The soybean-Phytophthora resistance locus Rps1-k encompasses coiled coil-nucleotide binding-leucine rich repeat-like genes and repetitive sequences

Impact of Rhg1 copy number variation on a soybean cyst nematode resistance transcriptional network

Soybean yield loss due to soybean cyst nematode (SCN) infestation has a negative impact on the U.S. economy. Most SCN-resistant soybeans carry a common resistance locus (Rhg1), conferred by copy number variation of a 31.2-kb segment at the Rhg1 locus. To identify the effects of Rhg1 copy number on the plant prior to SCN infection, we investigated genome-wide expression profiles in isogenic Fayette plants carrying different copy numbers at the Rhg1 locus (9-11 copies), that confer different levels of resistance to SCN. We found that even small differences in copy number lead to large changes in expression of downstream defense genes. The co-expression network constructed from differentially expressed genes (DEGs) outside the Rhg1 locus revealed complex effects of Rhg1 copy number on transcriptional regulation involving signal transduction and ethylene-mediated signaling pathways. Moreover, we report a variation in expression levels of phytoalexin biosynthesis-related genes that is correlated with copy number, and the activation of different NBS-LRR gene sets, indicating a broad effect of copy number on defense responses. Using qRT-PCR time series during SCN infection, we validated the SCN responses of DEGs detected in the copy number comparison and showed a stable upregulation of genes related to phytoalexin biosynthesis in resistant Fayette lines during the early stages of the incompatible interaction between soybeans and SCN, before syncytium formation. These results suggest additional genes that could enhance Rhg1-mediated SCN resistance.

The soybean plasma membrane GmDR1 protein conferring broad-spectrum disease and pest resistance regulates several receptor kinases and NLR proteins

Overexpression of Glycine max disease resistant 1 (GmDR1) exhibits broad-spectrum resistance against Fusarium virguliforme, Heterodera glycines (soybean cyst nematode), Tetranychus urticae (Koch) (spider mites), and Aphis glycines Matsumura (soybean aphids) in soybean. To understand the mechanisms of broad-spectrum immunity mediated by GmDR1, the transcriptomes of a strong and a weak GmDR1-overexpressor following treatment with chitin, a pathogen- and pest-associated molecular pattern (PAMP) common to these organisms, were investigated. The strong and weak GmDR1-overexpressors exhibited altered expression of 6098 and 992 genes, respectively, as compared to the nontransgenic control following chitin treatment. However, only 192 chitin- and 115 buffer-responsive genes exhibited over two-fold changes in expression levels in both strong and weak GmDR1-overexpressors as compared to the control. MapMan analysis of the 192 chitin-responsive genes revealed 64 biotic stress-related genes, of which 53 were induced and 11 repressed as compared to the control. The 53 chitin-induced genes include nine genes that encode receptor kinases, 13 encode nucleotide-binding leucine-rich repeat (NLR) receptor proteins, seven encode WRKY transcription factors, four ethylene response factors, and three MYB-like transcription factors. Investigation of a subset of these genes revealed three receptor protein kinases, seven NLR proteins, and one WRKY transcription factor genes that are induced following F. virguliforme and H. glycines infection. The integral plasma membrane GmDR1 protein most likely recognizes PAMPs including chitin and activates transcription of genes encoding receptor kinases, NLR proteins and defense-related genes. GmDR1 could be a pattern recognition receptor that regulates the expression of several NLRs for expression of PAMP-triggered immunity and/or priming the effector triggered immunity.

