Biology subjects

Ji, M.

Publications and source records attributed to Ji, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Isoleucine and asparagine influence the growth of staphylococcal strains in atopic dermatitis

Atopic dermatitis (AD) is a multifactorial, chronic skin disease associated with microbial factors. It is known that staphylococcal skin microbes play a role in the pathophysiology of AD, notably S. aureus. However, how staphylococcal strain variation affects disease aetiology and progression remains unclear. Using a culture-dependent approach, we analyzed the genomic and phenotypic profile of staphylococcal strains isolated from a Hong Kong children cohort (n = 70). Presence of S. aureus was positively associated with AD skin, whilst S. epidermidis and S. hominis were positively associated with healthy skin, but no overall strain type was associated with AD. In vitro experimentation revealed that there is demarcation in S. aureus strain growth, biofilm biomass formation, and metabolite production by disease severity. While isoleucine and asparagine promoted S. aureus growth, these amino acids suppressed S. hominis growth. These collective findings highlight the importance of strain-level and metabolic interactions of staphylococci in AD pathophysiology.

microbiology↗

bioRxiv2026

Trichome acylsugar defenses are equally effective against leaf-mining and free-living insects

Trichomes are epidermal projections, crucial components of plant defense systems. Whether these epidermal defenses are effective against leafminers, which infest the internal mesophyll layers, remains unclear. Using the devasting invasive tomato pest, Phthorimaea absoluta (tomato leafminer), and the trichome-rich wild tomato, Solanum pennellii, we demonstrate that trichome produced acylsugars effectively inhibit the growth of endophagous P. absoluta larvae feeding inside leaves. High spatial resolution leaf- and frass-metabolite analysis by MALDI-MSI and Stimulated Raman Scattering microscopy revealed that trichome-synthesized acylsugars are translocated into the mesophyll tissues when larvae infest leaves. We identified an ATP-binding cassette (ABC) transporter, SpABCB5, as the mediator of this translocation and as an essential component of defense against leafminers. These data reveal that epidermal trichomes not only defend against free-living (ectophagous) herbivores through direct contact or rapid deposition of chemical defenses onto leaf surfaces, but also defend against endophagous leafminers by rapidly depositing chemical defenses into internal tissues. By delivering mines against leaf miners, trichomes offer new avenues for breeding crops with resistance to leafminers.

plant biology↗

bioRxiv2026

Structure-guided discovery and engineering of miniature CRISPR-Cas12m for epigenome editing

CRISPR-based epigenome editing represents a programmable strategy to precisely modulate gene expression, holding immense promise for therapeutic applications. However, the large size of the dCas proteins substantially impedes the delivery via adeno-associated virus (AAV) vectors. Here, through iterative bioinformatics analysis, structure-guided predictions, and functional assays, we identified and characterized PmCas12m, a novel miniature subtype V-M CRISPR-Cas12m. PmCas12m exhibited flexible 5-YTN-3 PAM-dependent recognition and robust double-stranded DNA binding properties, while lacking DNA cleavage activity, thus positioning it as an ideal tool for epigenome editing. Cryogenic electron microscopy (cryo-EM) structures of PmCas12m unveiled its unique molecular mechanism of DNA binding facilitating interference. Guided by these structural insights, we employed deep mutational scanning (DMS) and protein engineering to develop xCas12m, a hypercompact variant with highly potent and specific epigenome editing capabilities in human cells. We further constructed the xCas12m-CRISPRoff platform in a single AAV vector, which achieved durable epigenetic silencing and effective inhibition of hepatitis B virus (HBV) infection in a mouse model. Collectively, these findings establish xCas12m as a versatile epigenome editing platform with transformative potential for treating diseases, paving the way for clinical translation of epigenetic therapies.

bioengineering↗

bioRxiv2026

Construction of a GnRH mRNA Immunocastration Vaccine and Evaluation of Its Immunogenicity and Safety in Mice and Cats

