Biology subjects

Lupo, Y.

Publications and source records attributed to Lupo, Y..

9 recordsLinked to original sources

bioRxiv2026

Genetic Mapping Reveals a Major Locus for Boron Exclusion in Wild Vitis

Boron toxicity constrains grapevine (Vitis) production in irrigated arid and semi-arid regions, yet most available rootstocks are sensitive to excessive boron. Although underutilized Vitis species may harbor sources of adaptation, the genetic basis of natural variation in boron exclusion remains poorly understood, limiting the development of boron-tolerant rootstocks. We screened 267 wild Vitis accessions representing 16 species for their ability to limit leaf boron accumulation under excess boron conditions. Leaf boron concentration varied 190-fold among accessions and was highly heritable (entry-mean H^2 = 0.71). Its correlation with stomatal conductance was modest (r = 0.34), indicating that transpiration rate explained only a small proportion of the variation in leaf boron accumulation. Leaf boron was correlated with leaf chloride (r = 0.36), but their largely non-overlapping association profiles supported distinct genetic control. Genome-wide association analysis identified a suggestive association on chromosome 11. Independent quantitative trait locus mapping in a full-sib F1 population (n = 158) derived from Longii-9018 (V. acerifolia) x GRN3 (commercial rootstock) identified qBEx11.1 in the same syntenic region on chromosome 11, which explained 19.5% of the phenotypic variance. Positional candidate genes near the association peak included a pectinesterase and a MATE efflux transporter, suggesting roles for cell wall modification and membrane transport. Leaf spectral reflectance was associated with leaf boron concentration in both populations, particularly at visible and red-edge wavelengths, indicating potential for high-throughput phenotyping. Together, these findings identify qBEx11.1 as a priority locus for boron exclusion and support integrated genetic and spectral approaches for breeding boron-tolerant grapevine rootstocks.

plant biology↗

bioRxiv2026

Low-cost rhizotron imaging and zero-shot deep-learning resolve temporal, spatial, and genetic variation in grapevine rootstock root systems

Root system architecture shapes how grapevine rootstocks take up water and nutrients, yet roots remain the least phenotyped grapevine organ because they are hidden and hard to image. We present a low-cost phenotyping pipeline that pairs custom acrylic rhizotrons (about US$30 each) with a consumer flatbed scanner and BiRefNet, a general-purpose deep-learning model used without training on root images, followed by automated mask cleaning, skeleton-based trait extraction, and soil moisture mapping. We tested it on nine commercial rootstocks scanned 16 times over 42 days after transplanting (DAT), with half under a ten-day water deficit. From 1,108 images we extracted 21 whole-root, depth-resolved, and topological traits. Genotypes differed in nearly every trait and in how they changed over time. Heritability of size and branching traits peaked at 0.92-0.93 between 21 and 31 DAT and fell for width, depth, and convex hull once roots reached the rhizotron walls, defining the best measurement window. The image-derived soil moisture map accurately tracked the deficit and its recovery. Deficit plants shifted new root growth to deeper soil without growing less overall, and the substrate dried fastest around older and denser roots. Root brightness decreased with root age and local moisture, and transport segments (axes serving several tips) were brighter than terminal laterals in every genotype. Root system size was associated with stomatal conductance in well-watered plants, and stomatal recovery after re-watering correlated with new root growth. The pipeline turns simple hardware into a quantitative, time-resolved root phenotyping platform suitable for breeding.

plant biology↗

bioRxiv2026

Harnessing Vitis germplasm diversity to dissect and predict adventitious rooting traits in grapevine

