Submitted to: The Plant Genome
Publication Type: Peer reviewed journal
Publication Acceptance Date: 6/22/2008
Publication Date: 11/17/2009
Citation: Hudson, K.A., Kim, K., Diers, B., Hudson, M. 2009. Microarray-Based Genetic Mapping Using Soybean Near-Isogenic Lines and Generation of SNP Markers in the Rag1 Aphid-Resistance Interval. The Plant Genome. 1:89-98. Interpretive Summary: In some plant species, hybridization of DNA to microarrays has already been used to find sequence polymorphisms that can be used as markers for genetic mapping. Currently, this technique does not work well when used with crop plants with large genomes. We developed a procedure that is effective for finding polymorphic markers in a large-genome crop, soybean, through DNA hybridization to expression microarrays. The procedure was tested on soybeans carrying a gene for resistance to soybean aphid, a major crop pest. Four genetic markers in close proximity to the aphid resistance gene were developed and shown to be useful for mapping this gene at a finer resolution. This procedure may be used by other researchers to develop new genetic markers quickly using array hybridization, and the markers developed in this study will be used by soybean breeders to genetically map the gene for aphid resistance.
Technical Abstract: 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. Selected SFPs were converted to SNP markers and four of these polymorphisms were genetically mapped to positions close 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 without the need for a genome sequence, genetic or physical map, or existing molecular markers.