Therhg1-a(Rhg1low-copy) nematode resistance source harbors a copia-family retrotransposon within theRhg1-encoded α-SNAP gene

Abstract

AbstractSoybean growers widely use theResistance toHeteroderaglycines1 (Rhg1) locus to reduce yield losses caused by soybean cyst nematode (SCN).Rhg1is a tandemly repeated four gene block. Two classes of SCN resistance-conferringRhg1haplotypes are recognized:rhg1-a(“Peking-type”, low copy number, 3 or fewerRhg1repeats) andrhg1-b(“PI 88788-type”, high copy number, 4 or moreRhg1repeats). Therhg1-aandrhg1-bhaplotypes encode α-SNAP (alpha-SolubleNSFAttachmentProtein) variants α-SNAPRhg1LC and α-SNAPRhg1HC respectively, with differing atypical C-terminal domains, that contribute to SCN-resistance. Here we report thatrhg1-asoybean accessions harbor a copia retrotransposon within theirRhg1 Glyma.18G022500(α-SNAP-encoding) gene. We termed this retrotransposon “RAC”, forRhg1alpha-SNAPcopia. Soybean carries multipleRAC-like retrotransposon sequences. TheRhg1 RACinsertion is in theGlyma.18G022500genes of all truerhg1-ahaplotypes we tested and was not detected in any examinedrhg1-borRhg1WT(single-copy) soybeans.RACis an intact element residing within intron 1, anti-sense to therhg1-a α-SNAPopen reading frame.RAChas intrinsic promoter activities, but overt impacts ofRACon transgenic α-SNAPRhg1LC mRNA and protein abundance were not detected. From the nativerhg1-a RAC+genomic context, elevated α-SNAPRhg1LC protein abundance was observed in syncytium cells, as was previously observed for α-SNAPRhg1HC (whoserhg1-bdoes not carryRAC). Using a SoySNP50K SNP corresponding withRACpresence, just ∼42% of USDA accessions bearing previously identifiedrhg1-aSoySNP50K SNP signatures harbor theRACinsertion. Subsequent analysis of several of these putativerhg1-aaccessions lackingRACrevealed that none encodedα-SNAPRhg1LC, and thus they are notrhg1-a.rhg1-ahaplotypes are of rising interest, withRhg4, for combating SCN populations that exhibit increased virulence against the widely usedrhg1-bresistance. The present study reveals another unexpected structural feature of manyRhg1loci, and a selectable feature that is predictive ofrhg1-ahaplotypes.