Immunocastration has emerged as an alternative to surgical and chemical castration for managing reproductive function in animals, yet the development of safe and effective vaccines remains challenging. This study aimed to develop a gonadotropin-releasing hormone (GnRH)-based messenger RNA (mRNA) vaccine and systematically evaluate its immunogenicity, reproductive suppression efficacy, long-term durability, and biosafety in mice and cats. GnRH epitopes were fused to three carrier proteins, Fc, Foldon, and lumazine synthase nanoparticles (pLS) via a flexible linker. After identifying pLS as the optimal scaffold, three mRNA vaccine candidates (GnRH-3, GnRH-4, and GnRH-5) were generated with one, five, or ten tandem GnRH repeats, encapsulated in lipid nanoparticles (LNPs), and assessed in rodent and feline models. Immunogenicity was determined by enzyme-linked immunosorbent assay, gonadal histopathology, hormone measurements, transcriptomic analysis, and mating trials. Among the fusion partners, the pLS-based vaccine (GnRH-3) induced the strongest antibody responses and most pronounced reproductive suppression. Further optimization showed that GnRH-4, containing five tandem GnRH repeats, elicited the highest antibody titers, induced severe gonadal atrophy, and reduced litter size by 93.8% in mice. Transcriptomic analysis revealed that differentially expressed genes in males were enriched in spermatogenesis and motility pathways, whereas those in females were associated with RNA splicing and immune responses. In cats, the optimal regimen was a twoLdose schedule with 50Lg per dose and a 21Lday interval, which induced robust antibody responses lasting at least 12 Lmonths and sustained reproductive suppression. HighLdose (500Lg) administration showed no clinical toxicity or histopathological abnormalities, confirming favorable biosafety. This study successfully developed a pLSLbased GnRH mRNA vaccine (GnRH-4) with five tandem GnRH epitopes that demonstrates strong immunogenicity, longLlasting contraceptive effects, and excellent safety in both rodent and feline models, supporting its potential for clinical application in immunocastration.

immunology↗

bioRxiv2026

CCycDB: an integrative knowledgebase to fingerprint microbially mediated carbon cycling processes

Microorganisms play essential roles in mediating biogeochemical cycling of carbon across Earths ecosystems. Understanding the processes and underlying mechanisms for microbially mediated carbon cycling is therefore critical for advancing global ecology and climate change research. To comprehensively depict these complex biogeochemical processes, we developed CCycDB, a knowledge-based functional gene database, to accurately fingerprint microbially-mediated carbon cycling pathways and gene families, particularly from shotgun metagenomes. The CCycDB database comprises 4,676 gene families classified into six major functional categories, further structured into 45 level-1 and 188 level-2 sub-categories, encompassing a total of 10,991,724 high-quality reference sequences. Validation using both synthetic and real-world datasets demonstrated that CCycDB outperforms existing orthology databases in terms of accuracy, coverage and specificity. By directly targeting carbon-cycling functional gene families, CCycDB provided promising routines to reconstruct both functional gene and taxonomic profiles associated with microbially mediated carbon cycling. Application of CCycDB to shotgun metagenomes from diverse and complex ecosystems revealed pronounced habitat-specific differences in carbon cycling processes and their associated microbial taxa. Collectively, CCycDB provides a powerful and reliable tool for profiling carbon cycling processes from both functional and taxonomic perspectives in complex ecosystems. CCycDB is accessible at https://ccycdb.github.io/. Impact StatementThe microbially mediated carbon cycling processes are the most complex biogeochemical processes in the Earths biosphere, playing profound regulatory roles on global climate changes. A key bottleneck in linking microbial communities to global change is the lack of integrated tools for comprehensive carbon cycle profiling. Here, we present CCycDB, a tool that serves a dual purpose--first being a reference database that obtains functional gene and taxonomic profiles and functioning as a customized routine for efficiently aligning sequences and querying associated functional information. CCycDB enables researchers to accurately link microbial community dynamics to carbon cycling and transforming pathways, thereby advancing integrated global change studies with microbes and ecological research via complex metagenomic datasets.