Adventitious root formation (ARF) is a critical trait for the cost-effective propagation of grapevines in commercial nurseries. Poor rooting ability can limit the use and adoption of new rootstocks derived from underutilized Vitis species, constraining breeding efforts largely to the traditional trio: Vitis riparia, V. rupestris, and V. berlandieri. Despite its agronomic relevance, the genetic basis of ARF remains poorly characterized across the broader Vitis genus. In this study, we evaluated 308 accessions representing 18 Vitis species over three growing seasons, quantifying rooting performance at two developmental stages, callus-stage and post-transplant, alongside root biomass, cutting weight, and a derived transplant-response index. We observed extensive phenotypic variation both within and across species, and species rankings depended on the trait considered. V. riparia, V. rupestris and V. californica ranked among the top five species for all four rooting traits, whereas V. cinerea and V. candicans ranked among the lowest for root weight and post-transplant rooting. V. arizonica and V. acerifolia rooted well at the callus stage but were intermediate after transplanting, and V. berlandieri was among the weakest at the callus stage yet intermediate for post-transplant rooting. Repeatability was moderate to high for root weight (0.74) and callus-stage rooting (0.66), and lower for post-transplant rooting (0.47), reflecting both genetic control and season-to-season variation. Between-species differences accounted for 68% of the genetic variance in callus-stage rooting but only 10% in cutting weight. Rooting was associated with the climate of each accession's wild site of origin: after removing differences among species, accessions originating from sites with lower dry-season precipitation rooted better and produced more root biomass. Genome-wide association analysis using 3.4 million SNPs identified 54 significant SNPs resolving into 18 independent loci across four traits, with root weight contributing 12 of them. Candidate genes in linkage with these loci include a mitogen-activated protein kinase, a SCARECROW-LIKE GRAS transcription factor, PASTICCINO1, expansin A1, an AP2/ERF-RAV1 transcription factor, a tandem array of caffeoyl-CoA O-methyltransferases, and several sugar, peptide and nitrate transporters, implicating auxin-linked cell proliferation, cell wall and lignin remodeling, and solute transport. Genomic and phenomic prediction models yielded moderate accuracies across traits and seasons; up to r = 0.67 for post-transplant rooting within a season and r = 0.65 for previously unevaluated accessions. Moreover, the integration of spectral and genotypic data further improved predictive performance. Prediction accuracy was essentially flat between 5,000 and 50,000 markers. This study establishes a foundational framework for the genetic improvement of grapevine rootstocks, promoting broader use of resilient, high-performing, and clonally-propagable germplasm in viticulture.

genetics↗

bioRxiv2025

Leveraging foundation models to dissect the genetic basis of cluster compactness and yield in grapevine

Grape cluster compactness is a key trait that influence fruit quality, yield, and disease susceptibility. Understanding the genetic basis of this trait is essential for optimizing vineyard management and improving grapevine cultivars. In this study, we performed quantitative trait locus (QTL) mapping to identify genomic regions associated with cluster architecture and yield components in a bi-parental population derived from Vitis vinifera cv. Riesling x Cabernet Sauvignon. A total of 138 full-sibling progeny were evaluated over two growing seasons at Oakville, Napa Valley, California. Traditional yield-related traits were measured, including cluster number, total cluster weight, and average cluster weight. Additionally, an image-based phenotyping pipeline leveraging the foundation model Segment Anything Model (SAM) was employed to segment individual berries, measure their size and shape, and compute cluster compactness with minimal manual intervention. Trait correlations revealed that compact clusters tended to have a higher berry count but smaller berry size, highlighting the role of compactness in modulating cluster structure. Heritability estimates varied across traits, with berry dimensions and compactness displaying moderate to high heritability, indicating strong genetic control. Two parental linkage maps were constructed using a pseudo-test cross strategy. QTL mapping identified multiple loci associated with cluster architecture and yield components, with several stable QTLs detected across both years. Notably, a QTL for cluster compactness was found in both seasons on chromosome 1 in Cabernet Sauvignon. Other stable QTLs were associated with berry size (chromosomes 6 and 17) and berry count (chromosome 5 in Cabernet Sauvignon and chromosome 7 in Riesling). Additional QTLs were detected in a single year, reflecting the influence of environmental variation. Our findings provide valuable insights into the application of foundation models requiring no prior training and minimal intervention for high-quality segmentation and enhance our understanding of the genetic architecture of cluster compactness and yield traits. The genomic regions identified in this study offer promising targets for breeding programs aimed at improving grape quality and disease resistance.

