High-throughput genotyping for a polymorphism linked to soybean cyst nematode resistance gene Rhg4 by using Taqman (TM) probes

An individual soybean breeder call generate over one hundred thousand new g enotypes each year. The efficiency of selection in these populations could be improved if these genotypes were effectively screened with one DNA marke r 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 meth od was developed with fluorogenic probes to distinguish between two inserti on polymorphisms in alleles of an AFLP market 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 fur each allele. The method can be used for scoring the polymorphism in a recombinant inbred li ne population and for screening parent lines in a breeding program. The Taq man(TM) method of determining genotype was accurate in 90% of scores in the RIL population compared to 95% accuracy with electrophoresis. Among 94 cul tivars that are patents in our breeding program allele 2 that is derived fr om the sources of resistance to SCN was common in resistant cultivars (30 o f 56) but rare in susceptible cultivars (3 of 38). Therefore, this: method can be applied to automated large-scale genotyping for soybean breeding pro grams.