microbiology↗

bioRxiv2024

Telocytes link epithelial nutrient sensing with amplification of the ILC2-tuft cell circuit

Group 2 innate lymphocytes (ILC2s) are prevalent in small intestine but engagement of type 2 immunity during basal processes are incompletely described. Thymic stromal lymphopoietin (TSLP), a cytokine implicated in ILC2 activation, was constitutively expressed in villus telocytes and crypt-associated trophocytes, specialized fibroblasts that sustain epithelial identity. Feeding increased TSLP and induced ILC2 type 2 cytokines that were attenuated by deletion of TSLP in PDGFR+ stromal cells or TSLP receptor on ILC2s. Mouse and human telocytes expressed receptors for glucagon-like peptide-2 (GLP-2), which is released by enteroendocrine cells (EECs) after eating. GLP-2 induced intestinal TSLP, TSLP-dependent ILC2 cytokine production, and tuft cell hyperplasia. The telocyte-alarmin relay couples EEC nutrient detection with amplification of a tuft cell chemosensory circuit that diversifies surveillance of ingested cargo. One-Sentence SummaryIntestinal telocyte TSLP relays signals from enteroendocrine cells to ILC2s to amplify the tuft cell circuit in response to feeding.

immunology↗

bioRxiv2024

Diversity and ecological roles of RNA viral communities in the cryosphere of the Tibetan Plateau

RNA viruses play crucial roles in modulating host communities, but their diversity and ecological roles in the cryosphere are poorly understood. We investigated the RNA virome from the cryosphere of the Tibetan Plateau (TPC), the largest area of the cryosphere in the mid-low latitude regions, which includes 79 metatranscriptomes from ecosystems including glaciers, proglacial lake sediments, permafrost wetland and upland soils. We obtained 8,799 RNA-dependent RNA polymerase encoding contigs, which clustered into 5,333 viral species, adding more than 4,900 new RNA viral species to the global RNA virome database. The recovered RNA viruses primarily infect prokaryotes, distinctively different from the dominance of eukaryotic RNA viruses in oceanic ecosystems. In addition to the known taxa such as Leviviricetes, we identified novel clades of putative prokaryotic RNA viruses, which greatly extended our understanding of their diversity. We further expanded the host of RNA virus by 20 additional prokaryotic phylum- or class-level taxonomic groups. Moreover, the TPC RNA viruses encoded dozens of auxiliary metabolic genes that could reprogram the metabolisms of diverse hosts, including photosynthesis in glacier eukaryotic algae and cyanobacteria, which may exert great impacts on glacier dynamics through modulating host adaptation. Furthermore, we identified potential pathogenic RNA viruses in various cryosphere environments, though their overall risks are low. This study provides the first comprehensive view of cryosphere RNA virome, highlighting their high diversity, vital ecological functions, and potential health impacts.

ecology↗

bioRxiv2024

Targeting protein tyrosine phosphatase non-receptor type 2 with a novel inhibitor for AML therapy

Acute myeloid leukemia (AML) is a fatal disease characterized by a bleak prognosis. For over four decades, treatment options for AML have been constrained to administering high-dose cytotoxic chemotherapy. However, the emergence of drug resistance and the resultant toxic side effects have created an urgent necessity for identifying novel therapeutic targets. In this study, non-receptor protein tyrosine phosphatase type 2 (PTPN2) is highly expressed in AML. Remarkably, knock down of PTPN2 expression markedly mitigated AML burden both in vitro and in vivo. Additionally, we unveiled the direct interaction between PTPN2 and C-MYC, establishing C-MYC as a direct acting substrate of PTPN2. Then, we performed a small-molecule compound screening to identify K73, a selective inhibitor of PTPN2. At the same time, K73 showed a good safety profile and exhibited strong activity against AML in vivo. In conclusion, we have pinpointed a considerable therapeutic potential in targeting PTPN2 for AML treatment and discovered a novel class of selective PTPN2 inhibitors suitable for AML therapy.

