Brassica rapa is an important Chinese vegetable crop that is beneficial to human health. The primary factor affecting B. rapa yield is low temperature, which promotes bolting and flowering, thereby lowering its commercial value. However, quickened bolting and flowering can be used for rapid breeding. Therefore, studying the underlying molecular mechanism of vernalization in B. rapa is crucial for solving production-related problems. Here, the transcriptome of two B. rapa accessions were comprehensively analyzed during different vernalization periods. During vernalization, a total of 974,584,022 clean reads and 291.28 Gb of clean data were obtained. Compared to the reference genome of B. rapa, 44,799 known genes and 2280 new genes were identified. A self-organizing feature map analysis of 21,035 differentially expressed genes was screened in two B. rapa accessions, ‘Jin Wawa’ and ‘Xiao Baojian’. The analysis indicated that transcripts related to the plant hormone signal transduction, starch and sucrose metabolism, photoperiod and circadian clock, and vernalization pathways changed notably at different vernalization periods. Moreover, different expression patterns of TPS, UGP, CDF, VIN1, and seven hormone pathway genes were observed during vernalization between the two accessions. The transcriptome results of this study provide a new perspective on the changes that occur during B. rapa vernalization, as well as serve as an excellent reference for B. rapa breeding.

The ADP-glucose pyrophosphorylase (AGPase) gene family plays an essential role in starch metabolism and stress adaptation. However, its function in antiviral defense remains largely uncharacterized. Cucumber (Cucumis sativus L.), a globally important vegetable crop, frequently experiences severe yield losses due to viral infections. In this study, we systematically identified five AGPase genes in cucumber, categorizing them into large and small subunits. Analysis of conserved motifs revealed ten conserved sequences, with the NTP (Nucleoside Triphosphate) transferase domain representing a signature feature of the AGPase family. Promoter regions contained multiple cis-regulatory elements associated with stress responses and hormone signaling. Transcriptomic profiling revealed tissue-specific expression patterns of CsAGP genes, with pronounced enrichment in leaves. Notably, CsAGP2, CsAGP4, and CsAGP5 were strongly induced under biotic and abiotic stresses. Of these, CsAGP4 exhibited rapid, transient induction specifically in the virus-resistant line ‘228’, but not in the susceptible line ‘65G’. Hormonal treatments showed that abscisic acid (ABA) rapidly activated most CsAGP genes and acted synergistically with viral infection to amplify CsAGP4 expression. Functional analysis via CRISPR/Cas9-mediated knockout of CsAGP4 revealed that the mutation disrupted starch granule formation and significantly altered resistance to watermelon mosaic virus (WMV) in ‘Poinsett 97’. Our work provides a systematic characterization of the AGPase gene family in cucumber and establishes its role in defense responses. Importantly, we identify CsAGP4 as a positive regulator of antiviral immunity, highlighting its potential as a target for breeding virus-resistant cucumber varieties.