Biology subjects

Gao, T.

Publications and source records attributed to Gao, T..

At least 55 records · Page 3Linked to original sources

bioRxiv2022

Structural and functional insights into the type III-E CRISPR-Cas immunity

The type III-E CRISPR-Cas system comprises a Cas effector (gRAMP), a TPR-CHAT and several ancillary proteins. However, both the structural features of gRAMP and the immunity mechanism remain unknown for this system. Here, we report a series of structures of gRAMP-crRNA, either its alone or in complex with target RNA or TPR-CHAT (called Craspase), and Craspase complexed with cognate (CTR) or non-cognate target RNA (NTR). Importantly, the 3 anti-tag region of NTR and CTR bind at two distinct channels in the Craspase, and CTR with a non-complementary 3 anti-tag induces a marked conformational change of the TPR-CHAT, which allosterically activates its protease activity to cleave an ancillary protein Csx30. This cleavage then triggers an abortive infection as the antiviral strategy of the type III-E system. Together, our study provides crucial insights into both the catalytic mechanism of the gRAMP and the immunity mechanism of the type III-E CRISPR-Cas system.

molecular biology↗

bioRxiv2022

Inhibition of Talin-induced Integrin Activation by a Double-hit Stapled Peptide

Integrins are ubiquitously expressed cell-adhesion proteins. Talin is required for integrin activation through an inside-out signaling pathway, during which talin is recruited to the plasma membrane (PM) by RAP1 directly or through its effector, RAP1-Interacting Adaptor Molecule (RIAM). RIAM also activates talin from autoinhibition by binding to talin head domain. A helical talin-binding segment (TBS) in RIAM mediates both talin activation and recruitment by binding to two distinct sites in talin head and rod domains respectively. The bi-specificity of the TBS fragment allows us to develop a new strategy to suppress talin-induced integrin activation through a "double-hit" approach. We designed an experimental peptidomimetic inhibitor by engineering a hydrocarbon "staple" in the helical TBS fragment to mask the integrin binding site in the talin head. The stapled peptide (S-TBS) exhibits a stronger binding affinity with talin and inhibits talin:integrin interaction. Crystal structure of S-TBS in complex with talin rod domains reveals an interface that overlaps with the TBS-binding site in talin. Consistently, S-TBS also exhibits an inhibitory effect on TBS:talin-rod interaction during the PM recruitment of talin. Importantly, S-TBS possesses excellent cell permeability and inhibits integrin activation in a talin-dependent manner. Hence, our results present a novel approach to design a new class of intracellular inhibitors targeting integrin functions.

biochemistry↗

bioRxiv2022

A non-destructive approach for measuring rice panicle-level photosynthetic responses using 3D-image reconstruction

Our understanding of the physiological response of rice inflorescence (panicle) to environmental stresses is limited by the challenge of accurately determining panicle photosynthetic parameters and their impact on grain yield. This is primarily due to lack of a suitable gas exchange methodology for panicles, as well as non-destructive methods to accurately determine panicle surface area. To address these challenges, we have developed a custom panicle gas exchange cylinder compatible with the LiCor 6800 Infra-red Gas Analyzer. Accurate surface area measurements were determined with a 3D panicle imaging platform to normalize the panicle-level photosynthetic measurements. We observed differential responses in both panicle and flag leaf for two temperate Japonica rice genotypes (accessions, TEJ-1 and TEJ-2) exposed to heat stress during early grain filling. There was a notable divergence in relative photosynthetic contribution of flag leaf and panicles for the genotype tolerant to heat stress (TEJ-2) compared to the less tolerant accession. The novelty of this approach is that it is non-destructive and more accurately determines panicle area and photosynthetic parameters, enabling researchers to monitor temporal changes in panicle physiology during the reproductive development. The method is useful for panicle-level measurements under diverse environmental stresses, and for evaluating genotypic variation for panicle physiology and architecture in other cereals with compact inflorescences.

