Biology subjects

Zhao, C.

Publications and source records attributed to Zhao, C..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Mental Imagery abilities affect visual working memory performance: evidence from aphantasic participants

Visual imagery refers to the mental generation of visual representations of stimuli, while visual working memory involves retaining visual information for a short period without external input. Due to the conceptual overlap between these two constructs, successful performance on visual working memory tasks may rely on the use of visual imagery to rehearse items during the retention interval. Consequently, individuals with aphantasia, who lack voluntary visual imagery, may experience difficulties with such tasks. However, prior research has suggested that some individuals with aphantasia might employ non-visual strategies to compensate for this deficit. In two experiments, we examined visual working memory performance in aphantasic and control participants across a range of stimulus types. In Experiment 1, participants completed a change localization task using color squares and complex fractals; in Experiment 2, stimuli included real words, phonologically valid pseudowords, and phonologically invalid pseudowords. Across both experiments, aphantasic participants demonstrated significantly impaired visual working memory compared to controls. Notably, their performance was equally impaired for stimuli that were easily verbalizable (i.e., colors and words) and those that were not (i.e., fractals and pseudowords). Furthermore, individual differences in visual imagery ability, as measured by the Vividness of Visual Imagery Questionnaire (VVIQ), significantly predicted working memory performance across all stimulus types. These findings provide direct evidence for the critical role of visual imagery in supporting visual working memory.

neuroscience↗

bioRxiv2025

Basal Cell-Contact Dynamics Influence Tissue Packing in a Proliferating Mammalian Epithelium

Animal tissue morphology is determined by the shape, position, and proliferative capacity of individual epithelial cells. Nevertheless, it remains incompletely understood how the dynamic shape transformations implicit in mitotic proliferation influence tissue packing, particularly at the level of basal cell contacts. Here, we use an in silico vertex model to show that epithelial mitotic rounding necessitates a sequence of dynamic basal contact rearrangements, including basal diminution of the mitotic cell volume, transient multicellular rosette assembly, basal reinsertion of daughter cells, and neighbor reorganization. We then leverage a mammalian intestinal organoid model to confirm nearly identical basal cell-contact dynamics as those predicted in silico. Pharmacological inhibition of mitotic progression reveals that two events--basal diminution of the cell body and daughter cell reinsertion--independently drive distinct contact rearrangements. Together, our results uncover a previously underappreciated topological role for basal mitotic cell dynamics in shaping epithelial packing and morphogenesis.

developmental biology↗

bioRxiv2025

Genomic analysis uncovers unique haplotype signatures from subspecies and agronomic types associated with blanchability in groundnut

Blanchability, defined as the ease of seed coat removal after roasting, is a vital trait for enhancing processing efficiency and product quality in groundnut (Arachis hypogaea L.). To enable a comprehensive haplotype-level genetic dissection of this trait, SNPs derived from whole-genome resequencing (WGRS) were used to perform genome-wide association study (GWAS) using multi-locus models (BLINK and FarmCPU) on a diverse groundnut mini-core collection phenotyped across two crop seasons. A total of 26 significant SNP-trait associations (STAs) were identified across multiple chromosomes, with major loci on chromosomes Ah05, Ah06, and Ah17, some of which were further validated using KASP (Kompetitive Allele-Specific PCR) markers. Candidate genes, such as those involved in cell wall biosynthesis (e.g., galactoside 2-alpha-L-fucosyltransferase-like protein, protein kinase superfamily members, and glycerophosphoryl diester phosphodiesterase 3), were found to be within linkage disequilibrium (LD) of the identified STAs, suggesting their plausible association with blanchability. Haplo-pheno analyses identified superior high-blanchability haplotypes; Ah05HapBL3, Ah06HapBL5, Ah06HapBL10, and Ah17HapBL6, which were predominantly found in the fastigiata subspecies (including Valencia and Spanish bunch agronomic types) from South Asia and South America, while the low-blanchability haplotypes were from hypogaea subspecies (including Virginia runner and Virginia bunch agronomic types) from Africa. Overall, this study provides valuable insights for customizing blanchability through haplotype-based breeding of processing-grade cultivars thereby improving groundnut value chains to meet diverse industrial demands.

genomics↗

bioRxiv2025

Desert Hedgehog mediates stem Leydig cell differentiation through Ptch2/Gli1/Sf1 signaling axis

