Molecular detection and characterisation of begomovirus causing bean yellowing disease in Sri Lanka

Bean (Phaseolus vulgaris L.) is one of the major vegetable crops cultivated in tropical, sub-tropical and temperate regions in the world. Bean yellowing disease (BYD), which was first reported in 1999 from Sri Lanka is still a serious viral threat to bean cultivation causing severe yield reduction. In this study, polymerase chain reaction (PCR) assays using degenerate (universal) primers were conducted with the aim of developing molecular techniques to detect the virus. Two degenerate primer pairs, namely, Deng 540/541 and AV494/AC1048 used in the PCR reactions confirmed the association of a begomovirus with the BYD by giving the desired core coat protein amplicons of 520 bp and 550 bp, respectively. The resulting amplicons were subjected to DNA sequencing and the sequence data were analysed to determine the phylogenetic and molecular evolutionary relationships with other related begomovirus sequences obtained from the GenBank. The analysis revealed that the virus associated with BYD (BYVD-GN-SL-Partial) is closely related to Horsegram [Macrotyloma uniflorum (Lam.) Verdc.] yellow mosaic virus isolate (HgYMV-LK: 09-Bean) reported in Sri Lanka. Further, the DNA sequence of BYVD-GN-SL-Partial was distinctively clustered with the Indian HgYMV sequences and positioned in between the Mungbean yellow mosaic virus (MYMV) sequences.