Exploring the Copy Number Variation of Multiple Genes at Rhg1 that Mediates Soybean Cyst Nematode Resistance in Soybean

The rhg1-b (PI88788-derived) allele of the soybean Rhg1 locus is used very widely in commercially grown germplasm as the primary source of resistance against soybean cyst nematode (SCN), the most economically damaging pathogen of soybeans in the United States.  We recently reported map-based cloning of the Rhg1 locus.  Gene silencing unexpectedly demonstrated that three genes in a 31 kb segment at rhg1-b, encoding an apparent amino acid transporter, an apparent α-SNAP protein, and a WI12 (wound-inducible domain) protein with no annotated functions, each contribute to resistance.  Strikingly, while there is one copy of the 31 kb segment per haploid genome in the soybean reference genome and in all other tested susceptible varieties, deep sequencing and fiber-FISH revealed that there are ten tandem copies of the 31 kb repeat in the rhg1-b haplotype.  The distinct Peking-derived Rhg1 allele (which, unlike the PI88788-source, requires the unlinked Rhg4 for effective function), carries three copies of the 31 kb repeat.  Overexpression of any one of the three implicated rhg1-b genes in roots from SCN-susceptible lines was ineffective at conferring SCN resistance, but overexpression together of the three identified genes conferred enhanced SCN resistance.  Hence Rhg1-mediated SCN resistance is conferred by copy number variation that increases the expression of a set of dissimilar genes in a repeated multi-gene segment.  The biochemical mechanism of SCN resistance remains unknown.  Our recent work to further characterize this economically important SCN resistance trait will be discussed.