STAY-GREEN (SGR) genes in tomato (Solanum lycopersicum): genome-wide identification, and expression analyses reveal their involvements in ripening and salinity stress responses

Chlorophyll (Chl) is present in many plant organs and plays vital roles during growth and development. Degradation of Chl causes the loss of green colour that typically occurs during senescence, and fruit ripening. The present study addresses genome-wide identification and bioinformatics analyses of tomato (Solanum lycopersicum), SlSGR1 (Solyc08g080090.2.1) SlSGR2 (Solyc12g056480.1.1) and SlSGR-like (Solyc04g063240.2.1) genes. Multiple sequence alignment indicated that the three tomato SGR proteins have conserved domains. Motif, sequence, and protein structure analysis showed that SlSGR-like differentially evolved from SlSGR proteins. Co-expression analyses were performed for each SlSGR using transcriptomic data of two fruit ripening stages [mature green (MG) and ripe fruit (R)] of Ailsa Craig (AC) tomato cultivar. According to the co-expression network analyses, SlSGRs participate in sulphur homeostasis, fatty acid biosynthesis, and biological processes of plant development during ripening stages of tomato. Six common genes were identified in the merged co-expression network. Also, 38 transcription factor families (TFFs) were searched in the co-expression network. Only 13 transcription factors, belonging to seven TFFs, were found to be involved in regulation of these two genes. Of these TFFs, GRAS and GeBP had five and three members for SlSGR-like and SlSGR1 in the network. The expression profiles of SlSGR1/2 and SlSGR-like in different tissues and different fruit ripening stages showed that SlSGR1/2 are highly expressed in ripening fruits, whereas SlSGR-like is more involved in leaf maturation. Moreover, expression of SlSGR1/2 and SlSGR-like in the leaves of ‘Ciko’ and ‘Black’ tomato varieties under 200mM salt stress indicated that significant expression changes occurred in SlSGR2 suggesting that SlSGR genes may be involved in signalling responses to abiotic stress. The findings provide new insight into the functions of these genes in growth and salinity stress.