines grafted to Teleki 5C, 1103 Paulsen, and Freedom rootstocks.We quantify clear differences between Cabernet Sauvignon and Chardonnay leaves. However, we also detect a separate, statistically independent source of shape variance that affects both Cabernet Sauvignon and Chardonnay leaves similarly. We find that this other shape difference is associated with differences in rootstock and location.The shape difference that arises from rootstock and location affects the basal part of the leaf near the petiole, known as the petiolar sinus, and affects its closure. This shape effect is independent from previously described shape differences that arise from genetic, developmental, or size effects. 

Grapevine leaves have diverse shapes and sizes which are influenced by many factors including genetics, vine phytosanitary status, environment, leaf and vine age, and node position on the shoot. To determine the relationship between grapevine leaf shape or size and leaf canopy temperature, we examined five seedling populations grown in a vineyard in California, USA. The populations had one parent with compound leaves of the Vitis piasezkii type and a different second parent with non-compound leaves. In previous work, we had measured the shape and size of the leaves collected from these populations using 21 homologous landmarks. Here, we paired these morphological data with canopy temperature measurements made using a handheld infrared thermometer. After recording time of sampling and canopy temperature, we used a linear model between time of sampling and canopy temperature to estimate temperature residuals. Based on these residuals, we determined if the canopy temperature of each vine was cooler or warmer than expected, based on the time of sampling. We established a relationship between leaf size and canopy temperature: vines with larger leaves were cooler than expected. By contrast, leaf shape was not strongly correlated with variation in canopy temperature. Ultimately, these findings indicate that vines with larger leaves may contribute to the reduction of overall canopy temperature; however, further work is needed to determine whether this is due to variation in leaf size, differences in the openness of the canopy or other related traits. 

Transition of grapevine buds from paradormancy to endodormancy is coordinated by changes in gene expression, phytohormones, transcription factors, and other molecular regulators, but the mechanisms involved in transcriptional and post-transcriptional regulation of dormancy stages are not well delineated. To identify potential regulatory targets, an integrative analysis of differential gene expression profiles and their inverse relationships with miRNA abundance was performed in paradormant (long day (LD) 15 h) or endodormant (short day (SD), 13 h) Vitis riparia buds. There were 400 up- and 936 downregulated differentially expressed genes in SD relative to LD buds. Gene set and gene ontology enrichment analysis indicated that hormone signaling and cell cycling genes were downregulated in SD relative to LD buds. miRNA abundance and inverse expression analyses of miRNA target genes indicated increased abundance of miRNAs that negatively regulate genes involved with cell cycle and meristem development in endodormant buds and miRNAs targeting starch metabolism related genes in paradormant buds. Analysis of interactions between abundant miRNAs and transcription factors identified a network with coinciding regulation of cell cycle and epigenetic regulation related genes in SD buds. This network provides evidence for cross regulation occurring between miRNA and transcription factors both upstream and downstream of MYB3R1. 

Hermaphroditic (perfect) flowers were a key trait in grapevine domestication, enabling a drastic increase in yields due to the efficiency of self-pollination in the domesticated grapevine ( Vitis vinifera L. ssp. vinifera ). In contrast, all extant wild Vitis species are dioecious, each plant having only male or female flowers. In this study, we identified the male (M) and female (f) haplotypes of the sex-determining region (SDR) in the wild grapevine species V. cinerea and confirmed the boundaries of the SDR. We also demonstrated that the SDR and its boundaries are precisely conserved across the Vitis genus using shotgun resequencing data of 556 wild and domesticated accessions from North America, East Asia, and Europe. A high linkage disequilibrium was found at the SDR in all wild grape species, while different recombination signatures were observed along the hermaphrodite (H) haplotype of 363 cultivated accessions, revealing two distinct H haplotypes, named H1 and H2. To further examine the H2 haplotype, we sequenced the genome of two grapevine cultivars, 'Riesling' and 'Chardonnay'. By reconstructing the first two H2 haplotypes, we estimated the divergence time between H1 and H2 haplotypes at ∼6 million years ago, which predates the domestication of grapevine (∼8,000 y ago). Our findings emphasize the important role of recombination suppression in maintaining dioecy in wild grape species and lend additional support to the hypothesis that at least two independent recombination events led to the reversion to hermaphroditism in grapevine.