Abstract
BACKGROUND: Shoot architecture is one of the fundamental traits in plants that diversifies their visual appearance. It is also an important agronomic trait as it substantially affects productivity and labor costs in crop species. Cucumber (Cucumis sativus L.) is a widely cultivated vegetable due to its economic value. As cucumber plants enter the vegetative and reproductive phases simultaneously, the shoot apical meristem continues to produce nodes bearing leaves, each capable of flower development in the axil. Therefore, the characteristics of node formation rate, which is generally recognized as a component of plant growth index ‘shoot vigor’ by growers, are expected to influence fruit yield. However, it remains unclear how and to what extent cultivar-dependent differences in node formation rate contribute to variation in yield. RESULTS: We examined four Japanese cucumber cultivars (‘Josho-661’ [‘Josho’], ‘S-30’, ‘Green-Flush’, and ‘Yusho’), which are considered to differ in shoot vigor. ‘Josho’ exhibited the highest node formation rate and the highest fruit yield (36.3 kg m(–2)), whereas ‘Yusho’ developed fewer nodes and achieved the lowest yield (28.1 kg m(–2)). However, ‘S-30’ showed the highest dry-matter productivity, although ‘Josho’ exhibited better dry-matter partitioning to fruits. These results revealed that node formation rate and the consequent dry-matter allocation rather than dry-matter productivity can become limiting factors in cucumber yield. In addition, we conducted a comparative mRNA sequencing analysis of shoot tips to explore transcriptomic diversity and functional enrichment underlying the cultivars, which implied that variations in SAM maintenance gene, mitotic activity in SAM, and shoot tip temperature might be behind the difference in node formation rate. CONCLUSIONS: The growth analysis revealed that dry-matter productivity was not necessarily correlated with fruit yield and highlighted the potential impact of shoot vigor, particularly node formation rate, on cucumber fruit yield. Transcriptomic diversity observed in this study would genetically reinforce cucumber yield model. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-025-07587-3.