Molecular and in silico characterization of tomato LBD transcription factors reveals their role in fruit development and stress responses

Abstract

LATERAL ORGAN BOUNDARIES DOMAIN (LBD) proteins represent a family of plant specific transcription factors associated with roles in plant organ development, pollen development, regeneration, disease susceptibility, photomorphogenesis, secondary growth and metabolism. LBD gene family has been studied in Arabidopsis thaliana, Glycine max, Medicago truncatula, Oryza sativa and Zea mays; however, there is no detail information about expression pattern and roles of LBD genes in tomato. In present study, a total of 47 SlLBD genes from tomato were in silico characterized by conserved motif analysis, cis-regulatory element analysis and interaction network analysis. Motif analysis of SlLBD proteins revealed close evolutionary relationship or similar motif compositions. Cis-regulatory elements analysis of promoters of SlLBD genes suggested their diverse functions associated with hormone and stress response, tissue specific expression, metabolite biosynthesis and light response. The interaction network analysis of SlLBD proteins suggests its interaction with ARF, GRAS, WRKY, MADS, MYB CONSTANS TFs as well as with other SlLBD members viz. SlLBD41-SlLBD3-SlLBD36 and SlLBD7-SlLBD19-SlLBD14. The combinatorial interaction between SlLBDs and other TFs is responsible to play role in regulating diverse functions in tomato. Further quantitative RT-PCR expression analysis of a total of 33 SlLBD genes in different vegetative and fruit tissues revealed spatio-temporal expression in different plant parts and fruit developing stages. Two of the SlLBD genes SlLBD20 and SlLBD47 were found exclusively expressing in fruit, suggesting their role in fruit development and ripening. Expression of SlLBD genes under different hormone treatments and stress (abiotic & biotic) conditions were analyzed using TomExpress database, suggested their role in defense and hormonal regulation.