A rapid molecular diagnostic tool to discriminate alleles of avirulence genes and haplotypes of Phytophthora sojae using high-resolution melting analysis

Effectors encoded by avirulence genes (Avr) interact with the Phytophthora sojae resistance gene (Rps) products to generate incompatible interactions. The virulence profile of P. sojae is rapidly evolving as a result of the large-scale deployment of Rps genes in soybean. For a successful exploitation of Rps genes, it is recommended that soybean growers use cultivars containing the Rps genes corresponding to Avr genes present in P. sojae populations present in their fields. Determination of the virulence profile of P. sojae isolates is critical for the selection of soybean cultivars. High-resolution melting curve (HRM) analysis is a powerful tool, first applied in medicine, for detecting mutations with potential applications in different biological fields. Here, we report the development of an HRM protocol, as an original approach to discriminate effectors, to differentiate P. sojae haplotypes for six Avr genes. An HRM assay was performed on 24 P. sojae isolates with different haplotypes collected from soybean fields across Canada. The results clearly confirmed that the HRM assay discriminated different virulence genotypes. Moreover, the HRM assay was able to differentiate multiple haplotypes representing small allelic variations. HRM-based prediction was validated by phenotyping assays. This HRM assay provides a unique, cost-effective and efficient tool to predict virulence pathotypes associated with six different Avr (1b, 1c, 1d, 1k, 3a and 6) genes from P. sojae, which can be applied in the deployment of appropriate Rps genes in soybean fields.

Breeding for disease resistance in soybean: a global perspective

KEY MESSAGE

This review provides a comprehensive atlas of QTLs, genes, and alleles conferring resistance to 28 important diseases in all major soybean production regions in the world. Breeding disease-resistant soybean [Glycine max (L.) Merr.] varieties is a common goal for soybean breeding programs to ensure the sustainability and growth of soybean production worldwide. However, due to global climate change, soybean breeders are facing strong challenges to defeat diseases. Marker-assisted selection and genomic selection have been demonstrated to be successful methods in quickly integrating vertical resistance or horizontal resistance into improved soybean varieties, where vertical resistance refers to R genes and major effect QTLs, and horizontal resistance is a combination of major and minor effect genes or QTLs. This review summarized more than 800 resistant loci/alleles and their tightly linked markers for 28 soybean diseases worldwide, caused by nematodes, oomycetes, fungi, bacteria, and viruses. The major breakthroughs in the discovery of disease resistance gene atlas of soybean were also emphasized which include: (1) identification and characterization of vertical resistance genes reside rhg1 and Rhg4 for soybean cyst nematode, and exploration of the underlying regulation mechanisms through copy number variation and (2) map-based cloning and characterization of Rps11 conferring resistance to 80% isolates of Phytophthora sojae across the USA. In this review, we also highlight the validated QTLs in overlapping genomic regions from at least two studies and applied a consistent naming nomenclature for these QTLs. Our review provides a comprehensive summary of important resistant genes/QTLs and can be used as a toolbox for soybean improvement. Finally, the summarized genetic knowledge sheds light on future directions of accelerated soybean breeding and translational genomics studies.

A Phosphoproteomics Study of the Soybean root necrosis 1 Mutant Revealed Type II Metacaspases Involved in Cell Death Pathway

The soybean root necrosis 1 (rn1) mutation causes progressive browning of the roots soon after germination and provides increased tolerance to the soil-borne oomycete pathogen Phytophthora sojae in soybean. Toward understanding the molecular basis of the rn1 mutant phenotypes, we conducted tandem mass tag (TMT)-labeling proteomics and phosphoproteomics analyses of the root tissues of the rn1 mutant and progenitor T322 line to identify potential proteins involved in manifestation of the mutant phenotype. We identified 3,160 proteins. When the p-value was set at ≤0.05 and the fold change of protein accumulation between rn1 and T322 at ≥1.5 or ≤0.67, we detected 118 proteins that showed increased levels and 32 proteins decreased levels in rn1 as compared to that in T322. The differentially accumulated proteins (DAPs) are involved in several pathways including cellular processes for processing environmental and genetic information, metabolism and organismal systems. Five pathogenesis-related proteins were accumulated to higher levels in the mutant as compared to that in T322. Several of the DAPs are involved in hormone signaling, redox reaction, signal transduction, and cell wall modification processes activated in plant-pathogen interactions. The phosphoproteomics analysis identified 22 phosphopeptides, the levels of phosphorylation of which were significantly different between rn1 and T322 lines. The phosphorylation levels of two type II metacaspases were reduced in rn1 as compared to T322. Type II metacaspase has been shown to be a negative regulator of hypersensitive cell death. In absence of the functional Rn1 protein, two type II metacaspases exhibited reduced phosphorylation levels and failed to show negative regulatory cell death function in the soybean rn1 mutant. We hypothesize that Rn1 directly or indirectly phosphorylates type II metacaspases to negatively regulate the cell death process in soybean roots.