cancer biology↗

bioRxiv2023

Adaptive Functions of Structural Variants in Human Brain Development

Quantifying the structural variants (SVs) in nonhuman primates could provide a niche to clarify the genetic backgrounds underlying human-specific traits, but such resource is largely lacking. Here, we report an accurate SV atlas in a population of 562 rhesus macaques, verified by two public SV benchmarks, an inhouse benchmark of eight macaque genomes with long-read sequencing and another inhouse benchmark of one macaque genome with whole-genome assembly. This accurate, quantitative SV map indicates stronger purifying selection on inversions, one type of poorly-clarified SVs to date, especially for those located on regulatory regions, suggesting a strategy for prioritizing inversions with the most important functions. Based on the distribution and the evolutionary features of these inversions in macaque population, we then identified 75 human-specific inversions, clarified their functional effects and prioritized them. Notably, the top-ranked inversions have substantially shaped the human transcriptome, through their dual-effects of reconfiguring the ancestral genomic architecture and introducing regional mutation hotspots at the inverted regions. As a proof-of-concept, we linked APCDD1, located on one of these inversions with the highest rank score and downregulated in human brains, to neuronal maturation. The accumulation of human-specific mutations on its promoter region, accelerated by the formation of the inversion, contributed to the decreased expression in humans. Notably, the overexpression of APCDD1 could accelerate the neuronal maturation, while its depletion in mice delays the neuronal maturation. This study thus highlights the contribution of SVs, especially the inversions, to the distinct features in human brain development.

evolutionary biology↗

bioRxiv2023

Pseudorabies virus hijacks DDX3X, initiating an addictive 'mad itch' and immune suppression, to facilitate viral spread.

Infections with defined Herpesviruses, such as Pseudorabies virus (PRV) and Varicella zoster virus (VZV) can cause neuropathic itch, referred to as "mad itch" in multiple species. The underlying mechanisms involved in neuropathic "mad itch" are poorly understood. Here, we show that PRV infections hijack the RNA helicase DDX3X in sensory neurons to facilitate anterograde transport of the virus along axons. PRV induces re-localization of DDX3X from the cell body to the axons which ultimately leads to death of the infected sensory neurons. Inducible genetic ablation of Ddx3x in sensory neurons results in neuronal death and "mad itch" in mice. This neuropathic "mad itch" is propagated through activation of the opioid system making the animals "addicted to itch". Moreover, we show that PRV co-opts and diverts T cell development in the thymus via a sensory neuron-IL-6-hypothalamus-corticosterone stress pathway. Our data reveal how PRV, through regulation of DDX3X in sensory neurons, travels along axons and triggers neuropathic itch and immune deviations to initiate pathophysiological programs which facilitate its spread to enhance infectivity.

neuroscience↗

bioRxiv2022

Abundant trans-driven variation in detoxification gene expression in the extreme generalist herbivore Tetranychus urticae