physiology↗

bioRxiv2022

Effects of seasonal changes on the carbon dynamics in mixed coniferous forests

We characterized seasonal changes in the residual rate and mass-loss rate of litter, as well as the carbon release dynamics of litter and soil, in mixed coniferous forests in the Xiaoxinganling region by conducting a controlled freeze-thaw experiment. The carbon release rate and mass-loss rate of litter at two levels of decomposition (undecomposed and semi-decomposed) were measured during four seasons: the unfrozen season, freeze-thaw season, frozen season, and thaw season. The temperature was higher, the mass-loss rate was faster, and the overall mass-loss rate of litter was higher in the unfrozen season than in the other three seasons; litter organic carbon increased and soil organic carbon increased due to the strong carbon sequestration capacity of plants. The temperature fluctuated above and below 0{degrees}C during the freeze-thaw season, which results in the physical breakage of the undecomposed litter and increases in the mass-loss rate. This leads to increases in the organic carbon of undecomposed litter and decreases in the soil organic carbon of undecomposed litter; the opposite patterns were observed for changes in the organic carbon of semidecomposed litter and soil organic carbon. There was noticeable mass loss of litter during the frozen season, and the rate of mass loss of litter during the thaw season was the lowest. Litter organic carbon decreased and soil organic carbon increased in both seasons. The organic carbon of undecomposed litter was highest in the thaw season, followed by the freeze-thaw season, frozen season, and unfrozen season. The organic carbon of semi-decomposed litter was highest in the frozen season, followed by the thaw season, freeze-thaw season, unfrozen season to freeze-thaw season, frozen season, thaw season, and unfrozen season. After freeze-thaw treatment, the organic carbon in deadfall soil was highest in the unfrozen season, freeze-thaw season, frozen season, thaw season to unfrozen season, frozen season, thaw season, and freeze-thaw season. The findings of this study provide new insights into the material cycling process under freeze-thawing, as well as information on the effect of seasonal freeze-thaws on the forest carbon cycle.

ecology↗

bioRxiv2022

Haplotype-enhanced inference of somatic copy number profiles from single-cell transcriptomes

Genome instability and aberrant alterations of transcriptional programs both play important roles in cancer. However, their relationship and relative contribution to tumor evolution and therapy resistance are not well-understood. Single-cell RNA sequencing (scRNA-seq) has the potential to investigate both genetic and non-genetic sources of tumor heterogeneity in a single assay. Here we present a computational method, Numbat, that integrates haplotype information obtained from population-based phasing with allele and expression signals to enhance detection of CNVs from scRNA-seq data. To resolve tumor clonal architecture, Numbat exploits the evolutionary relationships between subclones to iteratively infer the single-cell copy number profiles and tumor clonal phylogeny. Analyzing 21 tumor samples composed of multiple myeloma, breast, and thyroid cancers, we show that Numbat can accurately reconstruct the tumor copy number profile and precisely identify malignant cells in the tumor microenvironment. We uncover additional subclonal complexity contributed by allele-specific alterations, and identify genetic subpopulations with transcriptional signatures relevant to tumor progression and therapy resistance. We hope that the increased power to characterize genomic aberrations and tumor subclonal phylogenies provided by Numbat will help delineate contributions of genetic and non-genetic mechanisms in cancer.

bioinformatics↗

bioRxiv2021

Direct RNA sequencing of Respiratory Syncytial Virus infected human cells generates a detailed overview of RSV polycistronic mRNA and transcript abundance

To characterize species of viral mRNA transcripts generated during respiratory syncytial virus (RSV) infection, human fibroblast-like MRC5 lung cells were infected with subgroup A RSV for 6, 16 and 24 hours. Total RNA was harvested and polyadenylated mRNA was enriched and sequenced by direct RNA sequencing on an Oxford nanopore device. This yielded over 150,000 direct mRNA transcript reads which were mapped to the viral genome and analysed to determine relative mRNA levels of viral genes using our in-house ORF-centric pipeline. We were also able to examine frequencies with which polycistronic readthrough mRNAs were generated and to assess the length of the polyadenylated tails for each group of transcripts. We show that there is a general but non-linear decline in gene transcript abundance across the viral genome, as predicted by the model of RSV gene transcription. However, the decline in transcript abundance is not consistent. We show that the polyadenylate tails generated by the viral polymerase are similar in length to those generated by the host cells polyadenylation machinery and broadly declined in length for most transcripts as infection progressed. Finally, we observed that the steady state abundance of transcripts with very short polyadenylate tails is much less for N, SH and G transcripts compared to NS1, NS2, P, M, F and M2 which may reflect differences in mRNA stability and/or translation rates.

microbiology↗

bioRxiv2021

Effect of Aeromonas hydrophila infected on metabolomic response and gut microbial 16S rRna of Charybdis japonica