genetics↗

bioRxiv2025

Hyperspectral Sensing for High-Throughput Screening of Boron Tolerance in Grapevines

Boron (B) is an essential micronutrient for grapevine growth, yet excessive levels can impair photosynthesis, reduce yields, and diminish fruit quality. In this study, we evaluated the potential of hyperspectral radiometry combined with machine learning to identify B-tolerant rootstocks rapidly and cost-effectively. We screened both commercial grapevine rootstocks and wild Vitis germplasm under B treatments ranging from 0.5 to 8 ppm, measuring leaf B accumulation, stomatal conductance, photosystem II efficiency, and leaf reflectance (R380-R1100 nm). Our results revealed substantial genotypic variation in B exclusion, with some genotypes maintaining low leaf B content despite high external concentrations. Classification models (Partial Least Squares Discriminant Analysis and Random Forest classification) outperformed regression models (Partial Least Squares Regression and Random Forest regression) in distinguishing B-excluding genotypes, achieving moderate to high accuracy within just eight days after stress initiation. Vegetation indices such as Normalized Difference Vegetation Index (NDVI), Photochemical Reflectance Index (PRI), Structure Insensitive Pigment Index (SIPI), and Chlorophyll Index (CI) indicated that B stress reduces chlorophyll levels and may induce carotenoid accumulation, suggesting a photosynthetic tolerance mechanism. Although quantitative prediction of leaf B content proved more challenging, simulations showed that even modest prediction accuracies can substantially boost genetic gains if larger populations are screened, and selection intensities are increased. These findings underscore the value of hyperspectral radiometry for high-throughput phenotyping, allowing breeders to rapidly identify and advance B-tolerant rootstocks.

plant biology↗

bioRxiv2025

The Genetic Basis of Chloride Exclusion in Grapevines

Mediterranean regions are among the most important areas for global grape production, characterized by dry climates and frequent challenges associated with soil salinity. In these environments, chloride toxicity is a major factor limiting vine growth and fruit quality. Despite the critical role of chloride exclusion in salinity tolerance, the genetic mechanisms underlying this trait remain poorly understood. In this study, we leveraged one of the largest Vitis germplasm collections, comprising 335 accessions from 18 wild and cultivated Vitis species, to characterize natural variation in chloride exclusion. This diverse panel, which includes accessions from the southwestern United States and Mexico, captures a broad range of evolutionary adaptations to abiotic stress, providing an unprecedented opportunity to investigate the genetic basis of salinity tolerance. Using genome-wide association (GWA) and quantitative trait loci (QTL) mapping, we identified a major QTL on chromosome 8 containing candidate genes encoding cation/H exchangers (CHX), which are involved in ion transport and homeostasis. To validate these findings, we analyzed a mapping population derived from V. acerifolia longii 9018 and the commercial rootstock GRN3, confirming the chromosome 8 locus as a major determinant of chloride exclusion. Structural variant analysis revealed key non-synonymous substitutions within CHX genes, suggesting potential functional roles in salinity tolerance. Additionally, we discovered a novel QTL on chromosome 19 enriched with G-type lectin S-receptor-like serine/threonine-protein kinases, known regulators of stress signaling. By integrating extensive phenotypic and genomic data across a diverse Vitis collection, this study provides novel insights into the genetic architecture of chloride exclusion and identifies valuable candidate genes for breeding salt-tolerant rootstocks.

