S. A. Tolin

Recombination Within a Nucleotide-Binding-Site/Leucine-Rich-Repeat Gene Cluster Produces New Variants Conditioning Resistance to Soybean Mosaic Virus in Soybeans

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) × 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.

Fine mapping and candidate gene discovery of the soybean mosaic virus resistance gene, Rsv4.

Soybean mosaic virus (SMV) is a prevalent virus infecting soybean (Glycine max L. Merr) worldwide. The incorporation of Rsv4, conferring resistance to all currently known strains in the United States, can assist in creating durable virus resistance in soybean. Additionally, lines heterozygous at the Rsv4 locus often express a late susceptible phenotype, showing symptoms only in mid to late vegetative growth. In this study the whole‐genome shotgun sequence (WGS) of soybean was utilized for fine mapping and examining potential Rsv4 gene candidates in two populations. Six markers, designed from the WGS, were used to localize Rsv4 in the same, 1.3‐cM region in both mapping populations, a physical interval of less than 100 kb on chromosome 2. This region contained no sequences previously related to virus resistance, namely nucleotide binding site‐leucine rich repeat gene sequences or eukaryotic translation initiation factors. Instead, sequence analysis revealed several predicted transcription factors and unknown protein products. We conclude that Rsv4 likely belongs to a new class of resistance genes that interfere with viral infection and cell‐to‐cell movement, and delay vascular movement.

The Rsv3 Locus Conferring Resistance to Soybean Mosaic Virus is Associated with a Cluster of Coiled-Coil Nucleotide-Binding Leucine-Rich Repeat Genes

The Soybean mosaic virus (SMV) resistance locus, Rsv3, previously mapped between markers A519F/R and M3Satt in the soybean molecular linkage group B2 (chromosome 14), has been characterized by examination of the soybean genome sequence. The 154 kbp interval encompassing Rsv3 contains a family of closely related coiled‐coil nucleotide‐binding leucine‐rich repeat (CC‐NB‐LRR) genes. Tightly linked to this region are additional CC‐NB‐LRR genes and several leucine‐rich repeat receptor‐like kinase (LRR‐RLK) genes, thereby indicating that members of both multigene families constitute a heterogeneous cluster at the Rsv3 chromosomal region. To further confirm the sequence and genetic map concordance, we developed 16 markers from the genomic sequence including predicted CC‐NB‐LRR genes and their flanking sequences. Mapping of the resultant markers in three populations showed parallel alignment between the genetic and sequence maps in the Rsv3‐containing region. Phylogenetic analysis of five CC‐NB‐LRR genes including a pseudogene showed they were highly similar to each other and formed a subclade within a CC‐NB‐LRR gene clade with representatives from several plant families including legume species. These results demonstrate that the Rsv3 locus is associated with this cluster of CC‐NB‐LRR genes, thereby suggesting that the Rsv3 gene most likely encodes a member of this gene family. In addition, information from this study should facilitate marker‐assisted selection and pyramiding of resistance genes.

Genomics of Viral–Soybean Interactions

Virus infected soybean can be found in all soybean growing areas of the world. To date, over 67 viruses have been identified that are capable of replicating in the soybean plant. Twenty-seven of the 67 are currently a concern or have the potential to be a problem in soybean production systems (Tolin and Lacy 2004). The most prevalent viruses causing significant crop losses are made of single-stranded, positive-sense RNA from the Potyviridae and Comoviridae families, which this chapter will focus on. Soybean mosaic virus (SMV), which belongs to the Potyviridae, has been known to cause total crop loss (Kwon and Oh 1980) and occurs in all soybean growing areas of the world. Bean pod mottle virus (BPMV) is a member of the Comoviridae family and has increased its geographical distribution throughout the United States and poses a significant risk to soybean growers, particularly those in the North Central and Northern Great Plains states. Together the two viruses, BPMV and SMV, interact synergistically and drastically reduce yield and seed quality compared to each disease alone. Therefore, priority was placed on improving cultivar resistance often through utilization of molecular and genomic approaches. The most common method of controlling SMV in soybean is through development of resistant cultivars often carrying a single hypersensitive resistant (R) gene. However, recent reports of resistance-breaking (RB) stains in Japan and Korea (Choi et al. 2005; Koo et al. 2005; Saruta et al. 2005) shifted breeders and molecular biologists to incorporate durable forms of resistance into cultivars through gene pyramiding or transgenic methods. As SMV is seed borne, seed distribution processes such as those used in germplasm exchange programs, serve to spread the virus to different environments and other areas of the world. Disease management of BPMV through genetic resistance is not possible as no soybean cultivars with resistance to BPMV are commercially available. Only a few experimental transgenic lines conferring resistance against BPMV are available.

