Biology subjects

Zabotina, O. A.

Publications and source records attributed to Zabotina, O. A..

6 recordsLinked to original sources

bioRxiv2025

Sewing the future of cotton: a multi-omics study combining nanomechanics, transcriptomics, and phenotypic traits

Cellulose microfibrils that are essential for mechanical strength and overall quality of cotton fibers. This study quantifies and compares the nanoscale structural and mechanical properties of cellulose microfibrils such as microfibril dimensions, crossover count and angles, roughness, and Youngs modulus for two popular cotton species: Gossypium hirsutum (Gh) and Gossypium barbadense (Gb) fibers across four growth stages (8, 12, 18, and 22 days post-anthesis) using atomic force microscopy (AFM). Our results revealed for the first time that Gb fibers exhibit a better alignment, finer dimensions, and higher stiffness compared to Gh fibers at nanoscale, resulting in smoother fiber surfaces, and improved quality at macroscale. We are also the first to develop machine-learning models to predict macroscale phenotypic traits specifically boll length and cellulose content using nanoscale features alone and in combination with multi-omics modalities, substantially enhancing the predictive accuracy and highlighting opportunities for robust cross-species modeling of cotton fiber traits.

biophysics↗

bioRxiv2025

Comparative multi-omics profiling of Gossypium hirsutum and Gossypium barbadense fibers at high temporal resolution reveals key differences in polysaccharide composition and associated glycosyltransferases

Among the two allopolyploid cultivated species of cotton, Gossypium barbadense is known for its superior quality fiber compared to G. hirsutum. Length and strength are key determinants of the fiber quality. Although the mature fibers are dried cell walls consisting mainly cellulose, the dynamic remodeling of pectin, xyloglucan, and xylan polysaccharides during fiber growth significantly impact the final fiber quality. Comprehensive knowledge about polysaccharides and their biosynthesis during fiber development of the cultivated species is important for improving fiber quality. In this study, comparative large-scale glycome, transcriptome and proteome profiling were conducted daily on fibers of both cotton species covering critical stages of fiber development spanning primary cell wall synthesis and the transition to secondary wall synthesis. Interspecific comparisons revealed that a delayed accumulation of cellulose content, as well as the occurrence of lower levels and differential compositions of non-fucosylated/fucosylated xyloglucans, homogalacturonans, and highly branched Rhamnogalacturonan-I polysaccharides might be contributing to longer fiber phenotypes of G. barbadense relative to G. hirsutum. Our study also suggests, differential temporal compositions of heteroxylans might contribute to variation in cellulose microfibril arrangement and strength of fiber exists between the two species of cotton. Comparative transcriptomic analysis identified differentially expressed polysaccharide-synthesizing glycosyltransferases that might underlie fiber quality differences between the two species. Transcripts encoding many cell wall localized expansins were more abundant in G. barbadense than in G. hirsutum. Overall, these findings extend our knowledge regarding the molecular factors that contribute to fiber quality and provide insights for targeted cotton fiber improvement. SIGNIFICANCE STATEMENTComparative multi-omics profiling of two major commercial cotton species, Gossypium hirsutum and Gossypium barbadense revealed substantial differences in polysaccharide structures and expressed polysaccharide-synthesizing glycosyltransferases, that potentially contribute to differences in fiber length and strength. The molecular details elucidated in the present study contribute to the goal of improving fiber quality and its commercial value.

plant biology↗

bioRxiv2025

Proteomics-based models of gene expression and cellular control of cotton fiber development

The shapes and material properties of cotton seed coat trichoblasts are the basis of a multibillion-dollar natural fiber industry. As such, these highly specialized cells are low-hanging fruit for intentional trait engineering. However, broad successes will require more mechanistic knowledge about their systems-level cellular controls. This time-series study integrates daily measurements of purified fiber transcriptomes and proteomes with multiscale fiber phenotyping datasets that span the same developmental interval. Abundance profiles of the subcellular proteomes are the foundation of the analyses. This resource article provides direct information concerning which homoeologs operate and informative depictions of how compartmentalized cellular systems change during developmental transitions. Prediction accuracy was partially validated by analysis of the protein expression group 11, which contained multiple known secondary cell wall cellulose synthases and dozens of unknown proteins and an averaged profile that was strongly correlated with a sharp state transition in cellulose microfibril alignment and increased cellulose content. The dataset as a whole can serve as a hypothesis-generating machine to guide future experiments that relate to cell shape and growth rate control, reversible tissue formation, and cell wall remodeling. Integration of mRNA and protein abundance revealed widespread evidence for post-transcriptional control. In addition, there were hundreds of transcriptionally controlled genes with differing timepoints of transition. This latter gene set can be used to more reliably analyze transcriptional control networks and to generate collections of gene expression drivers for cotton fiber research. The protein and transcript data are organized into user-friendly tables and a web interface that can be searched using any plant ortholog of interest based on developmental time, abundance, annotations, or phenotypic association.

