Transcriptomic and the Pectinase Gene Family analysis reveals a particular pathway on malformed tomato development

Fruit malformation severely reduces the yield and quality of tomatoes, resulting in significant economic losses. However, the molecular mechanisms underlying malformed tomato fruit are far from being fully understood. Here, we first investigated the phenotypic characterization between the wild type "QT57" and the malformed fruit "QT2". Significant differences in flower organization were found. The expression of genes related to the CLAVATA-WUSCHEL pathway suggested that SlCRCa and SlCRCb are involved in the formation of QT2 misshapen fruits by acting in a compensatory manner. RNA-Seq analysis identified six pectinase genes as key candidate genes for misshapen fruit. They were significantly expressed and their expression was higher in "QT57" than in "QT2", suggesting a negative regulation of malformed fruit formation. Gene family analysis of pectinase genes was also performed. A total of 34 pectinase genes, including 6 PL, 15 PG and 13 PME genes, were used for in-depth bioinformatic analysis. We found that all genes except SlPL2 , SlPL11 and SlPG56-2 had gibberellin homeopathic effect elements; pectin lyase and pectin esterase were closely related and functioned in similar microenvironments. The results provide new insights into tomato fruit deformation.