A giant NLR gene confers broad-spectrum resistance to Phytophthora sojae in soybean

Phytophthora root and stem rot caused by P. sojae is a destructive soybean soil-borne disease found worldwide. Discovery of genes conferring broad-spectrum resistance to the pathogen is a need to prevent the outbreak of the disease. Here, we show that soybean Rps11 is a 27.7-kb nucleotide-binding site-leucine-rich repeat (NBS-LRR or NLR) gene conferring broad-spectrum resistance to the pathogen. Rps11 is located in a genomic region harboring a cluster of large NLR genes of a single origin in soybean, and is derived from rounds of unequal recombination. Such events result in promoter fusion and LRR expansion that may contribute to the broad resistance spectrum. The NLR gene cluster exhibits drastic structural diversification among phylogenetically representative varieties, including gene copy number variation ranging from five to 23 copies, and absence of allelic copies of Rps11 in any of the non-Rps11-donor varieties examined, exemplifying innovative evolution of NLR genes and NLR gene clusters.

Interaction of Phytophthora sojae Effector Avr1b With E3 Ubiquitin Ligase GmPUB1 Is Required for Recognition by Soybeans Carrying Phytophthora Resistance Rps1-b and Rps1-k Genes

Phytophthora sojae is an oomycete that causes stem and root rot disease in soybean. P. sojae delivers many RxLR effector proteins, including Avr1b, into host cells to promote infection. We show here that Avr1b interacts with the soybean U-box protein, GmPUB1-1, in yeast two-hybrid, pull down, and bimolecular fluorescence complementation (BIFC) assays. GmPUB1-1, and a homeologous copy GmPUB1-2, are induced by infection and encode 403 amino acid proteins with U-Box domains at their N-termini. Non-synonymous mutations in the Avr1b C-terminus that abolish suppression of cell death also abolished the interaction of Avr1b with GmPUB1-1, while deletion of the GmPUB1-1 C-terminus, but not the U box, abolished the interaction. BIFC experiments suggested that the GmPUB1-1-Avr1b complex is targeted to the nucleus. In vitro ubiquitination assays demonstrated that GmPUB1-1 possesses E3 ligase activity. Silencing of the GmPUB1 genes in soybean cotyledons resulted in loss of recognition of Avr1b by gene products encoded by Rps1-b and Rps1-k. The recognition of Avr1k (which did not interact with GmPUB1-1) by Rps1-k plants was not, however, affected following GmPUB1-1 silencing. Furthermore, over-expression of GmPUB1-1 in particle bombardment experiments triggered cell death suggesting that GmPUB1 may be a positive regulator of effector-triggered immunity. In a yeast two-hybrid system, GmPUB1-1 also interacted with a number of other RxLR effectors including Avr1d, while Avr1b and Avr1d interacted with a number of other infection-induced GmPUB proteins, suggesting that the pathogen uses a multiplex of interactions of RxLR effectors with GmPUB proteins to modulate host immunity.

Tightly linked Rps12 and Rps13 genes provide broad-spectrum Phytophthora resistance in soybean

The Phytophtora root and stem rot is a serious disease in soybean. It is caused by the oomycete pathogen Phytophthora sojae. Growing Phytophthora resistant cultivars is the major method of controlling this disease. Resistance is race- or gene-specific; a single gene confers immunity against only a subset of the P. sojae isolates. Unfortunately, rapid evolution of new Phytophthora sojae virulent pathotypes limits the effectiveness of an Rps ("resistance to Phytophthora sojae") gene to 8-15 years. The current study was designed to investigate the effectiveness of Rps12 against a set of P. sojae isolates using recombinant inbred lines (RILs) that contain recombination break points in the Rps12 region. Our study revealed a unique Rps gene linked to the Rps12 locus. We named this novel gene as Rps13 that confers resistance against P. sojae isolate V13, which is virulent to recombinants that contains Rps12 but lack Rps13. The genetic distance between the two Rps genes is 4 cM. Our study revealed that two tightly linked functional Rps genes with distinct race-specificity provide broad-spectrum resistance in soybean. We report here the molecular markers for incorporating the broad-spectrum Phytophthora resistance conferred by the two Rps genes in commercial soybean cultivars.