plant biology↗

bioRxiv2024

Developmental variability in cotton fiber cell wall properties linked to important agronomic traits

The economic value of cotton is based on its long, thin, strong, and twisted trichoblasts that emerge from the ovule epidermis. The mature dried fiber cell reflects the outcome of a rapid tapering of the nascent trichoblast, weeks of polarized diffuse growth, followed by a transition to persistent secondary cell wall synthesis. Highly conserved and dynamic microtubule and cellulose microfibril-based anisotropic growth control modules are central to all of these phases. In this paper, we developed novel quantitative phenotyping and computational modeling pipelines to analyze fiber growth behaviors at a daily resolution. We uncovered unexpected variability in growth rate, cell wall properties, and cell geometry across a critical window of fiber development. Finite element computational modeling of fiber growth was used to analyze the instability of cell diameter control and predict how spatial gradients of fiber and matrix material properties can interact to dictate the patterns of shape change. As an initial step toward gaining insight into the molecular orchestration of cellulose biosynthesis, expression profiles of a broad set of relevant genes were quantified across the same developmental timeline and correlated with fiber phenotypes. This analysis identified specific candidate genes that may serve as targets for fiber quality improvement.

plant biology↗

bioRxiv2024

A high-resolution model of gene expression during Gossypium hirsutum (cotton) fiber development

Cotton fiber development relies on complex and intricate biological processes to transform newly differentiated fiber initials into the mature, extravagantly elongated cellulosic cells that are the foundation of this economically important cash crop. Here we extend previous research into cotton fiber development by employing controlled conditions to minimize variability and utilizing time-series sampling and analyses to capture daily transcriptomic changes from early elongation through the early stages of secondary wall synthesis (6 to 24 days post anthesis; DPA). A majority of genes are expressed in fiber, largely partitioned into two major coexpression modules that represent genes whose expression generally increases or decreases during development. Differential gene expression reveals a massive transcriptomic shift between 16 and 17 DPA, corresponding to the onset of the transition phase that leads to secondary wall synthesis. Subtle gene expression changes are captured by the daily sampling, which are discussed in the context of fiber development. Coexpression and gene regulatory networks are constructed and associated with phenotypic aspects of fiber development, including turgor and cellulose production. Key genes are considered in the broader context of plant secondary wall synthesis, noting their known and putative roles in cotton fiber development. The analyses presented here highlight the importance of fine-scale temporal sampling on understanding developmental processes and offer insight into genes and regulatory networks that may be important in conferring the unique fiber phenotype.

cell biology↗

bioRxiv2024

Daily glycome and transcriptome profiling reveals polysaccharide structures and glycosyltransferases critical for cotton fiber growth

Cotton fiber length and strength are key determinants of its quality. Dynamic changes in the pectin, xyloglucan, xylan, and cellulose polysaccharide epitopes content during fiber growth contribute to complex remodeling of fiber cell wall (CW) and quality. Detailed knowledge about polysaccharide compositional and structural alteration in the fiber during fiber elongation and strengthening is vastly limited. Here, large-scale glycome profiling coupled with fiber phenotype and transcriptome profiling was conducted on fiber collected daily covering the most critical fiber developmental window. High temporal resolution profiling allowed us to identify specific polysaccharide epitopes associated with distinct fiber phenotypes that might contribute to fiber quality. This study revealed the critical role of highly branched RG-I pectin epitopes such as, {beta}-1,4-linked-galactans, {beta}-1,6-linked-galactans, and arabinogalactans, in addition to earlier reported homogalacturonans and xyloglucans in the formation of cotton-fiber-middle-lamella and contributing to fiber plasticity and elongation. We also propose the essential role of heteroxylans (Xyl-MeGlcA and Xyl-3Ar), as a guiding factor for secondary CW cellulose-microfibril arrangement, thus contributing to fiber strength. Correlation analysis of glycome and transcriptome data identified several key putative glycosyltransferases involved in synthesizing the critical polysaccharide epitopes. Novel details discovered here provide a foundation to identify molecular factors that dictate important fiber traits.

plant biology↗