Biology subjects

Coneva, V.

Publications and source records attributed to Coneva, V..

7 recordsLinked to original sources

bioRxiv2022

Integrated PET and confocal imaging informs a functional timeline for the dynamic process of vascular reconnection during grafting.

Grafting is a widely used agricultural technique that involves the physical joining of separate plant parts so they form a unified vascular system, enabling beneficial traits from independent genotypes to be captured in a single plant. This simple, yet powerful tool has been used for thousands of years to improve abiotic and biotic stress tolerance, enhance yield, and alter plant architecture in diverse crop systems. Despite the global importance and ancient history of grafting, our understanding of the fundamental biological processes that make this technique successful remains limited, making it difficult to efficiently expand on new genotypic graft combinations. One of the key determinants of successful grafting is the formation of the graft junction, an anatomically unique region where xylem and phloem strands connect between newly joined plant parts to form a unified vascular system. Here, we use an integrated imaging approach to establish a spatiotemporal framework for graft junction formation in the model crop Solanum lycopersicum (tomato), a plant that is commonly grafted worldwide to boost yield and improve abiotic and biotic stress resistance. By combining Positron Emission Tomography (PET), a technique that enables the spatio-temporal tracking of radiolabeled molecules, with high-resolution laser scanning confocal microscopy (LSCM), we are able to merge detailed, anatomical differentiation of the graft junction with a quantitative timeline for when xylem and phloem connections are functionally re-established. In this timeline, we identify a 72-hour window when anatomically connected xylem and phloem strands regain functional capacity, with phloem restoration typically preceding xylem restoration by about 24-hours. Furthermore, we identify heterogeneity in this developmental and physiological timeline that corresponds with microvariability in the physical contact between newly joined rootstock-scion tissues. Our integration of PET and confocal imaging technologies provides a spatio-temporal timeline that will enable future investigations into cellular and tissue patterning events that underlie successful versus failed vascular restoration across the graft junction.

plant biology↗

bioRxiv2021

small RNA can move long distances through plant vasculature to influence gene expression in shoot apical meristems

In plants, small RNA (sRNA) can regulate gene expression via post transcriptional gene silencing (PTGS) or through RNA-directed DNA methylation (RdDM) leading to transcriptional gene silencing (TGS). sRNA is mobile throughout the plant, with movement occurring short distances from cell-to-cell as well as long distances through the vasculature via phloem trafficking. The range of long-distance sRNA mediated signaling from the vasculature to the shoot apical meristem (SAM) is not clear. To investigate this, two independent transgenic approaches were used to examine trafficking of phloem-expressed sRNA to the SAM in Arabidopsis thaliana. First, the phloem companion-cell specific promoter SUC2 was used to drive expression of an inverted repeat complementary to FLOWERING LOCUS D (FD), a flowering time regulator expressed exclusively in the SAM. In a separate experiment, the SUC2 promoter was used to express an artificial microRNA (aMiR) designed to target a synthetic CLAVATA3 (CLV3) target in the SAM stem cells. Both systems provide evidence of a phloem-to-SAM sRNA communication axis connecting distal regions of the plant to the stem cells of the SAM, which ultimately gives rise to all shoot tissues, including gametes. Thus, phloem-to-SAM sRNA movement defines an important link between sRNA expressed in distal regions of the plant and the growing shoot. Importantly, phloem-to-SAM sRNA trafficking may allow somatic sRNA to direct SAM RdDM, fixing transient sRNA expression events into stable epigenetic changes.

plant biology↗

bioRxiv2021

Quantitative dissection of color patterning in the foliar ornamental Coleus reveals underlying features driving aesthetic value

O_LIColeus is a popular ornamental plant that exhibits a diverse array of foliar color patterns. New cultivars are currently hand selected by both amateur and experienced plant breeders. In this study, we reimagine coleus breeding using a quantitative color analysis framework. C_LIO_LIDespite impressive advances in high-throughput data collection and processing, complex color patterns remain challenging to extract from image datasets. Using a new phenotyping approach called "ColourQuant," we extract and analyze pigmentation patterns from one of the largest coleus breeding populations in the world. C_LIO_LIWorking with this massive dataset, we are able to analyze quantitative relationships between maternal plants and their progeny, identify features that underlie breeder-selections, and collect and compare consumer input on trait preferences. C_LIO_LIThis study is one of the most comprehensive explorations into complex color patterning in plant biology and provides new insights and tools for exploring the color pallet of the plant kingdom. C_LI

