Baiquan Sun

SUMMARY: Precise regulation of flowering time and maturity is critical for achieving high and stable soybean yields, and the circadian clock plays a central role in coordinating these developmental transitions. Soybean is a typical short‐day crop with a pronounced photoperiodic response; however, the molecular mechanisms linking circadian regulation to photoperiod‐dependent flowering and maturity remain incompletely understood. Here, we integrated genome‐wide association analysis with deep learning approaches using 257 soybean germplasm accessions spanning 14 maturity groups and identified GmRVE8a , a homolog of the Arabidopsis circadian clock gene REVEILLE , as a strong candidate locus associated with soybean maturity across two field environments. Haplotype analysis demonstrated that accessions carrying the GmRVE8a ^H1 haplotype consistently flowered and matured significantly later than those carrying GmRVE8a ^H2 . Functional validation revealed that knockout of GmRVE8a markedly accelerated flowering and maturity, whereas overexpression of GmRVE8a significantly delayed both processes. qRT‐PCR assays further suggested that GmRVE8a may repress flowering and delay maturity by promoting the expression of GmFT4 , a flowering‐inhibitory member of the FT family, and is unlikely to act by directly regulating E1 expression. Collectively, our findings suggest GmRVE8a as a circadian clock‐associated negative regulator of soybean flowering and maturity, and highlight it as a promising candidate for molecular breeding aimed at improving adaptation to diverse photoperiodic environments.

Photoperiod is a major environmental cue that regulates flowering, maturity, and ecological adaptation in soybean. Although soybean photoperiodic regulation has been extensively studied in true leaves and whole plants, the contribution of cotyledons, the first light-exposed organs after seedling emergence, remains poorly understood. In this study, we used cotyledons of the photoperiod-sensitive soybean cultivar ‘Zigongdongdou’ to investigate early transcriptional responses to day length. Seedlings were grown under short-day conditions, 12 h light/12 h dark, or long-day conditions, 16 h light/8 h dark, and cotyledons were collected every 4 h during the first 72 h after transfer from darkness to photoperiodic conditions, generating a 19-time-point RNA-seq dataset. A total of 663 differentially expressed genes were identified between short-day and long-day conditions, including 340 upregulated and 323 downregulated genes. Functional enrichment analysis showed that these genes were mainly associated with photoperiodic flowering, circadian regulation, hormone signaling, oxidative stress responses, glutathione metabolism, and primary metabolism. Core photoperiod-related genes, including photoreceptors, circadian clock genes, CONSTANS-like genes, E1-family genes, and FT genes, displayed clear photoperiod-dependent expression patterns in cotyledons. Weighted gene co-expression network analysis combined with predicted regulatory network analysis further identified C2H2, WRKY, ERF, NAC, Dof, MYB, and TCP transcription factors as candidate regulators associated with photoperiod-responsive modules. In particular, LATE and several GmNAC genes were connected with flowering- and hormone-related modules, suggesting possible links between transcription factor regulation and the COL–FT pathway. These results demonstrate that soybean cotyledons establish an active photoperiod-responsive transcriptional network shortly after emergence. Cotyledon expression profiling captures major regulatory features of the soybean photoperiod pathway and provides a compact, time-saving, and space-efficient system for investigating early photoperiodic regulation in soybean.

Timely flowering and maturity are crucial for plant reproduction and environmental adaptation. Light–dark cycle-associated regulatory networks integrate photoperiodic cues with intrinsic developmental programs and play pivotal roles in flowering, maturity and environmental adaptation. Soybean is a short-day crop with strong photoperiod responsiveness; however, the molecular mechanisms by which these networks mediate soybean adaptation to diverse environments remain largely elusive. Here, we combine genome-wide association analysis with deep learning-based assessment of soybean maturity variation and identify GmRVE4d, a homolog of the Arabidopsis clock-associated REVEILLE, as a maturity-associated locus across both field environments. Genetic analysis reveals evidence of domestication-related artificial selection at GmRVE4d and identifies the late-maturing haplotype GmRVE4d^H3. Functional analyses further demonstrate that the GmRVE4d protein directly binds to the promoter of GmPRR5a, a soybean homolog of the Arabidopsis clock-associated component PSEUDO-RESPONSE REGULATOR 5, and represses its transcription, thereby delaying soybean flowering and maturity. Taken together, our findings suggest that GmRVE4d is a negative regulator of soybean flowering and maturity that functions by directly repressing GmPRR5a expression and represents a promising molecular target for expanding cultivation latitudes through molecular breeding.