Chapter Two Biological and Molecular Diversity of Naturally Occurring Resistance Breaking Strains of Soybean mosaic virus

Resistance to Soybean mosaic virus (SMV; Genus Potyvirus; Family Potyviridae) is controlled by single dominant genes at three distinct loci, Rsv1, Rsv3 and Rsv4, in soybean (Glycine max [L.] Merr.). SMV isolates are classified into pathotypes G1 through G7 based on the differential reactions on resistant soybean cultivars. Most SMV isolated in the USA is of the G1 to G3 pathotypes. Since the cultivar Hutcheson carrying the Rsv1 allele for resistance to SMV G1 to G3 is widely used in the Mid-South region of the USA, SMV isolates that overcome that resistance are of particular interest for their biological and genomic diversity, as well as for their potential economic importance. Greenhouse experiments showed that SMV isolates collected between 1998 and 2002 have characteristics of the G5 and G6 pathotypes, and produce distinctive symptoms on Hutcheson. These resistance-breaking (RB) isolates systemically invaded cvs. Hutcheson and York, induced tip necrosis on Kwanggyo, and showed no symptoms on PI 96983 indicative of an extreme resistance (ER) response. These new isolates also induced a diversity of responses on Marshall and PI 507389 and on L29, an Rsv3 carrying cultivar. Regions of the SMV genome encoding the coat protein of these RB isolates were PCR amplified and sequenced. Phylogenetic analysis of the coat protein showed that RB isolates of SMV are G6-like based on their nucleotide sequence. The coat protein is diverse at the amino and carboxy termini and highly conserved in the core region. The RB isolates were also G6-like based on the amino acid sequence of the coat protein. Amino acid substitutions were detected at 16 positions, indicating higher diversity than previously reported for SMV. All of the RB isolates retained the DAG triplet required for aphid transmission Emergence of SMV-G6 like isolates is a threat to resistance in soybean carrying the Rsv1 allele.