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United States Department of Agriculture

Agricultural Research Service

Title: A Physical Map of a Gene-Dense Region in Soybean

Authors
item Lewers, Kimberly
item Heinz, Ruth -
item Beard, Hunter
item Marek, Laura - IOWA STATE UNIVERSITY
item Matthews, Benjamin

Submitted to: Plant Molecular Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 25, 2001
Publication Date: N/A

Interpretive Summary: The soybean cyst nematode is the major pest of soybean and causes an estimated 1.5 billion dollars loss to the soybean crop in the U.S. each year. We physically isolated a large genomic DNA sequence from the soybean cultivar Williams 82 which is susceptible to the soybean cyst nematode. The isolated DNA region resides close to the Rhg4 locus, one of the genes that confer resistance to the soybean cyst nematode race 3 in resistant soybean cultivars. The genomic DNA was subcloned as smaller pieces and portions of the DNA were sequenced and mapped to provide landmarks throughout the clone. The DNA sequences were compared to sequences in computer databases to determine their similarity to known genes. Several DNA sequnces had high similarity to known genes, such as chalcone synthase and peroxidase. These landmarks will be useful to researchers as probes to identify and order clones from a soybean cultivar resistant to soybean cyst nematode attack. Then DNA sequences from this region can be compared between soybean cultivars that are sensitive and those that are resistant to attack by the soybean cyst nematode. This information will be used by scientists to identify the gene responsible for conferring resistance to the soybean cyst nematode and will enable soybean breeders to develop soybean cultivars with better resistance to this nematode.

Technical Abstract: Soybean (Glycine max L. Merrill) Linkage Group A2 contains a major resistance gene to the soybean cyst nematode (Heterodera glycines Ichinohe) at the Rhg4 locus near a gene encoding aspartokinase homoserine dehydrogenase (AK-HSDH) and also near the I locus affecting seed coat color. A PCR assay using primers designed from a gene encoding AK-HSDH was used to screen approximately 40,000 clones from a bacterial artificia chromosome (BAC) library constructed from genomic DNA of the susceptible cultivar Williams 82 to physically isolate the Rhg4 genomic region. The BACs identified by the screen were assayed by PCR using primers designed from DNA sequence associated with the I locus. Only BAC Gm_ISb001_056_G02 (56G2) was positive for both assays. BAC 56G2, used as a probe against a library of cDNA clones from infected resistant soybean, identified cDNA clones having high sequence similarity to genes encoding chalcone synthase, peroxidase, benzoyl transferase, and a ribosomal protein. EcoR I subclones of the BAC had high sequence similarity to genes encoding AK- HSDH, chalcone synthase, glucosyl-transferase, a heat shock transcription factor, a membrane-associated salt-inducible protein, adenosyl homocysteinase, an RNA-binding protein, a protein kinase, and a G10-like protein. These genes provide landmarks to identify BAC clones near the Rhg4 locus in resistant soybean genomic libraries and provide a foundation for comparison of SCN resistant and susceptible DNA sequences in this region. Observed duplication on both the gene level and the regional level within this BAC may be responsible for reported organizational instability in this part of the genome.

Last Modified: 10/22/2014
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