The extreme adaptation potential of the generalist herbivore Tetranychus urticae (the two-spotted spider mite) to pesticides as well as diverse host plants has been associated with clade-specific gene expansions in known detoxifying enzyme families, and with extensive and rapid transcriptional responses. However, how this broad transcriptional potential is regulated remains largely unknown. Using a parental/F1 design in which four inbred strains were crossed to a common inbred strain, we assessed the genetic basis and inheritance of gene expression variation in T. urticae. Mirroring known phenotypic variation in the progenitor strains of the inbreds, we confirmed that the inbred strains we created were genetically distinct, varied markedly in pesticide resistance, and also captured variation in host plant fitness commonly observed in this species. By examining differences in gene expression between parents and allele-specific expression in F1s, we found that variation in RNA abundance was more often explained in trans as compared to cis, with the former associated with dominance in inheritance. Strikingly, in a gene ontology analysis, detoxification genes of the cytochrome P450 monooxygenase (CYP) family, as well as dioxygenases (DOGs) acquired from horizontal gene transfer from fungi, were specifically enriched at the extremes of trans-driven up- and downregulation. In particular, a clade of CYPs with documented broad substrate-specificity including multiple pesticides, as well as DOGs that have recently been shown to have broad substrate specificity against plant specialized compounds, were exceptionally highly upregulated as a result of trans effects (or in some cases synergism of cis and trans) in the most multi-pesticide resistant strains. Collectively, our findings highlight the potential importance of trans-driven expression variation in genes associated with xenobiotic metabolism and host plant use for rapid adaptation in T. urticae, and also suggest modular control of these genes, a regulatory architecture that might ameliorate negative pleiotropic effects. Author summaryThe two-spotted spider mite, Tetranychus urticae, is a generalist herbivore and pest of diverse crops globally. In response to the plethora of chemicals used for its control, the species rapidly evolves pesticide resistance. Further, experimental evolution studies with T. urticae populations have demonstrated adaptation to challenging host plants in as few as five generations. The adaptation of T. urticae to pesticides and host plants has been associated with large transcriptome changes, including for genes associated with detoxification of pesticides and toxic plant compounds. Nevertheless, the basis of the observed transcriptome variation has remained largely unknown. Here, we examined the genetic control and inheritance of expression differences among five inbred T. urticae strains, including several with histories of intense pesticide selection. With a parental/F1 experimental design, we found that trans effects were common in explaining variation in detoxification gene expression, with the trans-driven upregulation of a subset of cytochrome P450 monooxygenases of broad substrate specificity especially striking in the most pesticide resistant strains. Our findings suggest that genetic variation acting with dominant or additive inheritance to impact the regulation of modules of detoxification genes may be an important target of selection during rapid pesticide and host plant evolution in herbivores.

genetics↗

bioRxiv2022

MINE is a method for detecting spatial density of regulatory chromatin interactions based on a MultI-modal NEtwork

Chromatin interactions play essential roles in chromatin conformation and gene expression. However, few tools exist to analyze the spatial density of regulatory chromatin interactions. Here, we present the MultI-modal NEtwork (MINE) toolkit, including MINE-Loop, MINE-Density, and MINE-Viewer. MINE-Loop network modeling integrates Hi-C, ATAC-seq, and histone ChIP-seq data to enhance the detection of regulatory chromatin interactions (RCIs, i.e., chromatin interactions that are anchoring regulatory elements to chromatin); MINE-Density quantifies the spatial density of regulatory chromatin interactions identified by MINE-Loop within different chromatin conformations; and MINE-Viewer facilitates 3D visualization of the density of chromatin interactions and participating regulatory factors, such as transcription factors. We applied MINE to investigate the relationship between the spatial density of regulatory chromatin interactions (SD-RCI) and chromatin volume change in HeLa cells before and after liquid-liquid phase separation. Changes in SD-RCI before and after treating the HeLa cells with 1,6-hexanediol showed that the change in chromatin volume was related to the degree of activation or repression of genes in chromatin interactions. The MINE toolkit provides a new method for quantitative study of chromatin conformation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=187 HEIGHT=200 SRC="FIGDIR/small/499656v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@1705cc8org.highwire.dtl.DTLVardef@1db89adorg.highwire.dtl.DTLVardef@2be8e4org.highwire.dtl.DTLVardef@c6f1a6_HPS_FORMAT_FIGEXP M_FIG C_FIG In BriefGong et al. provide a toolkit MINE to explore the relationship between spatial density of regulatory chromatin interactions, gene expression and chromatin structure change. HighlightsO_LIMINE toolkit was provided to detect more regulatory chromatin interactions (RCI), count the spatial density of regulatory chromatin interactions and visualize the density of chromatin interactions with transcription factors in three-dimension. C_LIO_LIChromatin regions were divided into developed active hub, developing active hub, developed repressive hub, and developing repressive hub according to the density of active or repressive regulatory chromatin interactions. C_LIO_LIThe change of chromatin structure before and after liquid-liquid phase separation is quantitively described by using the MINE toolkit. C_LI