Meta-GWAS for quantitative trait loci identification in soybean

We report a meta-Genome Wide Association Study involving 73 published studies in soybean [Glycine max L. (Merr.)] covering 17,556 unique accessions, with improved statistical power for robust detection of loci associated with a broad range of traits. De novo GWAS and meta-analysis were conducted for composition traits including fatty acid and amino acid composition traits, disease resistance traits, and agronomic traits including seed yield, plant height, stem lodging, seed weight, seed mottling, seed quality, flowering timing, and pod shattering. To examine differences in detectability and test statistical power between single- and multi-environment GWAS, comparison of meta-GWAS results to those from the constituent experiments were performed. Using meta-GWAS analysis and the analysis of individual studies, we report 483 peaks at 393 unique loci. Using stringent criteria to detect significant marker-trait associations, 59 candidate genes were identified, including 17 agronomic traits loci, 19 for seed-related traits, and 33 for disease reaction traits. This study identified potentially valuable candidate genes that affect multiple traits. The success in narrowing down the genomic region for some loci through overlapping mapping results of multiple studies is a promising avenue for community-based studies and plant breeding applications.

Identification of three closely linked loci conferring broad-spectrum Phytophthora sojae resistance in soybean variety Tosan-231

KEY MESSAGE

A variable genomic region containing two Harosoy-derived loci related to Rps7 and one Nemashirazu-derived locus confers broad-spectrum Phytophthora sojae resistance in Tosan-231 and is useful for developing resistant cultivars. We investigated resistance to pathotypically variable Phytophthora sojae isolates in the soybean variety Tosan-231, which has broad-spectrum resistance. Mapping analysis using descendent lines from a cross between Shuurei and Tosan-231 demonstrated that a genomic region between SSR markers BARCSOYSSR_03_0209 and BARCSOYSSR_03_0385 (termed "Region T"), confers broad-spectrum resistance in Tosan-231 and contains three closely linked resistance loci. Inoculation tests with 20 P. sojae isolates of different pathotypes and simple sequence repeat (SSR) analysis of progenitors of Tosan-231 facilitated identification and characterization of Rps genes at the three resistance loci. Two resistance genes, RpsT1 and RpsT2, were found to be derived from Harosoy carrying Rps7. This result suggested two mutually exclusive possibilities: (1) either RpsT1 or RpsT2 is Rps7, and the other is a locally functional novel gene; (2) Rps7 is not a single gene but in fact comprises RpsT1 and RpsT2. The resistance locus containing RpsT3 is derived from Nemashirazu, in which Rps genes have remained poorly defined. Moreover, we identified two genomic regions with relatively high recombination frequencies on the basis of mapping information and proposed a strategy to readily assemble useful resistance genes in or around Region T.

Understanding Root Rot Disease in Agricultural Crops

Root rot diseases remain a major global threat to the productivity of agricultural crops. They are usually caused by more than one type of pathogen and are thus often referred to as a root rot complex. Fungal and oomycete species are the predominant participants in the complex, while bacteria and viruses are also known to cause root rot. Incorporating genetic resistance in cultivated crops is considered the most efficient and sustainable solution to counter root rot, however, resistance is often quantitative in nature. Several genetics studies in various crops have identified the quantitative trait loci associated with resistance. With access to whole genome sequences, the identity of the genes within the reported loci is becoming available. Several of the identified genes have been implicated in pathogen responses. However, it is becoming apparent that at the molecular level, each pathogen engages a unique set of proteins to either infest the host successfully or be defeated or contained in attempting so. In this review, a comprehensive summary of the genes and the potential mechanisms underlying resistance or susceptibility against the most investigated root rots of important agricultural crops is presented.

