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PubMed2026

MYC-bound enhancer RNAs in cis regulate gene transcription and tumorigenesis.

Emerging evidence suggests that MYC binds RNAs, but its functional consequences remain unclear. Here, we integrate multiomics data and reveal that MYC broadly binds enhancer RNAs (eRNAs), which exhibit high cancer- and tissue-specific expression in cancer cell lines and patient tumors. Moreover, we developed a computational pipeline to identify potential cis-regulatory MYC-eRNA target genes, with most predicted eRNA-target pairs supported by RNA polymerase II-mediated chromatin interaction data. Among these, we functionally characterized MERG1 as an oncogenic eRNA that promotes breast cancer tumorigenesis. Mechanistically, MERG1 interacts with MYC to enhance its occupancy at the GREB1 promoter, driving chromatin remodeling and epigenetic activation. This process specifically amplifies GREB1 expression and promotes tumor progression. Last, nanoparticle-mediated delivery of antisense oligonucleotides targeting MERG1 suppresses MYC-mediated breast cancer growth. These results advance our understanding of the enhancer-driven regulation of gene expression and tumorigenesis and provide insights into the regulatory landscape of MYC in cancer.

Humans↗
PubMed2026

Decoding gene regulation in plant genomes with artificial intelligence.

One of the central goals of plant functional genomics is to uncover regulatory mechanisms that shape agriculturally important traits to inform crop improvement. Recent advances in machine learning (ML) and artificial intelligence (AI), especially Large Language Models (LLMs), have greatly transformed our ability to derive regulatory information from complex genomics data. This review starts with a brief introduction of recent advances in AI and ML. We then present a plant-focused synthesis of emerging applications of AI- and LLM tools to: (i) predict epigenomic features, regulatory DNA elements, and gene expressions; (ii) infer gene regulatory network; and (iii) estimate post-transcriptional regulation.

Artificial intelligence↗
PubMed2025

Genomic context-dependent roles of 5-hydroxymethylcytosine in regulating gene expression during rice drought response.

DNA methylation (5-methylcytosine, 5mC) is a key epigenetic regulator of genome stability and stress adaptation in plants. However, the functional role of its oxidative derivative, 5-hydroxymethylcytosine (5hmC), remains poorly understood in plant systems, largely due to its low abundance and unresolved enzymatic origins. Here, we integrated ACE-seq (APOBEC-coupled epigenetic sequencing) with an optimized Tn5mC-seq (transposase-based library preparation in the context of whole-genome bisulfite sequencing, WGBS) approach to generate the first single-base resolution map of 5hmC in rice (Oryza sativa), unveiling its stress-responsive dynamics and regulatory interplay with 5mC during drought adaptation. Genome-wide profiling revealed a basal 5hmC level of ~0.03 (defined as the ratio of C/(C + T) at each site), with drought triggering a pronounced reduction in 5hmC abundance and locus number, followed by incomplete recovery post-rehydration. Unlike 5mC, which accumulates in heterochromatin, 5hmC preferentially localized to euchromatic regions, including promoters, exons, and intergenic elements, and exhibited enrichment at ABA-responsive transcription factors (e.g., OsATAF1, bZIP50). Strikingly, drought induced an antagonistic relationship between 5hmC and 5mC, with the latter increasing globally to reinforce transposon silencing. Multi-omics analyses demonstrated that 5hmC depletion in promoters correlated with transcriptional downregulation, while its accumulation in gene bodies (notably 5'-UTRs) suppressed stress-responsive genes. These findings highlight 5hmC's bifunctional regulatory capacity, contingent on genomic context, and its role in balancing transcriptional plasticity with genome stability during stress. Our work establishes 5hmC as a dynamic epigenetic mark in plant environmental adaptation and provides a foundation for leveraging DNA hydroxymethylation in crop resilience engineering.

Oryza↗
PubMed2026

Interplay between the role of DNA methylation in regulating gene expression and TE-silencing in a reptilian methylome.