Candidate Gene Sequence Analyses toward Identifying Rsv3 -Type Resistance to Soybean Mosaic Virus

Rsv3 locus confers strain‐specific resistance to Soybean mosaic virus The Rsv3 locus contains a cluster of five NB‐LRR resistance genes Comprehensive study of five Rsv3 candidate NB‐LRR gene sequences was conducted Comparisons were done between Rsv3‐type resistant vs. rsv‐type susceptible soybeans Glyma14g38533 gene was identified as the most likely candidate gene for Rsv3

Candidate Gene Sequence Analyses toward Identifying -Type Resistance to

Rsv3 locus confers strain‐specific resistance to Soybean mosaic virus The Rsv3 locus contains a cluster of five NB‐LRR resistance genes Comprehensive study of five Rsv3 candidate NB‐LRR gene sequences was conducted Comparisons were done between Rsv3‐type resistant vs. rsv‐type susceptible soybeans Glyma14g38533 gene was identified as the most likely candidate gene for Rsv3

Soybean mosaic virus: A successful potyvirus with a wide distribution but restricted natural host range

TAXONOMYnSoybean mosaic virus (SMV) is a species within the genus Potyvirus, family Potyviridae, which includes almost one-quarter of all known plant RNA viruses affecting agriculturally important plants. The Potyvirus genus is the largest of all genera of plant RNA viruses with 160 species.nnnPARTICLEnThe filamentous particles of SMV, typical of potyviruses, are about 7500xa0Å long and 120xa0Å in diameter with a central hole of about 15xa0Å in diameter. Coat protein residues are arranged in helices of about 34xa0Å pitch having slightly less than nine subunits per turn.nnnGENOMEnThe SMV genome consists of a single-stranded, positive-sense, polyadenylated RNA of approximately 9.6xa0kb with a virus-encoded protein (VPg) linked at the 5 terminus. The genomic RNA contains a single large open reading frame (ORF). The polypeptide produced from the large ORF is processed proteolytically by three viral-encoded proteinases to yield about 10 functional proteins. A small ORF, partially overlapping the P3 cistron, pipo, is encoded as a fusion protein in the N-terminus of P3 (P3Nxa0+xa0PIPO).nnnBIOLOGICAL PROPERTIESnSMVs host range is restricted mostly to two plant species of a single genus: Glycine max (cultivated soybean) and G.xa0soja (wild soybean). SMV is transmitted by aphids non-persistently and by seeds. The variability of SMV is recognized by reactions on cultivars with dominant resistance (R) genes. Recessive resistance genes are not known.nnnGEOGRAPHICAL DISTRIBUTION AND ECONOMIC IMPORTANCEnAs a consequence of its seed transmissibility, SMV is present in all soybean-growing areas of the world. SMV infections can reduce significantly seed quantity and quality (e.g. mottled seed coats, reduced seed size and viability, and altered chemical composition).nnnCONTROLnThe most effective means of managing losses from SMV are the planting of virus-free seeds and cultivars containing single or multiple R genes.nnnKEY ATTRACTIONSnThe interactions of SMV with soybean genotypes containing different dominant R genes and an understanding of the functional role(s) of SMV-encoded proteins in virulence, transmission and pathogenicity have been investigated intensively. The SMV-soybean pathosystem has become an excellent model for the examination of the genetics and genomics of a uniquely complex gene-for-gene resistance model in a crop of worldwide importance.

Candidate Gene Sequence Analyses towardIdentifying Rsv3-Type Resistance to SoybeanMosaic Virus

Rsv3 locus confers strain‐specific resistance to Soybean mosaic virus The Rsv3 locus contains a cluster of five NB‐LRR resistance genes Comprehensive study of five Rsv3 candidate NB‐LRR gene sequences was conducted Comparisons were done between Rsv3‐type resistant vs. rsv‐type susceptible soybeans Glyma14g38533 gene was identified as the most likely candidate gene for Rsv3