Desert Hedgehog (Dhh) mutations cause Leydig cell dysfunction, yet the mechanisms governing Leydig lineage commitment through Dhh-mediated receptor selectivity, transcriptional effector specificity, and steroidogenic coupling remain elusive. In this study, using CRISPR/Cas9-mediated gene knockout and stem Leydig cells (SLCs) transplantation, we identified a critical Dhh/Patched 2 (Ptch2)/Glioma-associated oncogene homolog 1 (Gli1)/steroidogenic factor 1 (Sf1) signaling axis essential for SLC differentiation in Nile tilapia (Oreochromis niloticus). Dhh deficiency resulted in defective adult Leydig cells and androgen insufficiency. Rescue experiments involving 11-ketotestosterone administration and a Dhh agonist treatment, combined with SLCs transplantation, demonstrated that Dhh regulates SLC differentiation, not survival. In vitro knockout of ptch1 and ptch2 in SLCs revealed that Ptch2 likely acts as the functional receptor for Dhh. This was further supported by in vivo genetic rescue experiments, where ptch2 mutation did not impair testicular development, yet completely rescued the testicular defects in dhh mutants--consistent with Ptch2 acting as an inhibitory receptor whose loss alleviates Dhh pathway suppression. Luciferase assays in Gli-knockout SLCs demonstrated that Gli1 acts as the primary transcriptional effector, and transactivates sf1 expression. Additionally, functional transplantation assays confirmed that Sf1 is indispensable for SLCs differentiation, as Sf1-overexpressing SLCs rescued differentiation, whereas sf1-mutant SLCs failed. Overall, our work delineates the Dhh-Ptch2-Gli1-Sf1 axis and provides fundamental insights into the endocrine regulation of Leydig cell lineage development. HighlightsO_LIDhh regulates the differentiation of SLCs rather than their survival C_LIO_LIPtch2 acts as the functional receptor for Dhh signaling in SLCs C_LIO_LIGli1 is the principal transcriptional activator for Dhh signaling in SLCs C_LIO_LISf1 is the critical downstream effector of Gli1 in SLCs differentiation C_LI

developmental biology↗

bioRxiv2025

Human meibomian gland organoids to study epithelial homeostasis and dysfunction

Meibomian glands (MGs) are holocrine glands that secrete lipids to maintain the homeostasis of ocular surface, and their dysfunction leads to dry eye disease. Herein, we established long-term 3D organoid culture for murine and human MGs, which retained the cell lineages and lipid-producing ability. The organoids mimicked the drug treatment responses and generated functional MGs after orthotopic transplantation. Inspired by organoid cultures, we found FGF10 eye drops could rescue all-trans retinoic acid-induced MG dysfunction in mice. Besides, nicotinamide uniquely hampered the human MG organoid expansion by inhibiting FGF10 signaling. Single-cell atlas and lipidome not only aligned the delineated cell types and featured lipids between human MGs and organoids, but highlighting MAPK signaling inhibition enhanced acinar cell differentiation and functional maturation of MG organoids. In summary, this study established an organoid platform to explore epithelial homeostasis and dysfunction of MGs, facilitating drug development and regenerative medicine for dry eye disease.

cell biology↗

bioRxiv2025

Linkage of nucleotide and functional diversity varies across gut bacteria.

Understanding the forces shaping genomic diversity within bacterial species is essential for interpreting microbiome evolution, ecology, and host associations. Here, we analyze over one hundred prevalent gut bacterial species using the Unified Human Gut Genome (UHGG) collection to characterize patterns of intra-specific genomic variability. Gene content divergence scales predictably with divergence in core genome single nucleotide polymorphisms (SNPs), though there is substantial variability in evolutionary dynamics across species. Overall, accessory genes exhibit consistently faster linkage decay compared to core SNPs, highlighting the fluidity of functional repertoires within species boundaries. This signal is strongest for mobile genetic elements, which show minimal linkage to core genome SNPs. Together, our findings reveal species-specific recombination regimes in the gut microbiome, underscoring the importance of accounting for horizontal gene transfer and genome plasticity in microbiome-wide association studies and evolutionary models.

