AUGUSTUS is a software tool for gene prediction in eukaryotes based on a Generalized Hidden Markov Model, a probabilistic model of a sequence and its gene structure. Like most existing gene finders, the first version of AUGUSTUS returned one transcript per predicted gene and ignored the phenomenon of alternative splicing. Herein, we present a WWW server for an extended version of AUGUSTUS that is able to predict multiple splice variants. To our knowledge, this is the first ab initio gene finder that can predict multiple transcripts. In addition, we offer a motif searching facility, where user-defined regular expressions can be searched against putative proteins encoded by the predicted genes. The AUGUSTUS web interface and the downloadable open-source stand-alone program are freely available from .

The soybean Rsv1 gene for resistance to soybean mosaic virus (SMV; Potyvirus) has previously been described as a single-locus multi-allelic gene mapping to molecular linkage group (MLG) F. Various Rsv1 alleles condition different responses to the seven (G1-G7) described strains of SMV, including extreme resistance, localized and systemic necrosis, and mosaic symptoms. We describe the cloning of a cluster of NBS-LRR resistance gene candidates from MLG F of the virus-resistant soybean line PI96983 and demonstrate that multiple genes within this cluster interact to condition unique responses to SMV strains. In addition to cloning 3gG2, a strong candidate for the major Rsv1 resistance gene from PI96983, we describe various unique resistant and necrotic reactions coincident with the presence or absence of other members of this gene cluster. Responses of recombinant lines from a high-resolution mapping population of PI96983 (resistant) ϫ Lee 68 (susceptible) demonstrate that more than one gene in this region of the PI96983 chromosome conditions resistance and/or necrosis to SMV. In addition, the soybean cultivars Marshall and Ogden, which carry other previously described Rsv1 alleles, are shown to possess the 3gG2 gene in a NBS-LRR gene cluster background distinct from PI96983. These observations suggest that two or more related non-TIR-NBS-LRR gene products are likely involved in the allelic response of several Rsv1-containing lines to SMV.

reaction to SMV (Buzzell and Tu, 1989). Finally, an SMV resistance locus was reported by Ma et al. (1995). Soybean mosaic virus (SMV) is a prevalent viral pathogen of soy-This gene, referred to in this paper as Rsv4, confers bean [Glycine max (L.) Merr.] wherever it is grown. Several genes that confer resistance in soybean to soybean mosaic virus have been resistance to all known strains of SMV. The Rsv4 allele identified. One of these resistance loci, Rsv4, confers resistance to all reported by Ma et al. (1995) is derived from the line the known strain groups of SMV. This study was conducted to deter-PI486355, which was shown to contain two resistance mine the map position of the Rsv4 locus in the soybean genome. A loci, one which is allelic to Rsv1 and another (Rsv4) population of 255 F 2 individuals from the cross of the SMV resistant which is not allelic at either the Rsv1 or Rsv3 locus. It is line LR2 (Rsv4) by the susceptible line Lee68 (rsv4) was evaluated of interest to note that this resistance gene is completely in a mapping study. DNA from 12 to 15 F 2 individuals being either dominant, in contrast to Rsv1 alleles which show syshomozygous resistant or susceptible were pooled to produce bulk temic necrosis in the heterozygous state (Chen et al., resistant and bulk susceptible DNA samples. Parents and bulks were 1994). The Rsv4 locus from PI486355 shows resistance screened with 101 AFLP primer pairs and two linked polymorphisms without necrosis in both the heterozygous and homozywere identified. A putative linked marker, amplified by the primers Mse-AAA and Eco-AAG, was converted to a restriction fragment

Soybean mosaic virus (SMV) is a major viral pathogen, affecting soybean [Glycine max (L.) Merr.] production worldwide. The Rsv3 gene of soybean confers resistance to three of the most virulent strains (G5-G7) of SMV. The objectives of this study were to map Rsv3 and develop polymerase chain reaction (PCR) based markers for marker-assisted selection (MAS) purposes. Disease-response data were collected from two F(2) mapping populations, L29 (Rsv3) x Lee68 (rsv3) and Tousan 140 (Rsv3) x Lee68 (rsv3). Bulk segregant analysis based on amplified fragment length polymorphism (AFLP) markers demonstrated that the Rsv3 locus maps to the soybean molecular linkage group (MLG) B2 between restriction fragment length polymorphism (RFLP) markers A519 and Mng247. These two tightly linked RFLP markers were converted to PCR-based markers to expedite MAS. Sequence analysis of the Mng247 genomic region revealed similarity to the consensus sequence of a leucine-rich repeat (LRR) characteristic of the extracellular LRR class of disease resistance genes. Results from this study will be useful in pyramiding viral resistance genes and in cloning the Rsv3 gene.

Soybean mosaic virus (SMV) and peanut mottle virus (PMV) are two potyviruses that cause yield losses and reduce seed quality in infested soybean (Glycine max (L.) Merr.) fields throughout the world. Rsv1 and Rpv1 are genes that provide soybean with resistance to SMV and PMV, respectively. Isolating and characterizing Rsv1 and Rpv1 are instrumental in providing insight into the molecular mechanism of potyvirus recognition in soybean. A population of 1056 F2 individuals from a cross between SMV- and PMV-resistant line PI 96983 (Rsv1 and Rpv1) and the susceptible cultivar 'Lee 68' (rsv1 and rpv1) was used in this study. Disease reaction and molecular-marker data were collected to determine the linkage relationship between Rsv1, Rpv1, and markers that target candidate disease-resistance genes. F2 lines showing a recombination between two of three Rsv1-flanking microsatellite markers were selected for fine mapping. Over 20 RFLP, RAPD, and microsatellite markers were used to map 38 loci at high-resolution to a 6.8-cM region around Rsv1 and Rpv1. This study demonstrates that Rsv1 and Rpv1 are tightly linked at a distance of 1.1 cM. In addition, resistance-gene candidate sequences were mapped to positions flanking and cosegregating with these resistance loci. Based on comparisons of genetic markers and disease reactions, it appears likely that several tightly linked genes are conditioning a resistance response to SMV. We discuss the specifics of these findings and investigate the utility of two disease resistance related probes for the screening of SMV or PMV resistance in soybean.