The innate immune response of Charybdis japonica treated with Aeromonas hydrophila was explored using bioinformatics. Metabolomics data were integrated with a gut microbial 16S rRNA dataset, together with information on corresponding enzyme activity. The results of the study showed that after being infected with A. hydrophila, some beneficial genera of bacteria in the gut of C. japonica, such as Photobacterium, Rhodobacter, Polaribacter, Psychrilyobacter, Mesoflavibacter, Fusibacter and Phormidium, could directly inhibit Vibrio or produce extracellular polysaccharides with highly effective antibacterial properties. The intestinal probiotics of C. japonica such as Mesoflavibacter have a mutually reinforcing relationship with Phaeobacter, Colwellia, Bacillus, Psychrobacter and Cohaesibacter. Conditional pathogenic bacteria in the gut of healthy crabs may also have such a symbiotic relationship with intestinal probiotics, promoting their growth and reproduction. For example, Phormidium has a mutualistic relationship with Aeromonas and Azopira. Metabolites in the gut of C. japonica infected with A. hydrophila, including beta-alanine metabolism, nitrogen metabolism, inositol phosphate metabolism, galactose metabolism, histidine metabolism, ascorbate and arginine and proline metabolism were increased, with alanine metabolism being the most abundant. The activity of metabolite related enzymes such as lipid peroxidase, phenoloxidase, superoxide dismutase, nitric oxide synthase, glutathione transferase and mid-glutathione decreased and NO levels also decreased. The positive correlation with the probiotic flora suggests that metabolites increase with bacterial abundance and that microbial metabolites or co-metabolites can, in turn, achieve many pleiotropic effects to resist invasion by A. hydrophila. These results may contribute to further research in the resistance of C. japonica to invading pathogens. ImportanceWith the rapid development of the C. japonica farming industry, investors, in pursuit of economic benefits, have encountered problems such as frequent outbreaks of various diseases, resulting in high mortality and huge economic losses. The open water circulation system can give rise to several crab bacterial diseases. Among these, A. hydrophila is a pathogenic bacterium affecting fish and crustaceans, which leads to huge economic losses. Our results suggest that metabolites increased with the abundance of bacteria. It is possible that the autoimmune system and the entry of A. hydrophila into the intestinal tissues of C. japonica react immunologically and that the organism is producing certain metabolites which may be metabolised by various bacteria and absorbed into the circulation. In addition, some of these metabolites are modified or bound in the hepatopancreas to produce microbiota-host co-metabolites. These microbial metabolites or co-metabolites can resist invasion by A. hydrophila.

immunology↗

bioRxiv2021

SARS-CoV-2 receptor ACE2 identifies immuno-hot tumors in breast cancer

Angiotensin-converting enzyme 2 (ACE2) is known as a host cell receptor for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which is identified to be dysregulated in multiple tumors. Although the characterization of abnormal ACE2 expression in malignancies has been preliminarily explored, in-depth analysis of ACE2 in breast cancer (BRCA) has not been elucidated. A systematic pan-cancer analysis was conducted to assess the expression pattern and immunological role of ACE2 based on RNA-sequencing (RNA-seq) data downloaded from The Cancer Genome Atlas (TCGA). Next, correlations between ACE2 expression immunological characteristics in the BRCA tumor microenvironment (TME) were evaluated. Also, the role of ACE2 in predicting the clinical features and the response to therapeutic options in BRCA was estimated. These findings were subsequently validated in another public transcriptomic cohort as well as a recruited cohort. ACE2 was lowly expressed in most cancers compared with adjacent tissues. ACE2 was positively correlated with immunomodulators, tumor-infiltrating immune cells (TIICs), cancer immunity cycles, immune checkpoints, and tumor mutation burden (TMB). Besides, high ACE2 levels indicated the triple-negative breast cancer (TNBC) subtype of BRCA, lower response to endocrine therapy and higher response to chemotherapy, anti-ERBB therapy, antiangiogenic therapy and immunotherapy. To sum up, ACE2 correlates with an inflamed TME and identifies immuno-hot tumors, which may be used as an auxiliary biomarker for the identification of immunological characteristics in BRCA.

immunology↗

bioRxiv2021

Evaluation of different concentrations antibiotics on gut bacteria and growth of Ectropis obliquaProut (Lepidoptera: Geometridae)

