The rhg1-a (Rhg1 low-copy) nematode resistance source harbors a copia-family retrotransposon within the Rhg1-encoded α-SNAP gene
Soybean growers widely use the Resistance to Heterodera glycines 1 (Rhg1) locus to reduce yield losses caused by soybean cyst nematode (SCN). Rhg1 is a tandemly repeated four gene block. Two classes of SCN resistance-conferring Rhg1 haplotypes are recognized: rhg1-a (\"Peking-type\", low copy number, 3 or fewer Rhg1 repeats) and rhg1-b (\"PI 88788-type\", high copy number, 4 or more Rhg1 repeats). The rhg1-a and rhg1-b haplotypes encode -SNAP (alpha-Soluble NSF Attachment Protein) variants -SNAPRhg1LC and -SNAPRhg1HC respectively, with differing atypical C-terminal domains, that contribute to SCN-resistance. Here we report that rhg1-a soybean accessions harbor a copia retrotransposon within their Rhg1 Glyma.18G022500 (-SNAP-encoding) gene. We termed this retrotransposon \"RAC\", for Rhg1 alpha-SNAP copia. Soybean carries multiple RAC-like retrotransposon sequences. The Rhg1 RAC insertion is in the Glyma.18G022500 genes of all true rhg1-a haplotypes we tested and was not detected in any examined rhg1-b or Rhg1WT (single-copy) soybeans. RAC is an intact element residing within intron 1, anti-sense to the rhg1-a -SNAP open reading frame. RAC has intrinsic promoter activities, but overt impacts of RAC on transgenic -SNAPRhg1LC mRNA and protein abundance were not detected. From the native rhg1-a RAC+ genomic context, elevated -SNAPRhg1LC protein abundance was observed in syncytium cells, as was previously observed for -SNAPRhg1HC (whose rhg1-b does not carry RAC). Using a SoySNP50K SNP corresponding with RAC presence, just [~]42% of USDA accessions bearing previously identified rhg1-a SoySNP50K SNP signatures harbor the RAC insertion. Subsequent analysis of several of these putative rhg1-a accessions lacking RAC revealed that none encoded -SNAPRhg1LC, and thus they are not rhg1-a. rhg1-a haplotypes are of rising interest, with Rhg4, for combating SCN populations that exhibit increased virulence against the widely used rhg1-b resistance. The present study reveals another unexpected structural feature of many Rhg1 loci, and a selectable feature that is predictive of rhg1-a haplotypes.