Molecular Diversity Analysis of Coat Protein Gene Encoded by Legume Begomoviruses and PCR Assay to Detect Yellow Mosaic Viruses Infecting Soybean in India

Abstract

Aim: Coat protein (CP) genes encoded by Legume yellow mosaic viruses (LYMVs) were analysed to study molecular diversity and to devise effective PCR based assay to distinguish major Begomovirus species (Mungbean yellow mosaic India virus and Mungbean yellow mosaic virus) infecting soybean Design of the Study: All the known coat protein gene sequences encoded by begomoviruses causing yellow mosaic disease (YMD) in legumes were obtained from GenBank. YMD infected soybean leaf samples were collected from different parts of India during Kharif 2012 and species of virus infections identified using CP gene based primers in a PCR assay. Methodology: DNA polymorphism, phylogeny, and test of theory of neutral evolution were studied to decode variability and molecular evolutionary lineage of LYMVs encoded CP gene. CP based primers have been designed and employed to differentiate MYMIV and MYMV using infected soybean samples collected across India. Results: Nucleotide diversity and DNA polymorphism studies revealed relatively low levels of diversity in CP genes encoded by LYMV isolates. Test of neutral evolution and codon substitution analysis also reiterated the operation of purifying selection indicating deleterious mutations in CP gene are not tolerated in the LYMV population. Geographical confinement of species of yellow mosaic viruses infecting soybean is further validated as diseased soybean samples collected from Northern and Central India showed infection due to MYMIV and samples obtained from Southern and Western India were infected with MYMV. Conclusion: Evolutionary genomic analysis revealed conserved nature of LYMV encoded CP gene however a variable region has been identified.PCR assay for differentiation of two major begomoviruses viz.,) MYMV and MYMIV infecting soybean in India has been standardised. This is the first report of population genetics in LYMVs and it’s implications for yellow mosaic disease (YMD) resistance breeding in soybean are also discussed.