microbiology↗

bioRxiv2025

BioLogical: a universal analysis framework for biosystem logical dynamic

Complex biosystems exhibit ordered, functional, self-organized features. How-ever, a universal framework for exploring their logical paradigms and dynamic characteristics remains lacking. Here we describe BioLogical, a user-friendly R package, designed for analyzing properties of biosystems. We demonstrate its versatile capacities of deciphering multi-valued logical paradigms, calculating order parameters, and simulating system dynamic, even multi-valued Quine-McCluskey and logical satisfiability analysis. The open-source software is available at https://github.com/YuxiangYao/BioLogical.

systems biology↗

bioRxiv2025

EBSn, a robust synthetic reporter for monitoring ethylene responses in plants

Ethylene is a gaseous plant hormone that controls a wide array of physiologically relevant processes, including plant responses to biotic and abiotic stress, and induces ripening in climacteric fruits. To monitor ethylene in plants, analytical methods, phenotypic assays, gene expression analysis, and transcriptional or translational reporters are typically employed. In the model plant Arabidopsis, two ethylene-sensitive synthetic transcriptional reporters have been described, 5xEBS:GUS and 10x2EBS-S10:GUS. These reporters harbor a different type, arrangement, and number of homotypic cis-elements in their promoters and thus may recruit the ethylene master regulator EIN3 in the context of alternative transcriptional complexes. Accordingly, the patterns of GUS activity in these transgenic lines differ and neither of them encompasses all plant tissues even in the presence of saturating levels of exogenous ethylene. Herein, we set out to develop and test a more sensitive version of the ethylene-inducible promoter that we refer to as EBSnew (abbreviated as EBSn). EBSn leverages a tandem of ten non-identical, natural copies of a novel, dual, everted, 11bp-long EIN3-binding site, 2EBS(-1). We show that in Arabidopsis, EBSn outperforms its predecessors in terms of its ethylene sensitivity, having the capacity to monitor endogenous levels of ethylene and displaying more ubiquitous expression in response to the exogenous hormone. We demonstrate that the EBSn promoter is also functional in tomato, opening new avenues to manipulating ethylene-regulated processes, such as ripening and senescence, in crops.

plant biology↗

bioRxiv2025

Mechanisms of Output Gating for visual working memory

Working memory (WM) tasks often require comparing remembered items to test displays, but little is known about how people selectively remove irrelevant information at test. Across three experiments, we used contralateral delay activity (CDA) to track WM load and examine selective removal. In Experiment 1, CDA amplitudes increased with set size even when only one item was probed, suggesting minimal removal based on spatial location. Experiment 2 ruled out spatial grouping by presenting items sequentially in the same location, yet more items were retained for larger set size. In Experiment 3, however, when items belonged to distinct mnemonic categories, CDA amplitudes at test were reduced, consistent with selective removal based on category relevance. Additionally, P3 old-new effects showed that decision speed and strength were influenced by the number of items maintained. Together, these results suggest that people selectively remove WM contents based on categorical relevance, not spatial cues, enabling more efficient memory-based decisions.

neuroscience↗

bioRxiv2025

Env-antibody coevolution identifies B cell priming as the principal bottleneck to HIV-1 V2 apex broadly neutralizing antibody development

Broadly neutralizing antibodies (bNAbs) are rarely elicited during HIV-1 infection. To identify obstacles to bNAb development, we longitudinally studied 122 rhesus macaques infected by one of 16 different simian-human immunodeficiency viruses (SHIVs). We identified V2 apex as the most common bNAb target and a subset of Envs that preferentially elicited these antibodies. In 10 macaques, we delineated Env-antibody coevolution from B cell priming to bNAb development. Antibody phylogenies revealed permissive developmental pathways guided by evolving Envs that contained few mutations in or near the V2 apex C-strand, which were a sensitive indicator of apex-targeted responses. The absence of such mutations reflected a failure in bNAb priming. These results indicate that efficiency of B cell priming, and not complexities in Env-guided affinity maturation, is the primary obstacle to V2 apex bNAb elicitation in SHIV-infected macaques and identify specific HIV-1 Envs to advance as novel vaccine platforms. One sentence summaryB cell priming is the primary bottleneck to HIV-1 V2 apex bNAb elicitation.

immunology↗

bioRxiv2025

Effect of Transcranial Light Stimulation on the Neurovascular Unit in the Human Brain