The use of antibiotics to remove gut bacteria is a commonly used method to study gut function of insects. We assessed the impact of the artificial diet made from tea powder with different concentrations of antibiotics mixture (containing tetracycline, gentamicin, penicillin, and rifampicin) on Ectropis obliqua Prout (Lepidoptera: Geometridae) survival, growth, and reproduction. Antibiotic-induced bacterial clearance was monitored by Polymerase Chain Reaction (PCR) and by Colony-counting Methods. The results indicated that administration of the antibiotic mixture at a concentration of 200g/ml caused the increase of gut bacteria, while a concentration of 300g/ml was more effective in clearing gut bacteria but the concentration of 400g/ml caused a large number of larval deaths. The concentration of 300g/ml had no significant effect on the growth and development of E. obliqua, but had impact on fecundity. Therefore, we could use 300g/ml concentrations of the antibiotic mixture to obtain sterile E. obliqua to study the function of intestinal microbes.

animal behavior and cognition↗

bioRxiv2020

Cognitive and neural bases of collateral damage during intergroup conflict

Civilian casualties occur during military attacks. Such "collateral damage" is prohibited by international laws but increases with substantial consequences when intergroup conflict escalates. Here, we investigate cognitive and neural bases of decision-making processes resulting in civilian harm, using a task that simulates punishment decision-making during intergroup conflict. We test two groups of Chinese participants in a laboratory setting, and two ethnic groups (Jewish and Palestinian) in Israel. The results dissociate two psychological constructs, harm preference and harm avoidance, which respectively characterize punishment decision-making related to outgroup combatants and outgroup noncombatants during intergroup conflict. In particular, individuals show decreased avoidance of harming outgroup noncombatants when conflict escalates. Brain imaging (functional magnetic resonance imaging) reveals that decreased harm avoidance is predicted by inhibition of the left middle frontal activity during selection of punishment decisions. Our findings provide insight into the cognitive and neural bases of decision-making involving civilian harm during intergroup conflict.

neuroscience↗

bioRxiv2020

Wild emmer introgressions alter root-to-shoot growth dynamics under water stress

Water deficit is a major limiting factor for wheat (Triticum sp.) development and productivity. One approach to increase water stress adaptation in wheat is incorporating novel alleles from the drought-adapted wheat progenitor, wild emmer (T. turgidum ssp. dicoccoides). We explored this idea in the context of vegetative growth by examining the phenotypic consequence of a series of wild emmer (acc. Zavitan) introgressions into elite durum wheat (cv. Svevo) under water-limited conditions. Using image-based phenotyping we cataloged divergent (from Svevo) growth responses to water stress ranging from high plasticity to high stability among the introgression lines. We identified an introgression line (IL20) that exhibits a highly plastic response to water stress by shifting its root-to-shoot biomass ratio for detailed characterization. By combining genotypic information with root transcriptome analysis, we propose several candidate genes (including a root-specific kinase) that can confer the shoot-to-root carbon resource allocation in IL20 under water stress. Discovery of high plasticity trait in IL20 in response to water stress highlights the potential of wild introgressions for enhancing stress adaptation via mechanisms that may be absent or rare in elite breeding material.

plant biology↗

bioRxiv2020

Sorcin stimulates Activation Transcription Factor 6α (ATF6) transcriptional activity

Levels of the transcription factor ATF6, a key mediator of the unfolded protein response, that provides cellular protection during the progression endoplasmic reticulum (ER) stress, are markedly reduced in the pancreatic islet of patients with type 2 diabetes and in rodent models of the disease, including ob/ob and high fat-fed mice. Sorcin (gene name SRI) is a calcium (Ca2+) binding protein involved in maintaining ER Ca2+ homeostasis. We have previously shown that overexpressing sorcin under the rat insulin promoter in transgenic mice was protective against high fat diet-induced pancreatic beta cell dysfunction, namely preserving intracellular Ca2+ homeostasis and glucose-stimulated insulin secretion during lipotoxic stress. Additionally, sorcin overexpression was apparently activating ATF6 signalling in MIN6 cells despite lowering ER stress. Here, in order to investigate further the relationship between sorcin and ATF6, we describe changes in sorcin expression during ER and lipotoxic stress and changes in ATF6 signalling after sorcin overexpression or inactivation, both in excitable and non-excitable cells. Sorcin mRNA levels were significantly increased in response to the ER stress-inducing agents thapsigargin and tunicamycin, but not by palmitate. On the contrary, palmitate caused a significant decrease in sorcin expression as assessed by both qRT-PCR and Western blotting despite inducing ER stress. Moreover, palmitate prevented the increase in sorcin expression induced by thapsigargin. In addition, sorcin overexpression significantly increased ATF6 transcriptional activity, whereas sorcin inactivation decreased ATF6 signalling. Finally, sorcin overexpression increased levels of ATF6 immunoreactivity and FRET imaging experiments following ER stress induction by thapsigargin showed a direct sorcin-ATF6 interaction. Altogether, our data suggest that sorcin down-regulation during lipotoxicity may prevent full ATF6 activation and a normal UPR during the progression of obesity and insulin resistance, contributing to beta cell failure and type 2 diabetes.

