Abstract
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, three or fewer Rhg1 repeats) and rhg1‐b (“PI 88788‐type,” high‐copy number, four or more Rhg1 repeats). The rhg1‐a and rhg1‐b haplotypes encode α‐SNAP (alpha‐Soluble NSF Attachment Protein) variants α‐SNAPRhg1LC and α‐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 (α‐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 α‐SNAP open reading frame. RAC has intrinsic promoter activities, but overt impacts of RAC on transgenic α‐SNAPRhg1LC mRNA and protein abundance were not detected. From the native rhg1‐a RAC+ genomic context, elevated α‐SNAPRhg1LC protein abundance was observed in syncytium cells, as was previously observed for α‐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 α‐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.
Highlights
To thrive in their natural environments, organisms must continually sense and respond to changing conditions, including biotic and abiotic stresses
The α-SNAPs encoded by the rhg1-a and rhg1-b loci play a key role in soybean cyst nematode (SCN)-resistance (Cook et al, 2012; Cook et al, 2014; Bayless et al, 2016; Liu et al, 2017; Bayless et al, 2018)
The increasing occurrence of SCN populations that at least partially overcome the overwhelmingly utilized "PI 88788-type" rhg1-b resistance source is an important concern for soybean breeders and growers (McCarville et al, 2017)
Summary
To thrive in their natural environments, organisms must continually sense and respond to changing conditions, including biotic and abiotic stresses. Transposable elements (TEs) may insertionally disrupt genes, or if TE activity is repressed by epigenetic transcriptional silencing, small interfering RNAs and chromatin condensation, this can impact the expression of nearby genes (Sigman and Slotkin, 2016). Cis-regulatory motifs within certain TEs can recruit stress-responsive host transcriptional factors, thereby influencing nearby host gene expression and potentially conferring a host benefit (Slotkin and Martienssen, 2007; Woodrow et al, 2010; Matsunaga et al, 2012; McCue and Slotkin, 2012; Cavrak et al, 2014; Makarevitch et al, 2015; Matsunaga et al, 2015; Negi et al, 2016; Galindo-Gonzalez et al, 2017). Numerous studies report TEs lying within or adjacent to putative plant immune genes, potential influences on host genes or positive effects are often not apparent (Bhattacharyya et al, 1997; Henk et al, 1999; Wawrzynski et al, 2008)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
