The rhg1‐a (Rhg1 low‐copy) nematode resistance source harbors a copia‐family retrotransposon within the Rhg1‐encoded α‐SNAP gene

Abstract

Soybean growers widely use the R esistance to H eterodera g lycines 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‐ S oluble N SF A ttachment P rotein) variants α‐SNAP Rhg1 LC and α‐SNAP Rhg1 HC, 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 R hg1 a lpha‐SNAP c opia. 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 Rhg1 WT (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‐SNAP Rhg1 LC mRNA and protein abundance were not detected. From the native rhg1‐a RAC + genomic context, elevated α‐SNAP Rhg1 LC protein abundance was observed in syncytium cells, as was previously observed for α‐SNAP Rhg1 HC (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‐SNAP Rhg1 LC , and thus, they are not rhg1‐a . ...

Sequence Composition of Bacterial Chromosome Clones in a Transgressive Root-Knot Nematode Resistance Chromosome Region in Tetraploid Cotton

“…TEs regulating defense or susceptibility genes also have been reported ( Tsuchiya and Eulgem, 2013 ; Berg et al, 2015 ). An intact copia retrotransposon ( RAC ) was found within intron 1, anti-sense to H. glycines resistance gene rhg1-a α-SNAP open reading frame, and RAC has intrinsic promoter activities in soybean ( Bayless et al, 2019 ). Hu et al (2019) identified the unevenly distributed presence/absence variants of gene structure across the genome between TM-1 and Hai7124 to be mostly copia elements (LTR type) that were found in coding DNA sequence.…”

“…The enzyme serine hydroxymethyltransferase (SHMT) encoded by Rhg4 is associated with the resistance ( Liu et al, 2012 ), and copy number of rhg1 determines soybean resistance or susceptibility ( Cook et al, 2012 , 2014 ). Recently, Bayless et al (2019) found a copia family retrotransposon was harbored within the Rhg1 -encoded α-SNAP (alpha-soluble NSF attachment protein) gene in the rhg1-a ( Rhg1 low-copy) nematode resistance source.…”

Molecular and Cellular Mechanisms Involved in Host-Specific Resistance to Cyst Nematodes in Crops

“…Three genes located in the 31-kilobase segment are required for resistance, which encode for an amino acid transporter, an alpha-soluble NSF (N-ethylmaleimide–sensitive factor) attachment protein (α-SNAP) protein and a wound-inducible domain (WI12) protein ( Cook et al, 2012 ; Guo et al, 2019 ). The rhg1-a and rhg1-b haplotypes encode two different α-SNAP variants ( Liu et al, 2017 ; Bayless et al, 2019 ), but both variants hyperaccumulate at SCN infection sites ( Bayless et al, 2016 , 2019 ; Lakhssassi et al, 2020a ). The rhg1-a encoded α-SNAP carries a copia retrotransposon in its structure named RAC ( Rhg1 α-SNAP copia), which harbors intrinsic transcriptional activity ( Bayless et al, 2019 ).…”

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“…TEs regulating defense or susceptibility genes also have been reported (Tsuchiya and Eulgem, 2013;Berg et al, 2015). An intact copia retrotransposon (RAC) was found within intron 1, anti-sense to H. glycines resistance gene rhg1-a α-SNAP open reading frame, and RAC has intrinsic promoter activities in soybean (Bayless et al, 2019). Hu et al (2019) identified the unevenly distributed presence/absence variants of gene structure across the genome between TM-1 and Hai7124 to be mostly copia elements (LTR type) that were found in coding DNA sequence.…”