cell biology↗

bioRxiv2020

Multiple particle tracking detects changes in brain extracellular matrix structure and predicts neurodevelopmental age

Abstract SummaryBrain extracellular matrix (ECM) structure mediates many aspects of neuronal function. Probing changes in ECM structure could provide insights into aging and neurological disease. Herein, we demonstrate the ability to characterize changes in brain ECM structure using multiple particle tracking (MPT). MPT was carried out in organotypic rat brain slices to detect induced and naturally occurring changes in ECM structure. Induced degradation of neural ECM led to a significant increase in nanoparticle diffusive ability in the brain extracellular space. For structural changes that occur naturally during development, an inverse relationship existed between age and nanoparticle diffusion. Using the age-dependent dataset, we applied extreme gradient boosting (XGBoost) to generate models capable of classifying nanoparticle trajectories. Collectively, this work demonstrates the utility of MPT combined with machine learning for measuring changes in brain ECM structure and predicting associated complex features such as developmental age.

developmental biology↗

bioRxiv2020

Immunity-and-Matrix-Regulatory Cells Derived from Human Embryonic Stem Cells Safely and Effectively Treat Mouse Lung Injury and Fibrosis

Lung injury and fibrosis represent the most significant outcomes of severe and acute lung disorders, including COVID-19. However, there are still no effective drugs to treat lung injury and fibrosis. In this study, we report the generation of clinical-grade human embryonic stem cells (hESCs)-derived immunity- and matrix-regulatory cells (IMRCs) produced under good manufacturing practice (GMP) requirements, that can treat lung injury and fibrosis in vivo. We generate IMRCs by sequentially differentiating hESCs with serum-free reagents. IMRCs possess a unique gene expression profile distinct from umbilical cord mesenchymal stem cells (UCMSCs), such as higher levels of proliferative, immunomodulatory and anti-fibrotic genes. Moreover, intravenous delivery of IMRCs inhibits both pulmonary inflammation and fibrosis in mouse models of lung injury, and significantly improves the survival rate of the recipient mice in a dose-dependent manner, likely through paracrine regulatory mechanisms. IMRCs are superior to both primary UCMSCs and FDA-approved pirfenidone, with an excellent efficacy and safety profile in mice and monkeys. In light of public health crises involving pneumonia, acute lung injury (ALI) and acute respiratory distress syndrome (ARDS), our findings suggest that IMRCs are ready for clinical trials on lung disorders.

cell biology↗

bioRxiv2020

Behavioral and neural decomposition of skull-induced death awareness

Death awareness influences multiple aspects of human lives, but its psychological constructs and underlying brain mechanisms remain unclear. We address these by measuring behavioral and brain responses to images of human skulls. We show that skulls relative to control stimuli delay responses to life-related words but speed responses to death-related words. Skulls compared to the control stimuli induce early deactivations in the posterior ventral temporal cortex followed by activations in the posterior and anterior ventral temporal cortices. The early and late neural modulations by perceived skulls respectively predict skull-induced changes of behavioral responses to life- and death-related words and the early neural modulation further predicts death anxiety. Our findings decompose skull-induced death awareness into two-stage neural processes of a lifeless state of a former life. One sentence summaryBehavioral and brain imaging findings decompose skull-induced death awareness into two-stage neural processes of a lifeless state of a former life.

neuroscience↗

bioRxiv2020

GOT1 Inhibition Primes Pancreatic Cancer for Ferroptosis through the Autophagic Release of Labile Iron