Transcranial light stimulation (tLS) is emerging as a non-invasive approach for enhancing brain function and treating neurological disorders; however, its impact on the human neurovascular unit (NVU) remains poorly understood. Herein, we combined photon transport modeling with multimodal neuroimaging to reveal how light influences vascular and neuronal responses in the human brain. Simulations of photon propagation through transcranial tissue captured key scattering and attenuation patterns, guiding the localization of light effects in vivo. Using simultaneous functional magnetic resonance imaging and arterial spin labeling, we showed that tLS significantly increased blood oxygenation level-dependent signals and cerebral blood flow in the light-affected regions. These hemodynamic changes co-occurred with a reduction in cortical excitability, as revealed by electroencephalographic source reconstruction and transcranial magnetic stimulation-evoked potentials. To probe the underlying mechanism, we incorporated inhibitory neural inputs into the computational NVU model. The model predicted that tLS enhances inhibitory neuronal activity and nitric oxide release, driving vasodilation and elevating metabolic support. These findings revealed that transcranial photons can differentially modulate neuronal and vascular components of the NVU--suppressing excitability while promoting perfusion--thereby suggesting a novel therapeutic avenue for targeting neurovascular dynamics in cognitive and clinical applications.

neuroscience↗

bioRxiv2025

A biGWAS strategy reveals the genetic architecture of the interaction between wheat and Blumeria graminis f. sp. tritici

BackgroundWheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt) is one of the most significant diseases affecting global wheat production. Breeding for disease resistance (R) genes against Bgt often follows a boom-bust cycles, where cultivars with effective resistance are widely deployed on an expanding area until virulence emerges in the avirulence (Avr) pathogen population. While extensive effort has been devoted to identifying and cloning R genes, Avr genes remain relatively understudied, limiting our understanding of R-Avr interactions. That said, understanding R-Avr interactions is crucial for developing durable resistance strategies. ResultsWe conducted whole genome sequencing on 245 Bgt isolates collected from major wheat-growing regions in China, identifying 120 genetically unique isolates. Each of these unique isolates was inoculated and phenotyped on a diverse panel of wheat germplasm. Through Genome-Wide Association Analysis (GWAS) in both Bgt and wheat, we identified 65 Avr loci and 251 R loci overlapping with nine and eight cloned Avr or R genes, respectively. On average, each isolate carries eight Avr alleles, ranging from one to 17. Little geographical preference for Avr alleles or their combinations was observed, suggesting that disease resistance breeding against this pathogen should be coordinated at the national level. The level of resistance level is positively correlated with the number of R alleles carried by a wheat line, and the average frequency of an R allele is 2% among the wheat panel, indicating the potential for accumulating R alleles in breeding programs. We mapped 212 R-Avr interactions based on joint GWAS using both plant and pathogen genomes and cross-species epistasis, where a network of interactions was formed between wheat and Bgt. These interactions indicate that pyramiding five major R loci has the potential to confer resistance to half of the Avr loci. As a proof of concept, we successfully verified two previously described R-Avr pairs using tobacco experiments. Furthermore, we provided molecular validation evidence for three new Avr genes, including Bgt-50651, BgtE-5826 and BgtE-20009, and two new R-Avr interactions. Among them, Bgt-50651 interacts with Pm1a, Pm2a, and another unidentified R gene located near the Pm6/Pm52 interval. ConclusionOur study provides a framework for understanding the genetic interaction between plants and pathogens. The discovery of novel R/Avr loci and their complex interaction network underscores the need to integrate crop and pathogen genetic background, particularly the R/Avr allele composition, into breeding program design. These findings have significant implications for developing durable resistance strategies in wheat alongside offering valuable insights into the broader dynamics of plant-pathogen interactions.

genomics↗

bioRxiv2025

Reshaping epistatic network modules enhances wheat yield potential

Increasing wheat yield is a key approach to ensuring global food security and an enduring focus in crop breeding. Here, we assembled a panel of 3,030 wheat lines to dissect the genetic mechanisms of yield improvement. We conducted large-scale field trials across five ecological environments over two consecutive years to evaluate yield performance and constructed a haplotype atlas using the Wheat 660K genotype array. 234 quantitative trait loci (QTLs) and 522 haplotype blocks (HBs) were identified for 14 traits through genome-wide association studies (GWAS), including 10 QTLs and 35 HBs associated with grain yield. Genomic analysis revealed that wheat yield improvement is primarily driven by changes in the epistatic network rather than the introduction of new haplotype segments. SNPs or HBs explain 53.3%-62.9% of the phenotypic variation in yield, whereas epistasis explains 70.4%, highlighting the role of epistasis in yield improvement. Moreover, yield improvement is significantly correlated with the accumulation of favorable epistatic modules. Pedigree-based analysis revealed that the modules remained relatively stable under the pressure of breeding selection, while new favorable modules were also created during hybrid breeding, highlighting that crop design breeding should be based on genetic modules. This study provides insights into genetic mechanism of wheat yield improvement and guidance for designing future wheat in the era of artificial intelligence.

