| Summary: | Watermelon (<i>Citrullus lanatus</i>) is a popular crop worldwide. Compared to diploid seeded watermelon, triploid seedless watermelon cultivars are in great demand. Grafting in triploid and tetraploid watermelon produces few seedlings. To learn more about how genome duplication affects graft compatibility, we compared the transcriptomes of tetraploid and diploid watermelons grafted on squash rootstock using a splicing technique. WGCNA was used to compare the expression of differentially expressed genes (DEGs) between diploid and tetraploid watermelon grafted seedlings at 0, 3, and 15 days after grafting (DAG). Only four gene networks/modules correlated significantly with phenotypic characteristics. We found 11 genes implicated in hormone, AOX, and starch metabolism in these modules based on intramodular significance and RT-qPCR. Among these genes, two were linked with IAA (r<sup>2</sup> = 0.81), one with ZR (r<sup>2</sup> = 0.85) and one with POD (r<sup>2</sup> = 0.74). In the MElightsteelblue1 module, <i>Cla97C11G224830</i> gene was linked with CAT (r<sup>2</sup> = 0.81). Two genes from the MEivory module, <i>Cla97C07G139710</i> and <i>Cla97C04G077300</i>, were highly linked with SOD (r<sup>2</sup> = 0.72). <i>Cla97C01G023850</i> and <i>Cla97C01G006680</i> from the MEdarkolivegreen module were associated with sugars and starch (r<sup>2</sup> = 0.87). Tetraploid grafted seedlings had higher survival rates and hormone, AOX, sugar, and starch levels than diploids. We believe that compatibility is a complicated issue that requires further molecular research. We found that genome duplication dramatically altered gene expression in the grafted plants’ IAA and ZR signal transduction pathways and AOX biosynthesis pathways, regulating hormone levels and improving plant survival.
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