Biology subjects

Cousins, P.

Publications and source records attributed to Cousins, P..

8 recordsLinked to original sources

bioRxiv2026

Disentangling blade and vasculature shape in grapevine leaves

The leaf blade and vasculature develop together within a shared morphological space. Despite shared molecular patterning pathways, it is unknown if developmental and evolutionary variation affect these tissues separately or together in a coordinated way. Grapevine leaves have a morphometric history and abundant data measuring the shape of the blade and vasculature together. Using a combination of topological data analysis and deep learning, we perform reciprocal semantic segmentation of leaf blade and vasculature. Each tissue contains sufficient information to predict the other. We hypothesize that this is due to a one-to-one relationship between blade and vein. Using thin plate splines to swap and warp different combinations of blade and vein shapes, we show that a set of leaves with a many-to-one relationship of blade and vein are distinguishable from true leaves. We also swap blade and vein across the developmental series and between species and show that only reversing the developmental series disrupts the relationship between blade and vasculature. We end by discussing the evolutionary and developmental implications that there is a unique, one-to-one mapping between blade and vein that allows each to be predicted from the other. Author summaryLeaves are made of two closely connected parts: the flat blade that captures light and the network of veins that transports water, nutrients, and developmental signals. Although these tissues grow together and share common molecular patterning pathways, it has remained unclear whether a particular blade shape is uniquely linked to a specific vein pattern. In this study, we use grapevine leaves as a model system and combine mathematical shape analysis with deep learning to examine this relationship. We show that the shape of the blade alone can accurately predict the vein network, and that the vein network can likewise predict the blade. This finding suggests a near one-to-one relationship between these two tissues. To test this idea, we created artificial leaves in which blade and vein shapes were deliberately mismatched. Although these synthetic leaves appeared realistic at a global level, a neural network was able to distinguish them from real leaves based on subtle differences. We further show that this tight coupling is maintained by the developmental sequence of leaf growth rather than by species identity, revealing a conserved constraint linking leaf form and internal structure.

plant biology↗

bioRxiv2024

The assembly and annotation of two teinturier grapevine varieties, Dakapo and Rubired

BackgroundTeinturier grapevine varieties were first described in the 16th century and have persisted due to their deep pigmentation. Unlike most other grapevine varieties, teinturier varieties produce berries with pigmented flesh due to anthocyanin production within the flesh. As a result, teinturier varieties are of interest not only for their ability to enhance the pigmentation of wine blends but also for their health benefits. Here, we assembled and annotated the Dakapo and Rubired genomes, two teinturier varieties. FindingsFor Dakapo, we used a combination of Nanopore sequencing, Illumina sequencing, and scaffolding to the existing grapevine genome assembly to generate a final assembly of 508.5 Mbp with an N50 scaffold length of 25.6 Mbp and a BUSCO score of 98.0%. A combination approach of de novo annotation and lifting over annotations from the existing grapevine reference genome resulted in the annotation of 36,940 genes in the Dakapo assembly. For Rubired, PacBio HiFi reads were assembled, scaffolded, and phased to generate a diploid assembly with two haplotypes 474.7-476.0 Mbp long. The diploid genome has an N50 scaffold length of 24.9 Mbp and a BUSCO score of 98.7%, and both haplotype-specific genomes are of similar quality. De novo annotation of the diploid Rubired genome yielded annotations for 56,681 genes. ConclusionsThe Dakapo and Rubired genome assemblies and annotations will provide genetic resources for future investigations into berry flesh pigmentation and other traits of interest in grapevine.

genomics↗

bioRxiv2024

Terroir and rootstock effects on leaf shape in California Central Valley vineyards

SummaryO_LIEmbedded 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. C_LIO_LIWe 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. C_LIO_LIUsing geometric morphometric approaches, we visualize a morphospace in which, in addition to clear separation of Cabernet Sauvignon and Chardonnay scion leaf shapes, an orthogonal source of shape variation affects both varieties. Comparing the Procrustes distances to within and between group means, the additional source of variance is found to arise from location and rootstock effects. C_LIO_LIWe describe and visualize a specific shape feature, the angle of the proximal lobe to the midvein that defines the closure of the petiolar sinus, that is attributable to location and rootstock effects and orthogonal to and separate from genetic, developmental, or allometric effects attributable to leaf size. C_LI Societal Impact Statement (EN)The 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 alter 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.

plant biology↗

bioRxiv2023

From buds to shoots: Insights into grapevine development from the Witch's Broom bud sport

Premise of StudyDevelopment is relatively understudied in woody vines, such as grapevine (Vitis vinifera). We used the Witchs Broom bud sport in grapevine to understand the developmental trajectories of the bud sports, as well as the potential genetic basis of the bud sport. MethodsWe phenotyped shoots, buds, and leaves of two independent cases of the Witchs Broom bud sport, in the Dakapo and Merlot varieties of grapevine, alongside wild-type counterparts of the same variety. We also performed Illumina and Oxford Nanopore sequencing on the two independent cases and two wild-type counterparts of the same variety. Key ResultsThe Dakapo and Merlot cases of Witchs Broom displayed severe developmental defects, with no fruit/clusters formed and dwarf vegetative features. However, the Dakapo and Merlot cases of Witchs Broom studied were also phenotypically different from one another, with distinct differences in bud and leaf development. We were able to identify unique genetic mutations in our two Witchs Broom cases that are strong candidates for the genetic basis of the bud sports. ConclusionsThe Witchs Broom bud sport in grapevine serves as a useful natural mutant in which to study grapevine development. The Witchs Broom bud sports in both varieties studied had dwarf phenotypes, but the two instances studied were also vastly different from one another. Future work on Witchs Broom bud sports in grapevine could provide more insight into development and the genetic pathways involved in grapevine.

