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Plant pathogens are constantly under selection pressure for host resistance adaptation. Soybean cyst nematode (SCN, Heterodera glycines) is a major pest of soybean primarily managed through resistant cultivars; however, SCN populations have evolved virulence in response to selection pressures driven by repeated monoculture of the same genetic resistance. Resistance to SCN is mediated by multiple epistatic interactions between Rhg (for resistance to H. glycines) genes. However, the identity of SCN virulence genes that confer the ability to overcome resistance remains unknown. To identify candidate genomic regions showing signatures of selection for increased virulence, we conducted whole genome resequencing of pooled individuals (Pool‐Seq) from two pairs of SCN populations adapted on soybeans with Peking‐type (rhg1‐a, rhg2, and Rhg4) resistance. Population differentiation and principal component analysis‐based approaches identified approximately 0.72–0.79 million SNPs, the frequency of which showed potential selection signatures across multiple genomic regions. Chromosomes 3 and 6 between population pairs showed the greatest density of outlier SNPs with high population differentiation. Conducting multiple outlier detection tests to identify overlapping SNPs resulted in a total of 966 significantly differentiated SNPs, of which 285 exon SNPs were mapped to 97 genes. Of these, six genes encoded members of known stylet‐secreted effector protein families potentially involved in host defence modulation including venom‐allergen‐like, annexin, glutathione synthetase, SPRYSEC, chitinase, and CLE effector proteins. Further functional analysis of identified candidate genes will provide new insights into the genetic mechanisms by which SCN overcomes soybean resistance and inform the development of molecular markers for rapidly screening the virulence profile of an SCN‐infested field. [ABSTRACT FROM AUTHOR]

Summary: The soybean cyst nematode (SCN) is one of the most important causes of soybean yield loss. The major source of genetic resistance to SCN is the Rhg1 repeat, a tandem copy number polymorphism of three genes. The roles of these genes are only partially understood. Moreover, nematode populations virulent on Rhg1‐carrying soybeans are becoming more common, increasing the need to understand the most successful genetic resistance mechanism. Here, we show that a Rhg1‐locus gene (Glyma.18G02270) encoding a wound‐inducible protein (WI12Rhg1) is needed for SCN resistance. Furthermore, knockout of WI12Rhg1 reduces the expression of DELLA18, and the expression of WI12Rhg1 is itself induced by either JA, SA or GA. The content of the defence hormone SA is significantly lower whilst GA12 and GA53 are increased in WI12Rhg1 knockout roots compared with unedited hairy roots. We find that WI12Rhg1 directly interacts with DELLA18 (Glyma.18G040000) in yeast and plants and that double knockout of DELLA18 and its homeolog DELLA11 (Glyma.11G216500) significantly reduces SCN resistance and alters the root morphology. As DELLA proteins are implicated in hormone signalling, we explored the content of defence hormones (JA and SA) in DELLA knockout and unedited roots, finding reduced levels of JA and SA after the knockout of DELLA. Additionally, the treatment of DELLA‐knockout roots with JA or SA rescues SCN resistance lost by the knockout. Meanwhile, the SCN resistance of unedited roots decreases after the treatment with GA, but increases with JA or SA. Our findings highlight the critical roles of WI12Rhg1 and DELLA proteins in SCN resistance through interconnection with hormone signalling. [ABSTRACT FROM AUTHOR]

Summary: Soybean cyst nematode (SCN; Heterodera glycines) is the largest pathogenic cause of soybean yield loss. The Rhg1 locus is the most used and best characterized SCN resistance locus, and contains three genes including one encoding an α‐SNAP protein. Although the Rhg1 α‐SNAP is known to play an important role in vesicle trafficking and SCN resistance, the protein's binding partners and the molecular mechanisms underpinning SCN resistance remain unclear. In this report, we show that the Rhg1 α‐SNAP strongly interacts with two syntaxins of the t‐SNARE family (Glyma.12G194800 and Glyma.16G154200) in yeast and plants; importantly, the genes encoding these syntaxins co‐localize with SCN resistance quantitative trait loci. Fluorescent visualization revealed that the α‐SNAP and the two interacting syntaxins localize to the plasma membrane and perinuclear space in both tobacco epidermal and soybean root cells. The two syntaxins and their two homeologs were mutated, individually and in combination, using the CRISPR‐Cas9 system in the SCN‐resistant Peking and SCN‐susceptible Essex soybean lines. Peking roots with deletions introduced into syntaxin genes exhibited significantly reduced resistance to SCN, confirming that t‐SNAREs are critical to resisting SCN infection. The results presented here uncover a key step in the molecular mechanism of SCN resistance, and will be invaluable to soybean breeders aiming to develop highly SCN‐resistant soybean varieties. Significance Statement: Although the soybean cyst nematode (SCN) is the most damaging pathogen of soybeans in the USA, resistance mechanisms are still only partially understood. In this study, we identify two genes encoding syntaxin proteins that interact with a key player in SCN resistance, the Rhg1 α‐SNAP protein. Using the CRISPR/Cas9 system, we knockout these syntaxins in soybean roots and demonstrate they are essential to maintain SCN resistance. These findings will aid in the development of yield‐protecting SCN resistance traits. [ABSTRACT FROM AUTHOR]

