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GENOMICS, MOLECULAR GENETICS & BIOTECHNOLOGY

Genomic Polymorphism Identifies a Subtilisin-Like Protease near the Rhg4 Locus in Soybean

^a Dep. of Crop and Soil Environmental Science, 276 Poole Agricultural Center, Clemson Univ., Clemson, SC 29634-0359
^b Agronomy College, Shanxi Agricultural Univ., Taigu, Shanxi Province 030801, P.R. China
^c USDA-ARS-PSI, Soybean Genomics & Improvement Lab., Bldg. 006, Room 118, BARC-West, 10300 Baltimore Blvd., Beltsville, MD 20705-2350

^* Corresponding author (hskrpsk{at}clemson.edu).

Soybean [Glycine max (L.) Merr.] germplasm PI 437654 exhibits broad resistance to soybean cyst nematode (Heterodera glycines Ichinohe, SCN). Probes derived from PI 437654 bacterial artificial chromosome (BAC) clone 15G19 at the Rhg4 locus detected a restriction fragment length polymorphism (RFLP) between resistant and susceptible germplasms. Detailed RFLP analysis using restriction fragments from BAC clone 15G19 associated the polymorphism with an 8-kb BamHI fragment containing the promoter region and partial coding sequence of a novel soybean subtilisin-like protease, GmSUB1. Complete sequence of GmSUB1 was determined (GenBank AY277949). Regulatory elements for root gene expression, pathogen response, coordinated multiple-gene expression, and a novel 90-bp direct repeat were identified. GmSUB1 shows 74% similarity to Arabidopsis thaliana AIR3. Hybridization analyses indicate that PI 437654 contains only full-length copies of GmSUB1, whereas susceptible germplasm ‘Williams 82’ contains both full-length and truncated copies of the gene. A 4-fold increase in GmSUB1 copy number, and a corresponding 2- to 3-fold increase in steady state GmSUB1 mRNA levels, was observed in PI 437654 compared with Williams 82. Localization and polymorphism of GmSUB1 within the Rhg4 resistance region, and increases in GmSUB1 gene copy number and expression in PI 437654 compared with Williams 82 infers a functional role in the pathogen response. GmSUB1 is believed to be secreted into the extracellular matrix, and may function in reorganization of cell wall components during plant development and in the defense response.

Abbreviations: BAC, bacterial artificial chromosome • cDNA, complementary DNA • mRNA, messenger RNA • PCR, polymerase chain reaction • RFLP, restriction fragment length polymorphism • SCN, soybean cyst nematode

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Crop Science 2004 44: 1-4. [Full Text]