Comparative transcriptomics and weighted gene co-expression correlation network analysis (WGCNA) identified genes associated with fruit shape in pumpkin (Cucurbita maxima)

• The shape of mature melons can be predicted by examining the ovary shape during the early developmental stages of the pumpkin. • At the cellular level, pumpkins with different fruit shapes exhibit variations in both cell number and size within their flesh. • Key genes and transcription factors involved in the auxin and cytokinin signaling pathways interact to collectively regulate the shape of pumpkin fruit. Pumpkin ( Cucurbita maxima ) is a prominent cultivar in China and is highly favored by consumers. Fruit shape is a critical agronomic trait in horticultural crops, which significantly contributes to their commercial value. In this study, we compared the two inbred lines of Cucurbita maxima , 'CNG2–3–1–1′ and 'BL27–3–2–1′, which exhibited significant difference in fruit shape. We observed that 'CNG2–3–1–1′ had a notably higher fruit shape index than 'BL27–3–2–1′, potentially due to variations in gene expression regulating cell division and expansion throughout fruit development. Furthermore, fruit shape was clearly discernible in both inbred lines at the ovary stage. Transcriptome sequencing was performed at five developmental stages of the inbred lines, coupled with weighted co-expression network analysis (WGCNA), to elucidate the molecular mechanisms and interaction networks of select differentially expressed genes involved in fruit shape regulation. The findings revealed the detection of 25,653 differentially expressed genes (DEGs). In the growth hormone signaling pathway, CmaAux/IAA, CmaAUX1, CmaGH3 , and CmaSAUR , as well as CmaARR, CmaCRE1 , and CmaAHP in the cytokinin signaling pathway, exhibited differential expression between the two inbred lines. Moreover, analysis of differentially expressed transcription factors across various developmental stages suggested that CmabHLH, CmaERF, CmaWRKY, CmaHD-ZIP , and CmaMYB transcription factors may be associated with fruit expansion. It is postulated that these factors interact with target genes to collectively govern cell division and expansion in both horizontal and vertical directions, thereby influencing fruit shape difference between the two inbred lines.