New Insights into Plant Extracellular DNA. A Study in Soybean Root Extracellular Trap

exDNA is found in various organisms, including plants. However, plant exDNA has thus far received little attention related to its origin and role in the RET (root extracellular trap). In this study, we performed the first high-throughput genomic sequencing of plant exDNA from a Fabaceae with worldwide interest: soybean (Glycine max (L.) Merr.). The origin of this exDNA was first investigated in control condition, and the results show high-coverage on organelles (mitochondria/plastid) DNA relative to nuclear DNA, as well as a mix of coding and non-coding sequences. In the second part of this study, we investigated if exDNA release was modified during an elicitation with PEP-13 (a peptide elicitor from oomycete genus Phytophthora). Our results show that treatment of roots with PEP-13 does not affect the composition of exDNA.

Genetic Mapping of a Resistance Locus to Phytophthora sojae in the Korean Soybean Cultivar Daewon

Phytophthora root and stem rot reduce soybean yields worldwide. The use of R-gene type resistance is currently crucial for protecting soybean production. The present study aimed to identify the genomic location of a gene conferring resistance to Phytophthora sojae isolate 2457 in the recombinant inbred line population developed by a cross of Daepung × Daewon. Single-marker analysis identified 20 single nucleotide polymorphisms associated with resistance to the P. sojae isolate 2457, which explained ~67% of phenotypic variance. Daewon contributed a resistance allele for the locus. This region is a well-known location for Rps1 and Rps7. The present study is the first, however, to identify an Rps gene locus from a major soybean variety cultivated in South Korea. Linkage analysis also identified a 573 kb region on chromosome 3 with high significance (logarithm of odds = 13.7). This genomic region was not further narrowed down due to lack of recombinants within the interval. Based on the latest soybean genome, ten leucine-rich repeat coding genes and four serine/threonine protein kinase-coding genes are annotated in this region, which all are well-known types of genes for conferring disease resistance in crops. These genes would be candidates for molecular characterization of the resistance in further studies. The identified R-gene locus would be useful in developing P. sojae resistant varieties in the future. The results of the present study provide foundational knowledge for researchers who are interested in soybean-P. sojae interaction.

Fine Mapping, Candidate Gene Identification and Co-segregating Marker Development for the Phytophthora Root Rot Resistance Gene RpsYD25

Phytophthora root rot (PRR) caused by Phytophthora sojae is a serious disease of soybean. The most effective disease-control strategy is to deploy resistant cultivars carrying Rps genes. Soybean cultivar Yudou25 can effectively resist pathotypes of P. sojae in China. Previous studies have mapped the Rps gene in Yudou25, RpsYD25, on chromosome 3. In this study, at first RpsYD25 was located between SSR markers Satt1k3 (2.2 cM) and BARCSOYSSR_03_0253 (4.5 cM) by using an F_2:3 population containing 165 families derived from Zaoshu18 and Yudou25. Then the recombination sites were identified in 1127 F_3:4 families derived from Zaoshu18 and Yudou25 using the developed PCR-based SNP, InDel and SSR markers, and RpsYD25 was finely mapped in the a 101.3 kb genomic region. In this region, a zinc ion binding and nucleic acid binding gene Glyma.03g034700 and two NBS-LRR genes Glyma.03g034800 and Glyma.03g034900 were predicted as candidate genes of RpsYD25, and five co-segregated SSR markers with RpsYD25 were identified and validated to be diagnostic markers. Combined with the resistance reaction to multiple P. sojae isolates, seven of 178 soybean genotypes were detected to contain RpsYD25 using the five co-segregated SSR markers. The soybean genotypes carrying RpsYD25 and the developed co-segregated markers can be effectively applied in the breeding for P. sojae resistance in China.

