Microarray-Based Genetic Mapping Using Soybean Near-Isogenic Lines and Generation of SNP Markers in the Rag1 Aphid-Resistance Interval

A strategy using near-isogenic lines (NILs) and Affymetrix Soybean GeneChip microarrays was employed to identify genetic markers closely linked to the soybean aphid [Aphis glycines Matsumura (Hemiptera: Aphididae)] resistance gene Rag1 in soybean [Glycine max (L.) Merr.]. Genomic DNA from the aphid-resistant cultivar Dowling and the aphid-susceptible cultivar Dwight was labeled and hybridized to arrays, identifying more than 1500 putative single feature polymorphisms (SFPs) between these genotypes. To find polymorphisms closely linked to the Rag1 aphid-resistance locus, genomic DNA samples from two NILs developed through backcrossing Rag1 from Dowling four times to Dwight were also hybridized. Comparison of hybridization signals between the NILs and the recurrent parent identified more than 70 SFPs in each NIL between the NIL and the recurrent parent genotype. There were 22 SFPs shared by both NILs, representing molecular markers putatively linked to Rag1. Four selected SFPs were converted to SNP markers and confirmed by conventional genetic mapping to be closely linked to Rag1. The technique that we describe can be used to identify polymorphisms in a genetic region of interest and generate molecular markers closely linked to an agronomically important trait using a suitable oligonucleotide microarray.