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.

Cyperus esculentus is a new industrial crop with the high comprehensive utilization value, which is a strongly resistant to stresses and has a great potential to grow in saline soil. In order to clarify its salt tolerance, five NaCl concentrations (0, 0.3%, 0.6%, 0.9%, and 1.2%) were set in this study to analyze the effects of NaCl stress on morphological and physiological indexes during germination and seedling growth. The results showed that the germination percentage, root length, and seedling height were less affected under 0.3% and 0.6% NaCl stresses. Meanwhile, the contents of indicator of membrane damage degree, malondialdehyde (MDA), and oxidative stress substance, hydrogen peroxide (H2O2), did not increase significantly. However, the contents of osmoregulation substances [glycine betaine (GB), and proline (Pro)] and the activities of antioxidant enzymes [superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT)] were significantly increased, and the damage of salt stress was less on the whole. However, under 0.9% and 1.2% NaCl stresses, the salt stress injury was very obvious and the germination and seedling growth of Cyperus esculentus were severely inhibited. In order to further identify the genes related to salt tolerance, RNA-seq technology was used to detect the gene expression in roots under 0, 0.3%, and 0.6% NaCl stresses. 24 GO terms mainly related to oxidoreduction, transmembrane transport, chitin hydrolysis was significantly enriched, among which 15 significantly up-regulated genes were involved, through gene differential expression analysis, weighted gene co-expression network analysis (WGCNA), and GO enrichment analysis. Among them, DN23985_c0_g1, DN2960_c0_g1, and DN8384_c1_g1 encoded zeaxanthin epoxidase, L-ascorbate peroxidase, and glutathione S-transferase, respectively, which had antioxidant effects and participated in antioxidant regulation. Both DN21785_c1_g1 and DN6596_c0_g1 encoded amino acid transporters, which may enhance osmoregulation by accumulating small amino acid molecules such as Pro. DN14393_c0_g1 encoded chitinase, which hydrolyzed chitin and promoted plant response to stress. In this study, it was confirmed that Cyperus esculentus had a good salt tolerance under 0.6% or less NaCl stress, and the salt-tolerance related genes were further screened out, which provided an important reference for the cultivation in saline soil and the breeding of salt-tolerant varieties.