genetics↗

bioRxiv2025

Differential representations of spatial location by aperiodic and alpha oscillatory activity in working memory

Decades of research have shown working memory (WM) relies on sustained pre-frontal cortical activity and visual extrastriate activity, particularly in the alpha (8-12 Hz) frequency range. This alpha activity tracks the spatial location of WM items, even when spatial position is task-irrelevant and there is no stimulus currently being presented. Traditional analyses of putative oscillations using bandpass filters, however, conflate oscillations with non-oscillatory aperiodic activity. Here, we reanalyzed seven different human electroencephalography (EEG) visual WM datasets to test the hypothesis that aperiodic activity-which is thought to reflect the relative contributions of excitatory and inhibitory drive-plays a distinct role in visual WM from true alpha oscillations. To do this, we developed a novel, time-resolved spectral parameterization approach to disentangle oscillations from aperiodic activity during WM encoding and maintenance. Across all seven tasks, totaling 112 participants, we captured the representation of spatial location from total alpha power using an inverted encoding model (IEM), replicating traditional analyses. We then trained separate IEMs to estimate the strength of spatial location representation from aperiodic-adjusted alpha (reflecting just the oscillatory component) and aperiodic activity, and find that IEM performance improves for aperiodic-adjusted alpha compared to total alpha power that blends the two signals. We also discover a novel role for aperiodic activity, where IEM performance trained on aperiodic activity is highest during stimulus presentation, but not during the WM maintenance period. Our results emphasize the importance of controlling for aperiodic activity when studying neural oscillations while uncovering a novel functional role for aperiodic activity in the encoding of visual WM information. Significance statementWorking memory is a crucial component of cognition, yet its neural mechanisms are not fully understood. Research shows that alpha activity - presumed to reflect neural oscillations - tracks the location of items we hold in memory. However, these analyses assume that all alpha power is oscillatory, even though oscillations are mixed with non-oscillatory, aperiodic activity that may be physiologically and functionally distinct. Here, we use a novel analytical approach for separating alpha oscillations and aperiodic activity dynamically across time. Our results reveal distinct roles for each in human visual working memory: aperiodic activity encodes the spatial location of information whereas alpha oscillations maintain the location of that information.

neuroscience↗

bioRxiv2025

Sustained attention is more closely related to long-term memory than to attentional control

Individuals differ in their ability to sustain attention. However, whether differences in sustained attention reflect differences in processes related to attentional control and working memory or long-term memory (LTM) remains underexplored. In Experiment 1, we conducted an online study (n = 136) measuring participants sustained attention, attention control and working memory, and LTM. We measured sustained attention with an audio-visual continuous performance task (avCPT) in which participants responded to images while inhibiting responses to infrequent targets; attention control and working memory with Flanker, change localization, and Simon tasks; and LTM with recognition and source memory tests. Factor analyses revealed that sustained attention formed a distinct factor from attention control and working memory and LTM. Individual differences in the sustained attention factor robustly predicted individual differences in LTM and, to a lesser extent, attention control and working memory. In Experiment 2, to test how neural signatures of sustained attention related to attention control and working memory and LTM, we analyzed fMRI functional connectivity patterns collected as 20 participants performed the avCPT. A pre-trained connectome-based model of sustained attention predicted participants performance on out-of-scanner LTM, but not attention control and working memory, tasks. Together these results suggest that individual differences in sustained attention, although correlated with attention control and working memory, are more closely related to LTM.

neuroscience↗

bioRxiv2025

Identification of Direct-acting nsP2 Helicase Inhibitors with Anti-alphaviral Activity