genetics↗

bioRxiv2024

Hyperspectral Sensing for High-Throughput Chloride Detection in Grapevines

Soil salinity affects major viticultural areas worldwide with chloride ions being the primary source of salt toxicity in grapevines. This toxicity impacts vine health and reduces fruit yield and quality. Current breeding efforts to improve grapevine salinity tolerance are limited by the low throughput of available phenotyping methods, which are time-consuming, labor-intensive, and destructive. This study demonstrated that hyperspectral proximal sensing can be utilized as a high-throughput, non-destructive screening technique to identify salinity-tolerant grapevine germplasm. The predictive abilities of two different hyperspectral devices, which varied in price, resolution, and sensitivity, were compared across 23 Vitis accessions spanning eight species. Prediction models were built using hyperspectral reflectance and leaf chloride content measured with a lab chloridometer. Three distinct approaches were studied: 1) analyzing the correlation between individual wavelengths and chloride content; 2) employing machine learning models, including Partial Least Squares Regression (PLSR), Random Forest (RF), and Support Vector Machine (SVM), utilizing all wavelengths; and 3) classification-based prediction using Partial Least Squares Discriminant Analysis (PLSDA). Multiple regions in the spectrum, including 613-660 nm, 689-696 nm, and 1357-1358 nm, showed a medium correlation (0.30-0.50) with chloride content in the leaves. PLSR was the most effective machine learning approach, demonstrating moderate predictive capability for chloride content (maximum R{superscript 2} = 0.67), though performance varied between the two devices tested. With PLSDA, predictions increased considerably, up to an accuracy of 0.97, depending on the instrument used and the spectral data transformation. Overall, the more expensive and sensitive device with a wider spectral range outperformed the more affordable, shorter-range device. However, when the prediction model was based on classes (chloride excluders vs. non-excluders) rather than chloride content, the differences in prediction abilities were minimal, with both instruments performing very well. This is promising for identifying breeding materials with chloride exclusion capabilities at low cost and high throughput.

plant biology↗

bioRxiv2023

Importance of Leaf Age in Grapevines Under Salt Stress

The combined effects of salt stress and leaf age on photosynthesis and stomatal conductance are not fully understood. Salt stress develops at different rates in various plant organs and tissues, leading to osmotic and ionic stresses. We studied the development of salt stress (30 mM NaCl) in two grapevine rootstocks by examining the gas exchange, photochemistry, and salt accumulation of leaves at different ages. Our results indicate that leaf age strongly affected photosynthesis but had a minor effect on stomatal conductance in both control and salinity conditions. Surprisingly, salt stress lowered stomatal conductance but had little effect on photosynthesis, opposite to the leaf age effects. Reduction in photosystem II efficiency explained the age-associated decline in photosynthesis, suggesting that the light-dependent phase of photosynthesis is the first process affected by leaf aging. We also found that the sodium exclusion capacity decreased as leaves matured and was age and variety dependent, indicating the importance of leaf age when sampling for salt tolerance studies. Therefore, we suggest that sampling only young leaves is missing critical information in the evaluation of salt-tolerant traits in grapevines.

plant biology↗

bioRxiv2023

Phenotypic plasticity in response to drought stress: Comparisons of domesticated tomato and a wild relative

Phenotypic plasticity is the ability of an organism to undergo reversible behavioral, morphological or physiological changes in response to environmental conditions. Phenotypic plasticity enables plants to cope with uncertain environmental conditions, such as drought. A primary plastic trait is the rate of stomatal response to changes in ambient conditions, which determines the amount of water lost via transpiration, as well as levels of CO2 absorption, growth and productivity. Here, we examined the differences between domesticated and wild tomato species and their responses to drought stress. We found that the domesticated tomato had a higher transpiration rate and higher stomatal conductance (gs). The domesticated tomato also had greater biomass and greater leaf area under drought conditions, as compared to the wild tomato. Despite the domesticated tomatos higher transpiration rate and higher gs, there was no difference between the photosynthetic rates of the two lines. Moreover, the wild tomato had a higher maximum rate of rubisco activity, which might explain its greater molecular and whole canopy water-use efficiency. The domesticated tomatos higher transpiration rate and greater leaf area led to its earlier exposure to drought stress, as compared to the wild tomato, which maintained higher levels of soil water, enabling it to maintain steady rates of whole-canopy stomatal conductance (gsc) for extended periods. The wild tomato was also more sensitive to the soil water availability and lowered its maximum transpiration rate at a higher soil-water-content level. Our results suggest that the domestication process of tomatoes favored morphological/anatomical performance traits over physiological efficiency.

plant biology↗