plant biology↗

bioRxiv2018

Function of the Pedicellate Spikelet and Awn in Sorghum and Related Grasses

Sorghum and its relatives in the grass tribe Andropogoneae bear their flowers in pairs of spikelets, in which one spikelet (seed-bearing, or SS) of the pair produces a seed and the other is sterile or male (staminate). This division of function does not occur in other major cereals such as wheat or rice. Additionally, one bract of the seed-bearing spikelet often produces a long extension, the awn, which is in the same position as but independently derived from that of wheat and rice. The function of the sterile spikelet is unknown and that of the awn has not been tested in Andropogoneae. We used radioactive and stable isotopes of carbon, as well as RNA-seq of metabolically important enzymes to show that the sterile spikelet assimilates carbon, which is translocated to the largely heterotrophic SS, thereby functioning as a nurse tissue. The awn shows no evidence of photosynthesis. These results apply to distantly related species of Andropogoneae. Thus, the sterile spikelet, but not the awn, could affect yield in the cultivated species and fitness in the wild ones.

plant biology↗

bioRxiv2017

Persistent homology demarcates a leaf morphospace

Current morphometric methods that comprehensively measure shape cannot compare the disparate leaf shapes found in seed plants and are sensitive to processing artifacts. We explore the use of persistent homology, a topological method applied across the scales of a function, to overcome these limitations. The described method isolates subsets of shape features and measures the spatial relationship of neighboring pixel densities in a shape. We apply the method to the analysis of 182,707 leaves, both published and unpublished, representing 141 plant families collected from 75 sites throughout the world. By measuring leaves from throughout the seed plants using persistent homology, a defined morphospace comparing all leaves is demarcated. Clear differences in shape between major phylogenetic groups are detected and estimates of leaf shape diversity within plant families are made. This approach does not only predict plant family, but also the collection site, confirming phylogenetically invariant morphological features that characterize leaves from specific locations. The application of a persistent homology method to measure leaf shape allows for a unified morphometric framework to measure plant form, including shape and branching architectures.

plant biology↗

bioRxiv2017

Genetic Architecture and Molecular Networks Underlying Leaf Thickness in Desert-Adapted Tomato Solanum pennellii

Thicker leaves allow plants to grow in water-limited conditions. However, our understanding of the genetic underpinnings of this highly functional leaf shape trait is poor. We used a custom-built confocal profilometer to directly measure leaf thickness in a set of introgression lines (ILs) derived from the desert tomato species Solanum pennellii, and identified quantitative trait loci (QTL). We report evidence of a complex genetic architecture of this trait and roles for both genetic and environmental factors. Several ILs with thick leaves have dramatically elongated palisade mesophyll cells and, in some cases, increased leaf ploidy. We characterized thick ILs 2-5 and 4-3 in detail and found increased mesophyll cell size and leaf ploidy levels, suggesting that endoreduplication underpins leaf thickness in tomato. Next, we queried the transcriptomes and inferred Dynamic Bayesian Networks of gene expression across early leaf ontogeny in these lines to compare the molecular networks that pattern leaf thickness. We show that thick ILs share S. pennellii-like expression profiles for putative regulators of cell shape and meristem determinacy, as well as a general signature of cell cycle related gene expression. However, our network data suggest that leaf thickness in these two lines is patterned by at least partially distinct mechanisms. Consistent with this hypothesis, double homozygote lines combining introgression segments from these two ILs show additive phenotypes including thick leaves, higher ploidy levels and larger palisade mesophyll cells. Collectively, these data establish a framework of genetic, anatomical, and molecular mechanisms that pattern leaf thickness in desert-adapted tomato.

plant biology↗

bioRxiv2017

Persistent homology: a tool to universally measure plant morphologies across organs and scales

Genetic contributions to plant morphology are not partitioned between shoots and roots. Yet, shoot and root architectures are rarely measured in the same plants. Even if shoot and root architectures are both studied, the application of mathematical methods flexible enough to accommodate the disparate topologies and shapes within a plant, and across scales, are lacking. Here, we advocate the use of persistent homology, a mathematical method robust to noise, invariant with respect to orientation, capable of application across diverse scales, and importantly, compatible with diverse functions to quantify disparate plant morphologies, architectures, and textures. To demonstrate the usefulness of this method, we apply persistent homology approaches to the shape of leaves, serrations, and root architecture as measured in the same plants of a domesticated tomato Solanum pennellii near-isogenic introgression line population under field conditions. We find that genetic contributions to morphology affect the plant in a concerted fashion, affecting both the shoot and root, revealing a pleiotropic basis to natural variation in tomato.

plant biology↗