DNA methylation is a major component of eukaryotic genomes with an important role in the defence against transposable elements, to transcriptionally silence their activity and prevent transposition. DNA methylation also plays a major role in the regulation of gene expression. This dual role can come into conflict, where DNA methylation in gene regulatory regions becomes perturbed due to transposable element transposition, leading to disruption of gene expression. Here, we describe how this conflict is reflected in DNA methylation patterns in the sand lizard genome where there is recent transposable element activity. Using long-read sequencing technology we show that CpG islands in gene transcriptional start sites are typically hypomethylated and associated with higher gene expression. Outside transcriptional start sites, a majority of CpG islands overlapped transposable elements and were associated with hypermethylation, consistent with a host-defence role in suppressing transposition activity. We identify 605 instances where transcriptional start sites were associated with transposable elements (4.3% of all genes). These instances were far rarer in conjunction with a CpG island, when methylation signatures would be in conflict. Transposable elements were found to be closer to and at higher density the more hypermethylated a transcriptional start site was, suggesting strong selection against selfish genetic elements transposing into hypomethylated transcriptional start sites.

CpG islands↗
PubMed2026

Probiotic Lacticaseibacillus casei 2S-1 Attenuates Escherichia coli-Induced Enteritis via Gut Microbiota Modulation and Host Gene Regulation.

Maintaining gut microbial homeostasis is crucial for host health, whereas infection with Escherichia coli (E. coli) is a major contributor to intestinal inflammation and microbial dysbiosis. Recent research has focused on probiotic strategies for managing enteric inflammatory disorders. Previous studies have shown that beneficial microorganisms show protection through modulating host immune responses, enhancing intestinal epithelial barrier integrity, and inhibiting pathogenic bacteria. To evaluate the prophylactic effectiveness of a recently isolated strain, Lacticaseibacillus casei 2S-1, in a murine model of E. coli-induced enteritis, this study focuses on interactions within the microbiota-intestinal-immune axis, together with host transcriptional responses and pathway enrichment associated with oxidative stress and mitochondrial function. In vitro analysis of probiotic features, including growth dynamics, acidogenic capacity, and tolerance to acidic and bile salt environments, as well as genetic safety profiling, followed the methodical isolation and taxonomic identification of L. casei 2S-1. A preventive intervention protocol was established, and a murine model of enteritis was induced by exposure to E. coli. Histopathological analyses were performed to observe in vivo safety and protective efficacy. Changes in gut microbial structure were characterized by 16S rRNA gene sequencing, while host responses were identified by intestinal immunohistochemistry and transcriptome profiling. L. casei 2S-1 showed probiotic properties. In vitro analyses showed that the strain exhibited tolerance to acidic and bile salt conditions, and its untreated culture supernatant showed antimicrobial activity against pathogenic bacteria. Its safety profile was supported by genomic analysis, which verified the lack of virulence-associated genes and antibiotic resistance factors. In vivo, L. casei 2S-1 pretreatment reduced mortality and intestinal inflammation, modulated gut microbial composition, and preserved intestinal barrier-associated protein expression in infected mice. This study provides experimental evidence supporting the prophylactic effects of L. casei 2S-1 and its associations with gut microbiota modulation and host transcriptional responses, providing a foundation for further investigation of probiotic-based preventive strategies against intestinal infections.

Animals↗
PubMed2025

Large-scale analysis of MYB genes in Cucurbitaceae identifies a novel gene regulating plant height.

