An in silico approach for characterization of encoded protein from Rdr1, a black spot resistance gene in Rosa multiflora

Abstract

Black spot disease is the most common diseases of landscape roses and is caused by Diplocarpon rosae Wolf. In Rosa multiflora, the screening of black spot-resistant tetraploids and diploids demonstrated the presence of dominant genes Rdr1 and Rdr2. A previous study has identified muRdr1H as the only TIR-NBS-LRR gene, which could restore black spot resistance in the susceptible genotypes. In this study, we selected the protein encoded by muRdr1H gene, AEE43932.1, for computational analysis. Its primary, secondary, and tertiary structures were obtained for further analysis. The results showed that the query protein was acidic, stable, and hydrophilic. The secondary structure prediction showed that the query protein consisted of 37 beta strands, 26 alpha-helices, and 28 coils and is probably localized in the cell membrane and cytoplasm. Five three-dimensional (3D) models were predicted by I-TASSER and validated. We found that model A showed the best results with the highest confidence score (−0.90) as well as enzyme commission-related confidence score and ligation binding sites (LI). The models developed were validated using PROCHECK program. These analyses validated that the predicted model A was the best and reliable enough to be used for future studies related to black spot resistance in Rosaceae plants.