An atypical N-ethylmaleimide sensitive factor enables the viability of nematode-resistant Rhg1 soybeans

Abstract

N-ethylmaleimide sensitive factor (NSF) and α-soluble NSF attachment protein (α-SNAP) are essential eukaryotic housekeeping proteins that cooperatively function to sustain vesicular trafficking. The "resistance to 1" () locus of soybean () confers resistance to soybean cyst nematode, a highly damaging soybean pest. loci encode repeat copies of atypical α-SNAP proteins that are defective in promoting NSF function and are cytotoxic in certain contexts. Here, we discovered an unusual allele (-associated NSF on chromosome 07; ) in germplasm. NSF protein modeling to mammalian NSF/α-SNAP complex structures indicated that at least three of the five NSF polymorphisms reside adjacent to the α-SNAP binding interface. NSF exhibited stronger in vitro binding with resistance-type α-SNAPs. NSF coexpression was more protective against α-SNAP cytotoxicity, relative to WT NSF Investigation of a previously reported segregation distortion between chromosome 18 and a chromosome 07 interval now known to contain the NSF gene revealed 100% coinheritance of the allele with disease resistance alleles, across 855 soybean accessions and in all examined progeny from biparental crosses. Additionally, we show that some-mediated resistance is associated with depletion of WT α-SNAP abundance via selective loss of WT α-SNAP loci. Hence atypical coevolution of the soybean SNARE-recycling machinery has balanced the acquisition of an otherwise disruptive housekeeping protein, enabling a valuable disease resistance trait. Our findings further indicate that successful engineering of -related resistance in plants will require a compatible NSF partner for the resistance-conferring α-SNAP.

Whole‐genome re‐sequencing reveals the impact of the interaction of copy number variants of the rhg1 and Rhg4 genes on broad‐based resistance to soybean cyst nematode

“…Recently, Bayless et al . () reported ~300‐bp deletion within the promoter of another SNAP paralog gene ( Glyma.11G234500 ; α‐SNAP Ch11‐ IR) in ‘Forrest’ genotype. The authors cloned the WT locus of the GmSNAP11 from W82 with native promoter and terminator and observed elevated SNAP protein expression in transgenic roots.…”

“…It has been reported that the interaction of two or more alleles (epistasis) plays a major role in an organism's resistance to diseases and pests (Bayless et al ., ; Meksem et al ., ; Nagel, ). The rhg1 GmSNAP18 protein interacts with NSF (N‐ethylmaleimide–sensitive factor) protein and disturbs vesicle trafficking (Bayless et al ., , ). We discovered that soybean germplasm provided a wide range of SCN resistance controlled by natural variants (SNP and CNV) at both the rhg1 and Rhg4 loci.…”

“…Different types of CNV have been observed in diverse organisms, including humans and chimpanzees (Perry et al, 2008), rats (Aitman et al, 2006), Arabidopsis (DeBolt, 2010), extremophile crucifer (Dassanayake et al, 2011) and Plasmodium falciparum (Heinberg et al, 2013). In soybean, it was reported that copy number of three genes collectively, at the rhg1-b locus, encoding a soluble NSF-attachment protein (a-SNAP), an amino acid transporter, and a wound-inducible domain (WI12), mediate nematode resistance in soybean PI 88788 type of resistance (Bayless et al, 2018;Cook et al, 2012). In this study, we provide a strong evidence that CNV of GmSHMT08 at the Rhg4 locus also plays a significant role in SCN resistance.…”

“…Variation in GmSHMT08 and GmSNAP18 promoters in combination with CNV confers additional level of resistance to SCN It is well documented that SNPs in the promoter region, including the 5 0 UTR, can abolish gene function, expression level and localization (Patil et al, 2015). Recently, Bayless et al (2018) reported~300-bp deletion within the promoter of another SNAP paralog gene (Glyma.11G234500; a-SNAP Ch11-IR) in 'Forrest' genotype. The authors cloned the WT locus of the GmSNAP11 from W82 with native promoter and terminator and observed elevated SNAP protein expression in transgenic roots.…”

“…To date, only two major sources of resistance lines, PI 88788 and 'Peking' have been commonly employed in soybean breeding programs (Bayless et al, 2018;Concibido et al, 2004). PI 88788 has eight copies at the rhg1 locus and is the primary source used in commercial breeding programs to reduce SCN damage.…”