A physical map of a gene-dense region in soybean linkage group A2 near the black seed coat and Rhg ₄ loci

Abstract 

Soybean (Glycine max L. Merrill) linkage group A2 contains a major resistance gene to the soybean cyst nematode (Heterodera glycines Ichinohe) at the Rhg ₄ locus near a gene encoding aspartokinase homoserine dehydrogenase (AK-HSDH) and also near the I locus affecting seed coat color. To identify clones related to this region of the genome, we used a PCR assay using primers designed from a gene encoding AK-HSDH to screen approximately 40,000 clones from a bacterial artificial chromosome (BAC) library constructed from genomic DNA of the susceptible cv. Williams 82. The identified BACs were screened with a second PCR assay using primers designed from DNA sequence associated with the I locus to confirm the location of the BACs. Only BAC Gm_ISb001_056_G02 (56G2) was positive for both assays. BAC 56G2 contains several genes previously associated with stress or defense response including genes with high sequence similarity to those encoding chalcone synthase, glucosyl-transferase, a heat-shock transcription factor, a membrane-associated salt-inducible protein, adenosyl homocysteinase, a protein kinase, and a G10-like protein. The map contributes to our understanding of the organization of the soybean genome and to the completion of a physical map of the soybean genome. In addition, the genes identified provide landmarks to identify BAC clones near the Rhg ₄ locus in resistant soybean genomic libraries and provide a foundation for comparison of soybean cyst nematode resistant and -susceptible DNA sequences in this region.