bioinformatics↗

bioRxiv2022

Novel Murine models of Mania and Depression

Neuropathological mechanisms triggering manic syndrome or manic episodes in bipolar disorder remain poorly characterised, as the research progress is severely limited by the paucity of appropriate animal models. Here we developed a novel manic mice model by combining a series of chronic unpredictable rhythm disturbances (CURD), which include disruption of circadian rhythm, sleep deprivation, exposure to cone light, with subsequent interference of followed spotlight, stroboscopic illumination, high temperature stress, noise disturbance and foot shock. To validate this novel manic model, we used multiple behavioural and cell biology approaches comparing the CURD-model with healthy controls and depressed mice. The depression model was created by an exposure to an improved chronic unpredictable mild stress, which we defined as chronic unpredictable mild restraint (CUMR). A novel manic mice model induced by environmental stressors and free from genetic or pharmacological interventions will benefit research into pathological mechanisms of mania.

animal behavior and cognition↗

bioRxiv2022

Distinct denitrifying phenotypes of predominant bacteria mould nitrous oxide metabolism in upland agricultural soils

Denitrifying nitrous oxide (N2O) emissions in agroecosystems result from variations in microbial composition and soil properties. However, the microbial mechanisms of differential N2O emissions in agricultural soils are less understood. Microcosm experiments of two types of Chinese farmland soil were conducted with nitrate (250 mg/kg) and a combination of glucose (1000 mg/kg) and nitrate, and a case with no addition was used as the control. The results show that N2O accumulation in black soil (BF) was significantly higher than that in fluvo-aquic soil (FF) independent of carbon and nitrogen supply. The abundance of denitrifying genes was significantly higher in FF, but the ratios of genes responsible for N2O production (narG, nirS, and nirK) to the gene for N2O reduction (nosZ) did not significantly differ between the two soils. However, the soils showed obvious discrepancies in denitrifying bacterial communities. High accumulation of N2O was verified by the isolates of Rhodanobacter, which is predominant in BF due to its truncated denitrifying genes and lack of N2O reduction capacity. The dominance of complete denitrifiers such as Castellaniella in FF led to a rapid reduction in N2O and reduced N2O accumulation, as demonstrated when its corresponding isolate was inoculated into both studied soils. Therefore, the different phenotypes of N2O metabolism of the distinct denitrifiers maintained in the two soils caused their differing N2O accumulation. This knowledge could guide the regulation of the denitrifying bacterial community and the phenotypes of N2O metabolism in agricultural soils to reduce N2O emissions.

microbiology↗

bioRxiv2022

Introduction of a condensed, reverse tricarboxylic acid cycle for additional CO2 fixation in plants

Plants employ the Calvin-Benson cycle (CBC) to fix atmospheric CO2 for the production of biomass. The flux of carbon through the CBC is limited by the activity and selectivity of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Alternative pathways that do not use RuBisCO to fix CO2 exist but occur only in anaerobic microorganisms. Rather than modifying existing routes of carbon metabolism in plants, we have developed a synthetic carbon fixation cycle that does not exist in nature, but is inspired by metabolisms of bacterial autotrophs. This synthetic cycle uses endogenous plant metabolites to fix CO2 and yield glyoxylate as a product. In this work, we build and characterize a condensed, reverse tricarboxylic acid (crTCA) cycle in vitro and in planta. We demonstrate that a simple, synthetic cycle can be used to fix carbon in vitro under aerobic and mesophilic conditions and that these enzymes retain activity when expressed transiently in planta. We then evaluate stable transgenic lines of Camelina sativa that have both phenotypic and physiologic changes. Transgenic C. sativa are shorter than controls with increased rates of photosynthetic CO2 assimilation and changes in photorespiratory metabolism. This first iteration of a build-test-learn phase of the crTCA cycle provides promising evidence that this pathway can be used to increase photosynthetic capacity in plants.

plant biology↗

bioRxiv2022

The infiltration pattern of microenvironmental cells and different immune escape mechanisms in colorectal cancer

