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Title: GENOME POLYMORPHISM IDENTIFIES A SUBTILISIN-LIKE PROTEASE NEAR THE RHG4 LOCUS IN SOYBEAN

Author
item NELSEN, N - CLEMSON UNIVERSITY
item LI, Z - CLEMSON UNIVERSITY
item WARNER, A - CLEMSON UNIVERSITY
item Matthews, Benjamin - Ben

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/28/2004
Publication Date: 11/28/2004
Citation: Nelsen, N., Li, Z., Warner, A., Matthews, B.F. 2004. Genome polymorphism identifies a subtilisin-like protease near the rhg4 locus in soybean. Crop Science 44: 264-273.

Interpretive Summary: The soybean cyst nematode is the major pest of soybean in the United States and causes an estimated one billion dollars in damage annually. There are genes in exotic soybean germplasm that provide some protection against some of the races of soybean cyst nematode. We identified a piece of DNA near one of these resistance genes. The DNA contains the full gene encoding a novel soybean protease responsible for the breakdown or digestion of protein molecules and the DNA includes the gene's expression controls. The expression of this gene is elevated about four-fold in the SCN-resistant soybean, PI 437.654 compared to Williams 82, which is susceptible to SCN. This finding is important to scientists studying plant resistance to pests and pathogens because the protein encoded by this gene is believed to be secreted to the plant cell wall and may play a role in reorganization of cell wall components during normal plant development and in the defense response to the soybean cyst nematode.

Technical Abstract: PI 437.654 BAC clone 15G19 was used to detect restriction fragment length polymorphism (RFLP) between Faribault, Essex, Williams 82, PI 209.332, and PI 437.654, which display different responses to soybean cyst nematode. The polymorphism was localized to an 8 kb BamHI fragment that contained the promoter region and partial coding sequence of a novel soybean subtilisin-like protease, GmSUB1. Promoter elements for root gene expression, regulation of pathogenesis-related genes, and coordination of multiple gene expression, and a novel 90 bp direct repeat were identified. The complete sequence of GmSUB1 (GenBank accession number AY277949) shows 74% similarity to AIR3 of Arabidopsis and less similarity with previously isolated soybean subtilases. A gene-specific probe identified a 4-fold increase in GmSUB1 copy number in PI 437.654 compared to Williams 82. A 2- to 3-fold increase in steady-state GmSUB1 mRNA levels in PI 437.654 was also observed using relative quantitative real-time PCR. Previous localization of BAC 15G19 to the Rhg4 resistance region, genomic polymorphism of GmSUB1 and difference in gene copy number at this region between PI 437.654 and Williams 82, and the increased level of gene expression in PI 437.654 may support a potential functional role in response to pathogen attack. GmSUB1 is believed to be secreted into the extracellular matrix, and may play a role in reorganization of cell wall components during normal plant development and in the defense response.