Alphaviruses are mosquito-borne RNA viruses that pose a significant public health threat, with no FDA-approved antiviral therapeutics available. The non-structural protein 2 helicase (nsP2hel) is an enzyme involved in unwinding dsRNA essential for alphavirus replication. This study reports the discovery and optimization of first-in-class oxaspiropiperidine inhibitors targeting nsP2hel. Structure-activity relationship (SAR) studies identified potent cyclic sulfonamide analogs with nanomolar antiviral activity against chikungunya virus (CHIKV). Biochemical analyses of nsP2hel ATPase and RNA unwindase activities showed these compounds act by a non-competitive mode suggesting that they are allosteric inhibitors. Viral resistance mutations mapped to nsP2hel and a fluorine-labeled analog exhibited direct binding to the protein by 19F NMR. The lead inhibitor, 2o, demonstrated broad-spectrum antialphaviral activity, reducing titers of CHIKV, Mayaro virus (MAYV), and Venezuelan equine encephalitis virus (VEEV). These findings support nsP2hel as a viable target for development of broad-spectrum direct-acting antialphaviral drugs. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/641060v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@856df5org.highwire.dtl.DTLVardef@1f6225borg.highwire.dtl.DTLVardef@4997d5org.highwire.dtl.DTLVardef@18f42f2_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2025

DASH: A versatile and high-capacity gene stacking system for plant synthetic biology

DNA assembly systems based on the Golden Gate method are popular in synthetic biology but have several limitations: small insert size, incompatibility with other cloning platforms, DNA domestication requirement, generation of fusion scars, and lack of post-assembly modification. To address these obstacles, we present the DASH assembly toolset, which combines features of Golden Gate-based cloning, recombineering, and site-specific recombinase systems. We developed (1) a set of donor vectors based on the GoldenBraid platform, (2) an acceptor vector derived from the plant transformation-competent artificial chromosome (TAC) vector, pYLTAC17, and (3) a re-engineered recombineering-ready E. coli strain, CZ105, based on SW105. The initial assembly steps are carried out using the donor vectors following standard GoldenBraid assembly procedures. Importantly, existing parts and transcriptional units created using compatible Golden Gate-based systems can be transferred to the DASH donor vectors using standard single-tube restriction/ligation reactions. The cargo DNA from a DASH donor vector is then efficiently transferred in vivo in E. coli into the acceptor vector by the sequential action of a rhamnose-inducible phage-derived PhiC31 integrase and arabinose-inducible yeast-derived Flippase (FLP) recombinase using CZ105. Furthermore, recombineering-based post-assembly modification, including the removal of undesirable scars, is greatly simplified. To demonstrate the utility of the DASH system, a 116 kb DNA construct harboring a 97 kb cargo consisting of 35 transcriptional units was generated. One of the CDSs in the final assembly was replaced through recombineering, and the in planta functionality of the entire construct was tested in both transient and stable transformants.

synthetic biology↗

bioRxiv2025

Population-scale gene expression analysis reveals the contribution of expression diversity to the modern wheat improvement

Changes in gene expression are crucial for crop breeding, yet population genomics has primarily focused on sequence polymorphisms rather than gene expression diversity. The strategy of using single genome reference for RNA-seq analysis could not handle introgression bias, especially for hexaploidy wheat. Here, we conducted RNA-seq for 328 wheat lines, including representative diverse landraces and elite cultivars from China and the United States, to investigate the role of gene expression variation in shaping agronomic traits. Using pan-genome resources, we identified 20,615 more transcripts than using the Chinese Spring reference genome alone. We constructed a pan-gene atlas regulatory map through eQTL analysis, demonstrating that genes introgressed from wild relatives were under tight genetic control. Genes responding to environmental stress show higher activity after introgressed into the wheat genome, demonstrating how long-term breeding selection impacted the gene expression regulation of targeted introgression. Multi-omics modeling identified 231 high-confidence candidate genes for 34 field agronomic traits and the seedling resistance phenotypes of 8 powdery mildew isolates. More than one fifth of those candidates have no homolog in Chinese Spring reference genome. By utilizing the indexed KN9204 EMS library, 80% candidates showed significant trait difference between wild type and mutant lines. Furthermore, directional shifts in genes of which expression were changed by breeding improvement demonstrated distinct adaptations to local environments. Our study constructed a pan-gene atlas to correct the reference bias of reads mapping in RNA-seq studies and revealed the expression patterns of introgressed genes within the wheat genome and their regulatory mechanisms, which highlighted the impact of breeding selection on gene expression of the worlds most important crop.

plant biology↗