RNA-seq analysis of watermelon (Citrullus lanatus) to identify genes involved in fruit cracking

Fruit cracking in watermelon (Citrullus lanatus) causes a great economic loss. To understand the molecular mechanisms underlying watermelon fruit cracking, the differentially expressed genes (DEGs) between resistant and susceptible-cracking watermelon were analyzed using transcriptome sequencing. We selected the parent inbred W11 (resistant-cracking) and W13 (susceptible-cracking), and Near-Isogenic Lines W96 (resistant-cracking) and W85 (susceptible-cracking) as materials. Differentially expressed genes (DEGs) analysis showed that 290 DEGs had detectable in “W11” VS “W13”, while 165 DEGs had detectable in “W96” VS “W85”. There were 56 DEGs between the four samples. Additionally, 14 DEGs related to fruit cracking were identified from the transcriptome. Only 8 DEGs among them, were involved in 14 KEGG pathway. The expression patterns of the 14 DEGs related to fruit cracking were analyzed by qRT-PCR to explore their putative functions. This transcriptome dataset will aid in understanding and carrying out future studies on the molecular basis of fruit cracking and contribute to watermelon breeding.