The ( low-copy) nematode resistance source harbors a copia-family retrotransposon within the encoded α-SNAP gene.

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