Background: Cyperus esculentus L. is a unique tuber oil crop, in which tuber size directly determines both yield and oil storage capacity. It is crucial to clarify the tuber expansion pattern and explore the key genes associated with tuber expansion in Cyperus esculentus for crop improvement. Methods: This study conducted comprehensive morphological and cytological observations as well as transcriptomic analysis of tubers at multiple developmental stages. Tubers at 1, 5, 10, and 15 d were collected for transcriptome sequencing to identify differentially expressed genes (DEGs) and differentially expressed transcription factors. Gene ontology (GO) enrichment analysis was used to determine key functional categories. RT-qPCR was employed to verify the expression patterns of key genes. Results: Cyperus esculentus tubers expanded rapidly from 1 d to 15 d after initial tuber formation, and the expansion rate exhibited a trend of increasing first (1~5 d) and then decreasing (5~15 d). Cell expansion, rather than number, mainly contributed to tuber expansion. By combining the analysis of differential expression and the variation pattern of tuber expansion rate, 822 DEGs were identified to be associated with tuber expansion. GO enrichment analysis revealed that 20 genes were significantly enriched in GO:0043231 (cell wall), especially five remarkable genes encoding expansin, which exercise the function of cell wall loosening and have been proven to be associated with cell expansion. In addition, 57 differentially expressed TFs were further identified to be associated with tuber expansion. Conclusions: This study revealed the tuber expansion pattern of Cyperus esculentus and identified several key genes and TFs, which will facilitate the construction of the regulatory network and the analysis of the mechanism of tuber expansion in Cyperus esculentus.

Cyperus esculentus L., commonly known as Yellow Nutsedge or Tiger Nut, belongs to the Sedge family (Cyperaceae), which is widely distributed in tropical and temperate regions around the world. The species is particularly noted for its underground tuber, which is rich in starch and oil, and can be used for both food and industrial purposes. However, cultivated C. esculentus rarely flowers in the field, and when it does, flowering is often accompanied by sterility, significantly hindering the development of superior varieties through sexual hybridization. Our investigation into the causes of pollen abortion in C. esculentus yielded several key findings. Initially, we observed pollen abortion within the anthers using Alexander’s red staining and starch-iodide staining techniques. Further examination through semi-thin sections of the anthers revealed that, although the pollen appeared normal during the pachytene stage, the pollen failed to stain blue in later developmental stages, indicating abnormal development. This was followed by vacuolation, collapse, and degradation of the pollen, ultimately resulting in abortion. Additionally, we monitored chromosome behavior throughout meiosis and observed premature chromosome separation during metaphase II, leading to disarray in the subsequent pseudomonad phase. Chromosomal karyotype analysis and ploidy predictions suggested that the triploid nature of C. esculentus contributes to meiotic disorders, which may explain the phenomenon of pollen abortion. These findings provide valuable insights into the reproductive challenges faced by this species and may inform future breeding efforts aimed at overcoming its sterility.