Pancreatic ductal adenocarcinoma (PDA) is one of the deadliest solid malignancies, with a 5-year survival rate at ten percent. PDA have unique metabolic adaptations in response to cell-intrinsic and environmental stressors, and identifying new strategies to target these adaptions is an area of active research. We previously described a dependency on a cytosolic aspartate aminotransaminase (GOT1)-dependent pathway for NADPH generation. Here, we sought to identify metabolic dependencies induced by GOT1 inhibition that could be exploited to selectively kill PDA. Using pharmacological methods, we identified cysteine, glutathione, and lipid antioxidant function as metabolic vulnerabilities following GOT1 withdrawal. Targeting any of these pathways was synthetic lethal in GOT1 knockdown cells and triggered ferroptosis, an oxidative, non-apoptotic, iron-dependent form of cell death. Mechanistically, GOT1 inhibition promoted the activation of autophagy in response to metabolic stress. This enhanced the availability of labile iron through ferritinophagy, the autolysosome-mediated degradation of ferritin. In sum, our study identifies a novel biochemical connection between GOT1, iron regulation, and ferroptosis, and suggests the rewired malate-aspartate shuttle plays a role in protecting PDA from severe oxidative challenge. HighlightsO_LIPDA exhibit varying dependence on GOT1 for in vitro and in vivo growth. C_LIO_LIExogenous cystine, glutathione synthesis, and lipid antioxidant fidelity are essential under GOT1 suppression. C_LIO_LIGOT1 inhibition sensitizes pancreatic cancer cell lines to ferroptosis. C_LIO_LIGOT1 inhibition represses anabolic metabolism and promotes the release of iron through autophagy. C_LI

cancer biology↗

bioRxiv2020

Optimum Threshold Minimizes Noise in Timing of Intracellular Events

How the noisy expression of regulatory proteins affects timing of intracellular events is an intriguing fundamental problem that influences diverse cellular processes. Here we use the bacteriophage {lambda} to study event timing in individual cells where cell lysis is the result of expression and accumulation of a single protein (holin) in the Escherchia coli cell membrane up to a critical threshold level. Site-directed mutagenesis of the holin gene was used to generate phage variants that vary in their timing of lysis from 30 to 190 min. Observation of the lysis times of single cells reveals an intriguing finding - the noise in lysis timing first decreases with increasing lysis time to reach a minimum, and then sharply increases at longer longer lysis times. A mathematical model with stochastic expression of holin together with dilution from cell growth was sufficient to explain the non-monotonic noise profile, and identify holin accumulation thresholds that generate precision in lysis timing.

biophysics↗

bioRxiv2019

PI-Plat: A high-resolution image-based 3D reconstruction method to estimate growth dynamics of rice inflorescence traits

BackgroundRecent advances in image-based plant phenotyping have improved our capability to study vegetative stage growth dynamics. However, more complex agronomic traits such as inflorescence architecture (IA), which predominantly contributes to grain crop yield are more challenging to quantify and hence are relatively less explored. Previous efforts to estimate inflorescence-related traits using image-based phenotyping have been limited to destructive end-point measurements. Development of non-destructive inflorescence phenotyping platforms could accelerate the discovery of the phenotypic variation with respect to inflorescence dynamics and mapping of the underlying genes regulating critical yield components. ResultsThe major objective of this study is to evaluate post-fertilization development and growth dynamics of inflorescence at high spatial and temporal resolution in rice. For this, we developed the Panicle Imaging Platform (PI-Plat) to comprehend multi-dimensional features of IA in a non-destructive manner. We used 11 rice genotypes to capture multi-view images of primary panicle on weekly basis after the fertilization. These images were used to reconstruct a 3D point cloud of the panicle, which enabled us to extract digital traits such as voxel count and color intensity. We found that the voxel count of developing panicles is positively correlated with seed number and weight at maturity. The voxel count from developing panicles projected overall volumes that increased during the grain filling phase, wherein quantification of color intensity estimated the rate of panicle maturation. Our 3D based phenotyping solution showed superior performance compared to conventional 2D based approaches. ConclusionsFor harnessing the potential of the existing genetic resources, we need a comprehensive understanding of the genotype-to-phenotype relationship. Relatively low-cost sequencing platforms have facilitated high-throughput genotyping, while phenotyping, especially for complex traits, has posed major challenges for crop improvement. PI-Plat offers a low cost and high-resolution platform to phenotype inflorescence-related traits using 3D reconstruction-based approach. Further, the non-destructive nature of the platform facilitates analyses of the same panicle at multiple developmental time points, which can be utilized to explore the genetic variation for dynamic inflorescence traits in cereals.

plant biology↗