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Development of SNP Assays for Marker-Assisted Selection of Two Southern Root-Knot Nematode Resistance QTL in Soybean

^a Dep. of Crop and Soil Sci., Univ. of Georgia, Center for Applied Genetic Technologies, 111 Riverbend Rd., Athens, GA 30602
^b Dep. of Plant Pathology, Univ. of Georgia, 2106 Miller Plant Sciences Bldg., Athens, GA 30602

View larger version (16K): [in this window] [in a new window]   Figure 1. Soybean composite genetic map in the region of the Mi resistance quantitative trait loci on linkage group (LG)-G (a) and LG-O (b) (http://soybase.org; verified 16 April 2007). The bacterial artificial chromosome (BAC) clones were positive clones for the SSR markers. The BAC clones prefixed with "IS" (Iowa State University) or "UM" (University of Minnesota) were from the ‘Williams 82’ and ‘Faribault’ BAC libraries, respectively.

View larger version (33K): [in this window] [in a new window]   Figure 2. Polymorphic sites identified from PI 96354 and Bossier. A) sequences from the Satt358 containing genomic DNA clone, B) sequences from the Satt199 containing genomic DNA clone, C) sequences from the Satt012 containing genomic DNA clone.

View larger version (14K): [in this window] [in a new window]   Figure 3. Optimization of direct hybridization (DH) assay. SNP358 marker was genotyped across the F2:3 population from the cross of PI 96354 x Bossier using different length of probes and different hybridization temperature conditions. Data are presented as the log10 [(fraction of PI 96354 allele signal + 0.01)/(fraction of Bossier allele signal + 0.01)] versus total mean fluorescence intensity (MFI) of two alleles (Hirschhorn et al., 2000). Genotypes are represented by homozygotes for PI 96354 allele (), heterozygotes (), and homozygotes for Bossier allele () determined by the band sizes of the Satt358 SSR marker. (H.T. = hybridization temperature; ASO = allele-specific oligonucleotide).

View larger version (15K): [in this window] [in a new window]   Figure 4. Multiplex single nucleotide polymorphism (SNP) genotyping across the F2:3 population from the cross of PI 96354 x Bossier. Data are presented as the log10 [(fraction of PI 96354 allele signal + 0.01)/(fraction of Bossier allele signal + 0.01)] versus total mean fluorescence intensity (MFI) of two alleles (Hirschhorn et al., 2000). Genotypes at SNP358 and SNP199 are represented by homozygotes for PI 96354 allele (), heterozygotes (), and homozygotes for Bossier allele () determined by the band sizes of the SSR marker Satt358 and SSR marker Satt199, respectively.