The MYB transcription factor (TF) family, which is involved in plant growth and development, is large and diverse. Previous studies on MYB family in Cucurbitaceae were mostly based on a single genome or focused on the R2R3 subfamily. Here, we analyzed 91 genomes of 11 Cucurbitaceae species and identified a total of 15 858 MYB genes. According to phylogenetic relationships, these genes were divided into 27 subgroups. The identified MYB genes were further classified into 121 MYB orthologous gene groups (OGGs), including 25 core, 57 softcore, 19 shell and 20 line-specific/cloud groups. Whole-genome duplication was the most common mechanism of MYB genes expansion. In core group, the higher proportions of MYB genes were found to be in the coexpression network constructed by the RNA-seq data. Through the comprehensive analysis including phylogeny and gene expression profile of cucumber MYB genes, as well as genetic variations in 103 cucumber germplasms, we identified a MYB gene CsRAX5, which may be related to cucumber plant height. We used gene editing technology to knockout and overexpress CsRAX5. In the knockout lines, Csrax5, the height was significantly increased compared with wild type (WT), whereas after overexpression the height of CsRAX5-OE plants was significantly decreased compared with WT. These results indicated that MYB gene CsRAX5 negatively regulated cucumber plant height. The large-scale analysis of MYB genes in Cucurbitaceae in this study provides insights for further investigating the evolution and function of MYB genes in Cucurbitaceae crops.

Journal Article↗
PubMed2026

Genome-wide CRISPRi screen in human iNeurons identifies novel negative mTOR regulator genes associated with focal cortical dysplasia.

Focal cortical dysplasia (FCD) is a common cause of focal epilepsy that typically results from brain mosaic mutations in the mTOR cell signaling pathway. To identify new potential FCD genes, we developed an in vitro CRISPRi screen in human neurons and used FACS enrichment based on the FCD biomarker, phosphorylated S6 ribosomal protein (pS6). Using whole-genome (110,000 gRNAs) and candidate (129 gRNAs) libraries, we discovered 6 new genes in which loss of function significantly increases pS6 levels: LRRC4, EIF3A, TSN, HIP1, PIK3R3, and URI1. Further analysis of the mTOR pathway showed that only two of the genes, PIK3R3 and HIP1, caused hyperphosphorylation throughout the AKT/mTOR/S6 signaling pathway. Importantly, potential pathogenic variants in these two genes have been reported in resected brain tissue from a single FCD patient each, supporting the predictive validity of our screen. Knocking down each of the 6 genes in iNeurons made mTOR signaling resistant to the loss of neurotrophic factor signaling, specifically GDNF; even without GDNF, pS6 levels remained comparable to GDNF-stimulated controls. Thus, we have identified negative regulators of neuronal mTOR signaling in the context of lost neurotrophic factor support. Our data expand the set of genes that are likely to regulate mTOR pathway signaling in neurons, provide biological confirmation for candidate genes identified in human tissue, and suggest additional targets for investigating somatic gene variants in resected FCD tissues. The identification of novel mTOR regulators using iNeurons also highlights the importance of genetic screening in disease-related cell types.

Brain mosaicism↗
PubMed2026

Genome-wide identification of HCT gene family in sugarcane (Saccharum spp. hybrid) and characterization of putative cis-elements in gene regulation.

BACKGROUND: Sugarcane (Saccharum spp. hybrid) is a globally important crop, and its bagasse can be converted into bioethanol and other industrial products. Lignin, a core component of sugarcane cell walls, plays a crucial role in bagasse quality and lodging resistance. Shikimic acid hydroxycinnamyl transferase (HCT) is the key enzyme in lignin biosynthesis. However, the HCT gene family in sugarcane and its regulatory roles in sugarcane remain poorly understood. RESULTS: A total of 663 HCT genes (including alleles) were identified in the Saccharum hybrid R570 genome, which were classified into six groups (I-VI) and were unevenly distributed across 77 chromosomes. Bioinformatics analysis revealed that the subgroups of R570HCTs had similar gene structures, suggesting conserved functions. Moreover, the different subgroups presented unique putative cis‑element distribution patterns. Transcriptome data indicated that some R570HCTs exhibited significant spatiotemporal and tissue‑specific expression patterns. Further Pearson correlation analysis between putative cis‑element distribution and normalized expression values at the subgroup level revealed that light-responsive elements (L‑box and GA‑motif) were positively correlated with R570HCT expression, and different subgroups formed a complex regulatory network by integrating hormone response and stress elements. Importantly, this subgroup-level correlation was cross-validated by comparing the cis‑element clustering heatmap with the expression heatmap, revealing consistent enrichment patterns. CONCLUSIONS: The study's findings provide novel insights into the correlation among motifs, putative cis‑elements, and gene expression, and propose a cross-validated framework for understanding regulatory divergence among HCT subfamilies in polyploid sugarcane, serving as a hypothesis generating resource for future research on R570HCT expression.