BackgroundThe tumour microenvironment (TME) plays a crucial role in tumour progression and metastasis. However, the infiltration pattern of TME cells in CRC samples and the immune escape mechanism underneath have not been studied sufficiently. MethodsTranscriptomic data from public datasets were retrieved online. In total, 1802 samples from the microarray dataset and 619 samples from the TCGA dataset were enrolled. The ssGSEA algorithm and unsupervised clustering were used for TME cells infiltration speculation and infiltration pattern recognition. ResultsCRC samples can be classified into three distinct TME cell subtypes. Subtype 1, the immune-active subtype, was characterised by high infiltration of activated adaptive immune cells. Subtype 2, the immune-desert subtype, featured high tumour purity and low infiltration of immune and stromal cells. And subtype 3, stroma-rich subtype, had high infiltration of stromal cells. The stroma-rich subtype conferred a significantly worse prognosis. Three subtypes had different immune escape mechanisms. The immune-active subtype has the highest immune checkpoint expression level. In comparison, the immune-desert subtype had the lowest immunogenicity and the defective antigen presentation. And the stroma-rich subtype lacked activated immune cells. ConclusionsDistinct TME cell subtypes and immune escape mechanisms may provide inspiration and direction for further researches on CRC immunotherapy.

cancer biology↗

bioRxiv2021

PHB3 Regulates Lateral Root Primordia Formation via NO-mediated Degradation of AUX/IAAs

We previously showed that PHB3 regulates auxin-stimulated lateral root (LR) formation; however, the underlying molecular mechanism is unknown. Here, we demonstrate that PHB3 regulates LR development mainly through influencing lateral root primordia (LRP) initiation via affecting nitric oxide (NO) accumulation. The reduced LRP in phb3 was largely rescued by exogenous NO donor SNAP treatment. The decreased NO accumulation in phb3 caused a lower expression of GATA23 and LBD16 through inhibiting the degradation of IAA14/28. Overexpression of either GATA23 or LBD16 in phb3 mutant background recovered the reduced LRP number phenotype. These results indicate that PHB3 regulates LRP initiation via NO-mediated auxin signaling through regulating the degradation of IAA14/28. HighlightPHB3 regulates IAA28 and IAA14 degradation by controlling NO accumulation, and thereby regulating LR founder cell identification and the transition to asymmetric division.

developmental biology↗

bioRxiv2021

Maize inbred line B96 is the source of large-effect loci for resistance to generalist but not specialist spider mites

Maize (Zea mays subsp. mays) yield loss from arthropod herbivory is substantial. While the basis of resistance to major insect herbivores has been comparatively well-studied in maize, less is known about resistance to spider mite herbivores, which are distantly related to insects and feed by a different mechanism. Two spider mites, the generalist Tetranychus urticae, and the grass-specialist Oligonychus pratensis, are notable pests of maize, especially during drought conditions. We assessed the resistance to both mite species of 38 highly diverse maize lines, including several previously reported to be resistant to one or the other mite species. We found that line B96, as well as its derivatives B49 and B75, were highly resistant to T. urticae. In contrast, neither these three lines, nor any others included in our study, were notably resistant to O. pratensis. Quantitative trait locus (QTL) mapping with F2 populations from crosses of B49, B75, and B96 to susceptible B73 identified a large-effect QTL on chromosome 6 as underlying T. urticae resistance in each line, with an additional QTL on chromosome 1 in B96. Genome sequencing and haplotype analyses identified B96 as the apparent sole source of resistance haplotypes. Our study identifies loci for use in maize breeding programs for T. urticae resistance, as well as to assess if the molecular-genetic basis of spider mite resistance is shared with insect pests of maize, as B96 is also among the most resistant known maize lines to several insects, including the European corn borer, Ostrinia nubilalis. Key message Maize(Zea mays subsp. mays) inbred lines B49, B75, and B96 harbor large-effect loci for resistance to the generalist spider mite Tetranychus urticae, but not the specialist Oligonychus pratensis.

genetics↗