Characterization and in silico analyses of RTCS gene from sugarcane encoding LOB protein family of transcription factors: a key regulator of shoot-borne root initiation

RTCS (Rootless concerning Crown and Seminal roots) is a member of the plant-specific LATERAL ORGAN BOUNDARIES (LOB) domain (LBD) protein family of transcription factors. The RTCS gene has been identified as a key regulator of shoot-borne root initiation in maize. In this study an attempt has been made to characterize RTCS from a wild related genus of sugarcane Erianthus arundinaceus and compared to the RTCS gene isolated from commercial sugarcane hybrid genotypes. The candidate gene has been successfully isolated from two genotypes of E. arundinaceus (SES 288 and IND 04- 1335: EaRTCS) and two commercial sugarcane hybrid genotypes (Co 775 and Co 86032: ShRTCS). The isolated RTCS full-length gene showed significant variation between EaRTCS and ShRTCS at the DNA and protein level. The RTCS amino acid sequence of all the four genotypes indicated the presence of the characteristic structural features of LBD proteins such as a C-motif, LOB domain sequence and leucine zipper-like dimerization domain. Prediction and analysis of the secondary structure of RTCS protein in SES 288 and IND 04-1335 showed the presence of 65% alpha helix, 1% β strand and 38% disorder, while sugarcane commercial genotypes showed 58 % alpha-helix, 1% β strand and 47% disorder. Both the sequences of EaRTCS and ShRTCS was found to be closely related to Zea mays RTCS.