Saccharum↗
PubMed2026

Cell-specific DNA methylation in human alpha and beta cells regulates gene expression in type 2 diabetes.

Epigenome-wide studies of pancreatic islets provide valuable insights into type 2 diabetes (T2D) but lack methylomes from individual cell types. Here we show changes to alpha and beta cell-specific methylomes and transcriptomes from people with or without T2D, using whole-genome bisulfite sequencing and RNA sequencing. We discover 22,544 differentially methylated regions annotated to 7,975 genes in alpha versus beta cells, such as INS, GCG, PDX1 and PCSK1, with ~50% showing differential expression. CRISPR-dCas9-DNMT3A-based epigenetic editing increases INS and TH DNA methylation, while CRISPR-dCas9-TET1-based editing decreases GCG methylation, each altering INS, TH or GCG expression and content in beta cells. Pre-T2D/T2D-associated differentially methylated regions in alpha and beta cells overlap 12-18% of T2D-associated genome-wide association study candidates. Additionally, ONECUT2 is epigenetically upregulated in beta cells from people with pre-T2D/T2D and elevated in male Goto-Kakizaki rat islets. ONECUT2 overexpression in beta cells/islets downregulates gene sets impacting insulin secretion and glucose homeostasis, and reduces mitochondrial activity, ATP/ADP ratio and insulin secretion. We also provide 'alpha-beta-methylome' ( https://alpha-beta-methylome.serve.scilifelab.se/app/alpha-beta-methylome/ ), a resource exploring T2D, age and sex associations on methylation, highlighting cell-specific epigenetic regulation and dysfunctions contributing to T2D.

Humans↗
PubMed2026

Mining of CtOPR2 as an essential gene regulating jasmonic acid mediated insect tolerance in Camellia tachangensis through genome-wide association studies.

Jasmonic acid (JA), a pivotal lipid-derived phytohormone, serves as a critical regulator in plant growth and defense mechanisms. However, the genetic mechanisms of OPR2 gene in JA-dependent biotic defenses of Camellia tachangensis have rarely been investigated. In this study, we performed a genome-wide association study to analyze 100,720 high-quality single nucleotide polymorphisms (SNPs) among 350 tea accessions from Guizhou province to identify genetic variations associated with JA. Analysis showed C. tachangensis displayed higher levels of JA content, further analysis identified 60 high-quality SNPs and nine candidate genes related to JA. Among them, CtOPR2 encoding 12-oxophytodienoic acid reductase 2 is responsible for catalyzing the conversion of 4,5-didehydro-JA (4,5-ddh-JA) to JA. The expression level of CtOPR2 in three tea accessions with different JA content was consistent with the dynamic changes of JA content. The expression level of synthetic (AOS, AOC, and ACX) and responsive (WRKY18 and MYC2) genes were significantly decreased and increased in asODN-CtOPR2-treated shoot tips and transgenic tobacco lines overexpressing CtOPR2, respectively, which were consistent with the JA content. These results further revealed that CtOPR2 gene played essential roles in promoting JA biosynthesis. A significant reduction in insect bite area was observed on transgenic tobacco leaves compared to wild-type leaves in feeding experiments with Spodoptera litura, highlighting that the positive regulatory function of CtOPR2 gene in JA-mediated immune responses. This study provides a robust theoretical foundation for marker-assisted selection breeding in tea, aimed at developing high-JA germplasm with potentially enhanced pest resistance for cultivation in Guizhou.

Journal Article↗
PubMed2026

Dynamic and non-additive gene regulation shapes maize responses to simultaneous salt and cold stress.

