Whole-transcriptome dynamics reveal distinct regulatory networks during sugar beet vernalization

Sugar beet ( Beta vulgaris L.) is a biennial crop that requires prolonged cold exposure to initiate flowering—a process known as vernalization. This cold requirement restricts the growing season and limits cultivation options. However, the molecular networks that distinguish vernalization from general cold stress remain poorly characterized in this crop. Here, we performed a time-course whole-transcriptome analysis across five vernalization stages (0, 2, 6, 10, and 14 weeks) and identified 3,598 mRNAs that were specifically altered only after sufficient cold exposure. Many of these encode histone modifiers (including enzymes involved in histone phosphorylation, methylation, and acetylation) and transcription factors. Their expression patterns suggest a chromatin-based regulatory mechanism, although this inference is derived from transcript abundance rather than direct chromatin measurements. In contrast to the FLC -centered pathway in Arabidopsis , sugar beet may employ a putatively distinct regulatory logic: long non-coding RNAs (lncRNAs) such as MSTRG.54931.1 and MSTRG.64283.2 are predicted to preferentially associate with stress-related kinases rather than floral repressors, and microRNAs (miRNAs) predominantly respond at early cold stages, with limited contribution to later vernalization memory. These findings suggest a new regulatory framework for vernalization in a non-model crop and may provide a foundation for breeding bolting-tolerant varieties.