plant biology↗

bioRxiv2022

Grapevine leaf size influences vine canopy temperature

PremiseGrapevine leaves have diverse shapes and sizes. Their shape and size is known to be influenced by many factors including genetics, vine phytosanitary status, environment, leaf and vine age, and node position on the shoot. In order to determine the importance of grapevine leaf shape and size to canopy temperature, we examined the relationship in five seedling populations grown in a vineyard in California, USA. MethodsAll of the populations had one parent with compound leaves of the Vitis piasezkii type and each population had a different second parent with non-compound leaves. In previous work, we measured leaf shape and size using 21 homologous landmarks. Here, we paired these morphology data with measurements taken using an infrared thermometer to measure the temperature of the canopy. By recording time of sampling and canopy temperature, we were able to determine which vines were cooler or hotter than expected, using a linear model. ResultsWe established a relationship between leaf size and canopy temperature: vines with larger leaves were cooler than expected. In contrast, leaf shape was not strongly correlated with variation in temperature. ConclusionsUltimately, these findings indicate that vines with larger leaves may contribute to the reduction of overall vine canopy temperature, but further work is needed to determine if this is due to variation in leaf size, differences in the openness of the canopy, or other related traits.

plant biology↗

bioRxiv2022

X-ray imaging of 30 year old wine grape wood reveals cumulative impacts of rootstocks on scion secondary growth and harvest index

O_LIAnnual rings from 30 year old vines in a California rootstock trial were measured to determine the effects of 15 different rootstocks on Chardonnay and Cabernet Sauvignon scions. Viticultural traits measuring vegetative growth, yield, berry quality, and nutrient uptake were collected at the beginning and end of the lifetime of the vineyard. C_LIO_LIX-ray Computed Tomography (CT) was used to measure ring widths in 103 vines. Ring width was modeled as a function of ring number using a negative exponential model. Early and late wood ring widths, cambium width, and scion trunk radius were correlated with 27 traits. C_LIO_LIModeling of annual ring width shows that scions alter the width of the first rings but that rootstocks alter the decay thereafter, consistently shortening ring width throughout the lifetime of the vine. The ratio of yield to vegetative growth, juice pH, photosynthetic assimilation and transpiration rates, and stomatal conductance are correlated with scion trunk radius. C_LIO_LIRootstocks modulate secondary growth over years, altering hydraulic conductance, physiology, and agronomic traits. Rootstocks act in similar but distinct ways from climate to modulate ring width, which borrowing techniques from dendrochronology, can be used to monitor both genetic and environmental effects in woody perennial crop species. C_LI

plant biology↗

bioRxiv2022

Increases in vein length compensate for leaf area lost to lobing in grapevine

PremiseThere is considerable variation in leaf lobing and leaf size, including among grapevines, some of the most well-studied leaves. We examined the relationship between leaf lobing and leaf size across grapevine populations which varied in extent of leaf lobing. MethodsWe used homologous landmarking techniques to measure 2,632 leaves across two years in 476 unique, genetically distinct grapevines from 5 biparental crosses which vary primarily in the extent of lobing. We determined to what extent leaf area could explain variation in lobing, vein length, and vein to blade ratio. ResultsAlthough lobing was the primary source of variation in shape across the leaves we measured, leaf area varied only slightly as a function of lobing. Rather, leaf area increases as a function of total major vein length, total branching vein length, and decreases as a function of vein to blade ratio. These relationships are stronger for more highly lobed leaves, with the residuals for each model differing as a function of distal lobing. ConclusionsFor a given leaf area, more highly lobed leaves have longer veins and higher vein to blade ratios, allowing them to maintain similar leaf areas despite increased lobing. These findings show how more highly lobed leaves may compensate for what would otherwise result in a reduced leaf area, allowing for increased photosynthetic capacity through similar leaf size.

plant biology↗

bioRxiv2019

Rootstock choice can dramatically affect grapevine growth

Grape growers use rootstocks to provide protection against pests and pathogens and to modulate viticulture performance such as shoot growth. Our study examined two grapevine scion varieties ( Chardonnay and Cabernet Sauvignon) grafted to 15 different rootstocks and determined the effect of rootstocks on eight traits important to viticulture. We assessed the vines across five years and identified both year and variety as contributing strongly to trait variation. The effect of rootstock was relatively consistent across years and varieties, explaining between 8.99% and 9.78% of the variation in growth-related traits including yield, pruning weight, berry weight, and Ravaz index (yield to pruning weight ratio). Increases in yield due to rootstock were generally the result of increases in berry weight, likely due to increased water uptake by vines grafted to a particular rootstock. We demonstrated a greater than 50% increase in yield, pruning weight, or Ravaz index by choosing the optimal rootstock, indicating that rootstock choice is crucial for grape growers looking to improve vine performance.

plant biology↗