Salt and cold stresses often occur together in nature and severely impact crop productivity, yet their transcriptional regulation remains poorly understood. Here, we conducted a time-series transcriptomic analysis of maize under salt, cold, and their combination at 0, 6, 12, and 24 h. Differential expression analysis revealed dynamic, condition-specific gene responses grouped into eight distinct temporal patterns. Promoter motif analysis of genes within each pattern identified 5-39 significantly enriched motifs, with over 40% lacking known counterparts, suggesting the involvement of previously uncharacterized cis-regulatory elements in stress-responsive transcriptional regulation. By comparing combined stress responses to the sum of single-stress effects, we found that about 74% of DEGs showed non-additive patterns, suggesting that combined stress triggers a distinct transcriptional program. Evolutionary analysis showed that additive DEGs tend to be more recently evolved, subject to weaker purifying selection, and enriched in transposed duplications, contrasting with the stronger constraint observed in non-additive DEGs. WGCNA identified 24 co-expression modules, among which 65 hub DEGs were detected in modules significantly correlated with specific stress conditions. Furthermore, we reconstructed 228, 20, and 200 sequential transcription factor cascades spanning 6 h, 12 h, and 24 h under cold, salt, and combined stress, respectively, with no cascade shared across all three conditions. Together, these results reveal that maize responses to combined salt and cold stress are largely non-additive and temporally dynamic, with distinct evolutionary patterns underlying different response types, offering insights and candidate regulators for enhancing crop stress resilience.

Zea mays↗
PubMed2026

Transcriptomic shift in ethanol and amino acid metabolic genes regulated by Med15 during alcoholic fermentation.

Organisms that thrive in extreme environments provide natural experiments in evolution, revealing the genetic regulators that orchestrate complex phenotypic change. Wine yeast (WY) are specialized strains that are adapted to survive in the wine making environment while producing high concentrations of ethanol. In addition to large genomic changes that differentiate WY from yeast used in other industries, SNP and polyglutamine tract polymorphism in the transcriptional regulator Med15 are associated with the fermentation efficiency and stress response phenotypes of WY. In this study, we investigated the transcriptional differences during wine fermentation in transgenic lab strain yeast having integrated WY MED15 alleles. Compared to the unmodified lab strain (MED15 LAB), the same strain in which the MED15 locus was replaced with a MED15 allele from yeast isolated from palm wine, the fermented sap of palm (oil, date, coconut) trees (MED15 WY23), exhibited enhanced expression of amino acid biosynthesis genes as well as stress resistance and metabolic adaptation genes. Our experimental data confirm the role of arginine in efficient fermentation and suggest that certain MED15 alleles alter the expression patterns of arginine pathway genes in some cases improving carbon flux under nitrogen stress. The global benefits conferred by natural polymorphisms in a single transcriptional regulator highlight Med15 as a target for engineering of strains devoted to various types of alcohol production.

Ethanol↗
PubMed2026

Transcriptomic shift in ethanol and amino acid metabolic genes regulated by Med15 during alcoholic fermentation.

Organisms that thrive in extreme environments provide natural experiments in evolution, revealing the genetic regulators that orchestrate complex phenotypic change. Wine yeast are specialized strains that are adapted to survive in the wine making environment while producing high concentrations of ethanol. In addition to large genomic changes that differentiate wine yeast from yeast used in other industries, single nucleotide and polyglutamine tract polymorphisms in the transcriptional regulator Med15 are associated with the fermentation efficiency and stress response phenotypes of wine yeast. In this study we investigated the transcriptional differences during wine fermentation in transgenic lab strain yeast having integrated wine yeast MED15 alleles. Compared to the unmodified lab strain (LAB or MED15 LAB ), the same strain in which the MED15 locus was replaced with a MED15 allele from yeast isolated from palm wine, the fermented sap of palm (oil, date, coconut) trees, (WY23, or MED15 WY23 ) exhibited enhanced expression of glycolytic, fermentation, and amino acid biosynthesis genes. Our experimental data confirms the importance of arginine biosynthetic genes during the fermentation process and suggests that the improvement in fermentation efficiency in strains with MED15 alleles from some wine yeast strains may be related to the role of Med15 in expression of the genes of the arginine biosynthetic pathway. The global benefit conferred by polymorphisms in a single transcriptional regulator, makes Med15 a prime target for engineering of strains devoted to various types of alcohol production.

