The genus Allium belongs to the botanical family Amaryllidaceae and includes economically important crops such as onion, garlic, bunching onion, and leek, used as vegetables, spices, and traditional medicines. The large sizes of Allium genomes hamper the genetic dissection of agronomically important traits and molecular breeding. With the growing accumulation of genomic, resequencing, transcriptome, and phenotypic data, the demand for an integrative Allium database is increasing. Here we present a user-friendly database, AlliumDB (https://allium.qau.edu.cn), as a functional genomics hub integrating public and in-house data. The database contains all currently available nuclear and organelle genomes for Allium species, with genes comprehensively annotated based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, orthology, gene families, protein families (Pfam), and non-coding RNA families (Rfam). Transcriptome and variation profiles are integrated into dynamic visualization tools. We took phenotypic photographs and generated trait records for hundreds of Allium germplasms collected worldwide, which are included in the database. We incorporated JBrowse for the visualization of gene structures, RNA sequencing data, and variation data. Analysis tools such as the basic local alignment search tool (BLAST), sequence fetch, enrichment, and motif analyses are available to explore potential gene functions. This database incorporates comprehensive Allium genotypic and phenotypic datasets. As the community assembles new genomes and generates resequencing data for Allium germplasms, the database will be improved and continuously updated with these multi-omics data and comparative genomic studies. We expect the AlliumDB database to become a key resource for the study of Allium crops.

Background: Aegilops tauschii, a winter annual grass weed native to Eastern Europe and Western Asia, has become a widespread invasive species in the wheat-growing regions of China due to its high environmental adaptability. This study aims to explore the molecular mechanisms underlying the stress resistance of Tausch’s goatgrass, focusing on the HSP70 gene family. Methods: A genome-wide analysis was conducted to identify and characterize the HSP70 gene family in A. tauschii. Afterward, their physicochemical properties, phylogenetic relationships, gene structures, and chromosomal distributions were analyzed. Additionally, cis-acting regulatory elements were predicted to understand their potential role in stress resistance. Results: A total of 19 identified HSP70 family genes were classified into four subfamilies and distributed across all chromosomes. The syntenic analysis revealed extensive homology between Tausch’s goatgrass and wheat HSP70 genes. Segmental duplication was found to play a crucial role in the expansion of the HSP70 gene family. The prediction of cis-acting elements suggested that these genes are involved in stress resistance to various environmental conditions. Conclusions: This study provides a comprehensive overview of the HSP70 gene family in A. tauschii, offering insights into their role in stress resistance and their potential application in understanding invasive species behavior and improving wheat resilience. Further research is needed to validate their functional roles in stress adaptation.

Welsh onion (Allium fistulosum L.), a globally significant vegetable, flavoring agent, and phytomedicine resource, has remained unavailable with established transient expression platforms for functional genomic investigations. To address this critical methodological limitation, we present systematically optimized protocols for both Agrobacterium-mediated hairy root transformation and protoplast transient expression systems, achieving significant advances in transformation efficiency for this species. Through systematic optimization of key parameters, including Agrobacterium rhizogenes (A. rhizogenes) strain selection (with Ar.Qual demonstrating superior performance), explant type efficacy, bacterial suspension optical density (OD₆₀₀ = 0.3), and acetosyringone induction concentration (100 μM), we established a highly efficient stem disc infection methodology, achieving 88.75% hairy root induction efficiency. Subsequent optimization of protoplast isolation protocols identified the optimal enzymatic digestion conditions: 6-h dark digestion of young leaves using 1.0% (w/v) Cellulase R-10, 0.7% (w/v) Macerozyme R-10, and 0.4 M mannitol, yielding 3.3 × 10⁶ viable protoplasts g⁻¹ FW with 90% viability. System functionality validation through PEG-mediated transient transformation demonstrated successful green fluorescent protein (GFP) reporter gene expression, confirmed by fluorescence microscopy. As the first documented transient expression platforms for Welsh onion, these protocols enable essential molecular investigations, including in planta promoter activity profiling, subcellular protein localization, and CRISPR-based genome-editing validation. This methodological breakthrough overcomes previous technical constraints in Welsh onion molecular biology, providing critical tools for accelerated gene functional characterization in this agriculturally important species.

Plants exhibit diverse pathways to regulate the timing of flowering. Some plant species require a vegetative phase before being able to perceive cold stimuli for the acceleration of flowering through vernalization. This research confirms the correlation between the vernalization process and seedling age in Welsh onions. Findings from two vernalization experiments conducted at different time intervals demonstrate that seedlings must reach a vegetative phase of at least 8 weeks to consistently respond to vernalization. Notably, 8–week–old seedlings subjected to 6 weeks of vernalization displayed the shortest time to bolting, with an average duration of 138.1 days. Transcriptome analysis led to the identification of genes homologous to those in Arabidopsis thaliana that regulate flowering. Specifically, AfisC7G05578 (CO), AfisC2G05881 (AP1), AfisC1G07745 (FT), AfisC1G06473 (RAP2.7), and AfisC2G01843 (VIM1) were identified and suggested to have potential significance in age–dependent vernalization in Welsh onions. This study not only presents a rapid vernalization method for Welsh onions but also provides a molecular foundation for understanding the interplay between seedling age and vernalization.

Soil salinization is a significant global challenge that severely impacts agricultural productivity, particularly through its negative effects on crop growth and yield. Peanuts (Arachis hypogaea L.) are an important oil crop. One of the major goals in peanut breeding programs is to develop varieties with both high oil content and salt tolerance. Previously, we obtained a peanut line (HO) with high oil content through mutagenesis, which showed higher salt tolerance than its parental line (HY20). In this study, we employed multiple approaches including anatomical, physiological, and transcriptomic analyses to elucidate salt tolerance mechanisms of the HO peanut line. Under salt stress, the HO line exhibited better-developed vascular structures, with increased root vessel diameter and higher crystal idioblast density in leaves compared to HY20. HO also showed enhanced antioxidant enzyme activities, with POD and SOD activities higher than HY20. Photosynthetic efficiency was substantially improved in HO, with Fv/Fm decreasing under severe salt stress. Additionally, HO maintained a lower Na⁺/K⁺ ratio and higher linolenic acid content under salt stress. Transcriptomic analysis revealed up-regulated lignin biosynthesis genes in HO. This study established potential connections between salt stress tolerance and oil biosynthesis in peanuts, providing insights that could be leveraged for the development of high-yield and salt-resistant varieties.