High-throughput genotyping for a polymorphism linked to soybean cyst nematode resistance gene Rhg4 by using TaqmanTM probes

An individual soybean breeder can generate over one hundred thousand new genotypes each year. The efficiency of selection in these populations could be improved if these genotypes were effectively screened with one DNA marker that identified an important gene, and if laboratory throughput was high and costs were low. Our aim was to develop a rapid genotyping procedure for resistance to the soybean cyst nematode. A high-throughput genotyping method was developed with fluorogenic probes to distinguish between two insertion polymorphisms in alleles of an AFLP marker that is located about 50 kbp from the Rhg4 gene candidate. The assay uses the 5 exonuclease activity of Taq polymerase in conjunction with fluorogenic probes for each allele. The method can be used for scoring the polymorphism in a recombinant inbred line population and for screening parent lines in a breeding program. The Taqman^TM method of determining genotype was accurate in 90% of scores in the RIL population compared to 95% accuracy with electrophoresis. Among 94 cultivars that are parents in our breeding program allele 2 that is derived from the sources of resistance to SCN was common in resistant cultivars (30 of 56) but rare in susceptible cultivars (3 of 38). Therefore, this method can be applied to automated large-scale genotyping for soybean breeding programs.