Fine mapping of a Phytophthora-resistance locus RpsGZ in soybean using genotyping-by-sequencing

BACKGROUND

Phytophthora root rot (PRR) caused by Phytophthora sojae (P. sojae) is one of the most serious limitations to soybean production worldwide. The identification of resistance gene(s) and their incorporation into elite varieties is an effective approach for breeding to prevent soybean from being harmed by this disease. A valuable mapping population of 228 F8:11 recombinant inbred lines (RILs) derived from a cross of the resistant cultivar Guizao1 and the susceptible cultivar BRSMG68 and a high-density genetic linkage map with an average distance of 0.81 centimorgans (cM) between adjacent bin markers in this population were used to map and explore candidate gene(s).

RESULTS

PRR resistance in Guizao1 was found to be controlled by a single Mendelian locus and was finely mapped to a 367.371-kb genomic region on chromosome 3 harbouring 19 genes, including 7 disease resistance (R)-like genes, in the reference Willliams 82 genome. Quantitative real-time PCR assays of possible candidate genes revealed that Glyma.03 g05300 was likely involved in PRR resistance.

CONCLUSIONS

These findings from the fine mapping of a novel Rps locus will serve as a basis for the cloning and transfer of resistance genes in soybean and the breeding of P. sojae-resistant soybean cultivars through marker-assisted selection.

Genome-Wide Mining of Disease Resistance Gene Analogs Using Conserved Domains

The production of legume crop species is severely affected by disease, imposing a significant yield loss annually worldwide. Plant resistance gene analogs (RGAs) play specific roles in plant resistance responses, and their identification and subsequent application in breeding programs help to reduce this yield loss. RGAs contain conserved domains and motifs, which can be used for their identification and classification. Nucleotide-binding site-leucine-rich repeat (NLR), receptor like kinase (RLK), and receptor like protein (RLP) genes are the main types of RGAs. Computational identification and characterization of RGAs has been performed successfully among different plant species. Here, we explain the computational workflow for genome-wide RGA identification in legumes.

Construction and comparison of three reference-quality genome assemblies for soybean

We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.

Dissecting Resistance to Phytophthora cinnamomi in Interspecific Hybrid Chestnut Crosses Using Sequence-Based Genotyping and QTL Mapping

The soilborne oomycete Phytophthora cinnamomi-which causes root rot, trunk cankers, and stem lesions on an estimated 5,000 plant species worldwide-is a lethal pathogen of American chestnut (Castanea dentata) as well as many other woody plant species. P. cinnamomi is particularly damaging to chestnut and chinquapin trees (Castanea spp.) in the southern portion of its native range in the United States due to relatively mild climatic conditions that are conductive to disease development. Introduction of resistant genotypes is the most practical solution for disease management in forests because treatment with fungicides and eradication of the pathogen are neither practical nor economically feasible in natural ecosystems. Using backcross families derived from crosses of American chestnuts with two resistant Chinese chestnut cultivars Mahogany and Nanking, we constructed linkage maps and identified quantitative trait loci (QTLs) for resistance to P. cinnamomi that had been introgressed from these Chinese chestnut cultivars. In total, 957 plants representing five cohorts of three hybrid crosses were genotyped by sequencing and phenotyped by standardized inoculation and visual examination over a 6-year period from 2011 to 2016. Eight parental linkage maps comprising 7,715 markers were constructed, and 17 QTLs were identified on four linkage groups (LGs): LG_A, LG_C, LG_E, and LG_K. The most consistent QTLs were detected on LG_E in seedlings from crosses with both 'Mahogany' and 'Nanking' and LG_K in seedlings from 'Mahogany' crosses. Two consistent large and medium effect QTLs located ∼10 cM apart were present in the middle and at the lower end of LG_E; other QTLs were considered to have small effects. These results imply that the genetic architecture of resistance to P. cinnamomi in Chinese chestnut × American chestnut hybrid progeny may resemble the P. sojae-soybean pathosystem, with a few dominant QTLs along with quantitatively inherited partial resistance conferred by multiple small-effect QTLs.