Journal Article↗
PubMed2026

A human-specific non-coding RNA for EFHC1, an epilepsy-associated gene, regulates neural stem cell proliferation for cortical development.

Epilepsy is a prevalent brain disorder in humans but rarely occurs naturally in other species, highlighting the potential for human-specific mechanisms in its pathogenesis, and thus, current animal models fail to recapitulate human symptoms. Comparing RNA sequencing (RNA-seq) datasets from human and mouse neural stem cells (NSCs), we identified EFHC1, a juvenile myoclonic epilepsy gene, as exhibiting a human-biased expression. EFHC1 knockdown reduced human NSC proliferation, while its overexpression in mouse embryonic brains increased cortical NSC number. Mechanistically, EFHC1 prevented endoplasmic reticulum stress, thereby reducing inflammatory activation of p38 MAPK and promoting continuous proliferation of human NSCs. We also identified pancEFHC1, a bidirectional promoter-associated non-coding RNA (pancRNA), located at the human EFHC1 promoter. Knockdown of pancEFHC1 in human NSCs increased DNA methylation to reduce EFHC1 expression, with the resulting phenotype rescued by EFHC1 overexpression. We propose that the evolutionary acquisition of pancEFHC1 has introduced a complex regulatory mechanism for EFHC1 expression that allows distinguishing it in humans.

Humans↗
PubMed2025

Genotypes of SNPs of key genes regulate susceptibility and drug sensitivity to neovascular AMD in the human population.

OBJECTIVE: To compare the genetic characteristics of the normal control group to those of neovascular age-related macular degeneration (AMD) patients and to detect single-nucleotide polymorphisms (SNPs) related to the pathogenesis of neovascular AMD and the sensitivity to anti-VEGF drug, combercept. METHOD: This is a prospective case-controlled study. A total of 104 neovascular AMD patients were treated with combercept and 106 normal subjects were served as the control group. SNPs associated with neovascular AMD and disease susceptibility and drug sensitivity were analysed. RESULTS: Significant differences existed between neovascular AMD patients and normal subjects among genotypes of the SNPs of two genes, ARMS2 (rs10490924 T) and HTRA 1 (rs11200638 A). The T alleles in rs1065489 of CFH and the rs2230205 of C3 significantly promoted neovascular AMD in males while having no significant effect in females. Six SNPs of five genes, including C3 (rs2250656 G), CFB (rs2072633 G), CFH (rs2274700 A, rs3766405 T), KDR (rs6828477 A) and FZD 4 (rs10898563 T), had significant impact in reducing neovascular AMD. Two SNPs of the CFH gene (rs2274700 A and rs3766405 T) and one SNP of the CFB gene, rs2072633 G, were statistically significantly associated with good response to combercept. Conversely, the other two SNPs of the CFH gene, rs1065489 T and rs3753396 G, and the rs7412 T of the APOE gene were associated with a relatively poor patient response to drug action. Two sets of SNPs of CFB have a combined positive effect on disease. The two SNPs of CFH (rs1065489 T and rs3753396 G) and the combination of the two SNPs of CFH and rs7412T of APOE have negative effects on the drug effectiveness. CONCLUSIONS: These genotype differences facilitate the selection of individualised treatment options towards obtaining the most efficacious clinical treatment. These findings need to be validated by studies with different ethnic populations and/or larger samples.

Humans↗
PubMed2025

Aberrant DNA methylation of genes regulating CD4+ T cell HIV-1 reservoir in women with HIV.

