Transcriptome Profiling to Dissect the Role of Genome Duplication on Graft Compatibility Mechanisms in Watermelon

SIMPLE SUMMARY: Triploid seedless watermelon cultivars have high demand globally, and they are excellent in quality compared to diploid seeded watermelons. A low number of seedlings are produced as a result of grafting in triploid and tetraploid watermelons. In this regard, to understand the influencing factors of genome duplication on graft compatibility, we performed a comparative transcriptome analysis between tetraploid and diploid watermelons grafted on squash rootstock with the splice method. A weighted gene co-expression network analysis (WGCNA) was performed using the common differentially expressed genes (DEGs) between diploid and tetraploid plants of watermelon grafted seedlings and the contents of hormones antioxidants (AOX), sugars, and starch at 0, 3, and 15 days after grafting (DAG). Higher survival rates and contents of hormones, AOX, sugars, and starch were observed in tetraploid grafted seedlings compared to diploid ones. We concluded that genome duplication significantly affected gene expression in the IAA and ZR signal transduction and AOX biosynthesis pathways in the grafted plants, resulting in the regulation of hormone levels’ signal pathways, promoting plant survival. These genes are identified for the first time, and no previous reports about their role or functions in watermelon are available. ABSTRACT: Watermelon (Citrullus lanatus) 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(2) = 0.81), one with ZR (r(2) = 0.85) and one with POD (r(2) = 0.74). In the MElightsteelblue1 module, Cla97C11G224830 gene was linked with CAT (r(2) = 0.81). Two genes from the MEivory module, Cla97C07G139710 and Cla97C04G077300, were highly linked with SOD (r(2) = 0.72). Cla97C01G023850 and Cla97C01G006680 from the MEdarkolivegreen module were associated with sugars and starch (r(2) = 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.