Key message: Novel QTL conferring resistance to both the SDS and SCN was detected in two RIL populations. Dual resistant RILs could be used in breeding programs for developing resistant soybean cultivars.Abstract: Soybean cultivars, susceptible to the fungus Fusarium virguliforme, which causes sudden death syndrome (SDS), and to the soybean cyst nematode (SCN) (Heterodera glycines), suffer yield losses valued over a billion dollars annually. Both pathogens may occur in the same production fields. Planting of cultivars genetically resistant to both pathogens is considered one of the most effective means to control the two pathogens. The objective of the study was to map quantitative trait loci (QTL) underlying SDS and SCN resistances. Two recombinant inbred line (RIL) populations were developed by crossing ‘A95-684043’, a high-yielding maturity group (MG) II line resistant to SCN, with ‘LS94-3207’ and ‘LS98-0582’ of MG IV, resistant to both F. virguliforme and SCN. Two hundred F7 derived recombinant inbred lines from each population AX19286 (A95-684043 × LS94-3207) and AX19287 (A95-684043 × LS98-0582) were screened for resistance to each pathogen under greenhouse conditions. Five hundred and eighty and 371 SNP markers were used for mapping resistance QTL in each population. In AX19286, one novel SCN resistance QTL was mapped to chromosome 8. In AX19287, one novel SDS resistance QTL was mapped to chromosome 17 and one novel SCN resistance QTL was mapped to chromosome 11. Previously identified additional SDS and SCN resistance QTL were also detected in the study. Lines possessing superior resistance to both pathogens were also identified and could be used as germplasm sources for breeding SDS- and SCN-resistant soybean cultivars. [ABSTRACT FROM AUTHOR]

The soybean cyst nematode ( SCN) resistance locus Rhg1 is a tandem repeat of a 31.2 kb unit of the soybean genome. Each 31.2-kb unit contains four genes. One allele of Rhg1, Rhg1-b, is responsible for protecting most US soybean production from SCN. Whole-genome sequencing was performed, and PCR assays were developed to investigate allelic variation in sequence and copy number of the Rhg1 locus across a population of soybean germplasm accessions. Four distinct sequences of the 31.2-kb repeat unit were identified, and some Rhg1 alleles carry up to three different types of repeat unit. The total number of copies of the repeat varies from 1 to 10 per haploid genome. Both copy number and sequence of the repeat correlate with the resistance phenotype, and the Rhg1 locus shows strong signatures of selection. Significant linkage disequilibrium in the genome outside the boundaries of the repeat allowed the Rhg1 genotype to be inferred using high-density single nucleotide polymorphism genotyping of 15 996 accessions. Over 860 germplasm accessions were found likely to possess Rhg1 alleles. The regions surrounding the repeat show indications of non-neutral evolution and high genetic variability in populations from different geographic locations, but without evidence of fixation of the resistant genotype. A compelling explanation of these results is that balancing selection is in operation at Rhg1. [ABSTRACT FROM AUTHOR]

The article discusses the results of a gene silencing study of soybean that showed genes in a 31-kilobase segment at the rhg1-b soybean allele, which encodes an amino acid transporter, an a-SNAP protein, and a WI12 (wound-inducible domain) protein, each contribute to resistance. Topics include the role of the rhg1-b allele for resistance against the soybean cyst nematode (SCN), which the author's note is the most economically damaging pathogen of soybeans in the U.S., the discovery of 10 tandem copies present in an rhg1-b haplotype, and the impact of copy number variation of multiple genes at Rhg1 in mediating nematode SCN resistance mediated in soybean.