BACKGROUND: The HIV-1 reservoir in CD4+ T cells (HRCD4) pose a major challenge to curing HIV, with many of its mechanisms still unclear. HIV-1 DNA integration and immune responses may alter the host's epigenetic landscape, potentially silencing HIV-1 replication. METHODS: This study used bisulphite capture DNA methylation sequencing in CD4+ T cells from the blood of 427 virally suppressed women with HIV to identify differentially methylated sites and regions associated with HRCD4. RESULTS: The average total HRCD4 size was 1409 copies per million cells, with most proviruses defective and only a small proportion intact. The study identified 245 differentially methylated CpG sites and 85 regions linked to HRCD4 size, with 52% of significant sites in intronic regions. Genes associated with HRCD4 were involved in viral replication, HIV-1 latency and cell growth and apoptosis. HRCD4 size was inversely related to DNA methylation of interferon signalling genes and positively associated with methylation at known HIV-1 integration sites. HRCD4-associated genes were enriched on the pathways related to immune defence, transcription repression and host-virus interactions. CONCLUSIONS: These findings suggest that HIV-1 reservoir is linked to aberrant DNA methylation in CD4+ T cells, offering new insights into epigenetic mechanisms of HIV-1 latency and potential molecular targets for eradication strategies. KEY POINTS: Study involved 427 women with HIV. Identified 245 aberrant DNA methylation sites and 85 methylation regions in CD4+ T cells linked to the HIV-1 reservoir. Highlighted genes are involved in viral replication, immune defence, and host genome integration. Findings suggest potential molecular targets for eradication strategies.

Humans↗
PubMed2026

CRISPR-Cas9 screen to identify genes regulating cell death.

Regulated cell death mediated by dedicated molecular machines, known as programmed cell death, plays important roles in health and disease. Understanding the mechanisms of cell death is crucial for elucidating the control of cellular homeostasis and developing therapies for related diseases. Despite extensive research efforts spanning decades, many aspects of cell death mechanisms remain elusive, highlighting the need for continued exploration. Here, we describe how to identify novel regulators involved in cell death pathways using a genome-wide screening approach.

CRISPR-Cas Systems↗
PubMed2026

Multidimensional GWAS analyses on longitudinal phenotypes reveal candidate genes regulating multi-stage egg production traits in Wannan yellow chicken.

Egg production performance directly determines the economic viability of indigenous chicken breeding. However, the genetic regulation of multi-stage egg production traits remains difficult to characterize due to their complex and dynamic nature. Here, we integrated a multidimensional GWAS framework, including single-trait GWAS, multi-trait GWAS (MTAG), and longitudinal trajectory-based GWAS (TrajGWAS), to identify stage-specific and shared genetic effects underlying egg production traits in Wannan yellow chickens (WNY). Whole-genome sequencing of 354 WNY hens (10× depth) and quality control yielded 14,253,816 SNPs for analysis. Selective sweep analyses comparing red jungle fowl, commercial layers, and WNY identified a genomic region containing IGF1 under significant selection pressure. Single-trait GWAS identified SNPs 4_57990480 (BMPR1B) and 17_370912 (LOC112531479) associated with egg production across three laying stages (21-30, 31-40, and 21-40 weeks). MTAG further identified loci 8_4336468 (FASLG) and 21_654726 (CHD5) with shared effects across the laying period, whereas TrajGWAS revealed longitudinal associations involving PRKG1 and identified dynamic loci associated with clutch traits, including GRID1. For clutch traits, stage-specific loci were detected for average clutch size (ACS) and maximum clutch size (MCS), including SNP 8_8542036 at 21-30 weeks, PROK1 at 31-40 weeks, and CUL5, ALKBH8 across the entire laying period. These results demonstrate that integrating complementary GWAS strategies improves the resolution of genetic architecture underlying egg production traits by capturing trait-specific, shared, and stage-dependent genetic effects. The identified GWAS loci and selective-sweep candidate regions provide insights into the genetic architecture of egg production traits and breed differentiation.

Egg production↗