Genetic Mapping and Molecular Characterization of a Broad-spectrum Phytophthora sojae Resistance Gene in Chinese Soybean

Phytophthora root rot (PRR) causes serious annual soybean yield losses worldwide. The most effective method to prevent PRR involves growing cultivars that possess genes conferring resistance to Phytophthora sojae (Rps). In this study, QTL-sequencing combined with genetic mapping was used to identify RpsX in soybean cultivar Xiu94-11 resistance to all P. sojae isolates tested, exhibiting broad-spectrum PRR resistance. Subsequent analysis revealed RpsX was located in the 242-kb genomic region spanning the RpsQ locus. However, a phylogenetic investigation indicated Xiu94-11 carrying RpsX is distantly related to the cultivars containing RpsQ, implying RpsX and RpsQ have different origins. An examination of candidate genes revealed RpsX and RpsQ share common nonsynonymous SNP and a 144-bp insertion in the Glyma.03g027200 sequence encoding a leucine-rich repeat (LRR) region. Glyma.03g027200 was considered to be the likely candidate gene of RpsQ and RpsX. Sequence analyses confirmed that the 144-bp insertion caused by an unequal exchange resulted in two additional LRR-encoding fragments in the candidate gene. A marker developed based on the 144-bp insertion was used to analyze the genetic population and germplasm, and proved to be useful for identifying the RpsX and RpsQ alleles. This study implies that the number of LRR units in the LRR domain may be important for PRR resistance in soybean.

Plant NLRs: From discovery to application

Plants require a complex immune system to defend themselves against a wide range of pathogens which threaten their growth and development. The nucleotide-binding leucine-rich repeat proteins (NLRs) are immune sensors that recognize effectors delivered by pathogens. The first NLR was cloned more than twenty years ago. Since this initial discovery, NLRs have been described as key components of plant immunity responsible for pathogen recognition and triggering defense responses. They have now been described in most of the well-studied mulitcellular plant species, with most having large NLR repertoires. As research has progressed so has the understanding of how NLRs interact with their recognition substrates and how they in turn activate downstream signalling. It has also become apparent that NLR regulation occurs at the transcriptional, post-transcriptional, translational, and post-translational levels. Even before the first NLR was cloned, breeders were utilising such genes to increase crop performance. Increased understanding of the mechanistic details of the plant immune system enable the generation of plants resistant against devastating pathogens. This review aims to give an updated summary of the NLR field.

Fine mapping Ruv2, a new rust resistance gene in cowpea (Vigna unguiculata), to a 193-kb region enriched with NBS-type genes

A new rust resistance gene Ruv2 was fine-mapped in cowpea to a 193-kb region on chromosome 2, which harboured 23 predicted gene models enriched with NBS-type genes. ZN016 is a landrace vegetable cowpea highly resistant to rust. Two previous studies using mixed-spores inoculation suggested different modes of inheritance of rust resistance in ZN016. In this study, we initially developed a detached leaf assay with a purified single-rust isolate (Auv-LS). Using this approach, we assessed the inheritance of rust resistance in a recombinant inbred line (RIL) population and an F₂ population, both derived from the cross of "ZN016" and the susceptible cultivar "Zhijiang282." A single dominant gene mode against Auv-LS was revealed in both populations. QTL mapping showed that this gene was coincident with the Ruv2 locus on LG7, one of the three resistance QTLs previously mapped based on mixed-spores inoculation data. Therefore, Ruv2 was considered as specifically against the rust isolate Auv-LS. Through an analysis of the RIL recombinants at Ruv2, we fine-mapped the gene to an ~ 0.45-cM interval between SNP markers 2_09656 and 2_00973, which corresponded to an ~ 193-kb region on chromosome 2 that harboured 23 predicted gene models enriched with NBS-type genes. Re-sequencing of the two parents revealed polymorphisms in four genes predictively to cause substantial protein structural changes, rendering them valuable candidate genes for future validation. Cross-species syntenic analysis indicated that Ruv2 may represent a novel rust resistance gene in food legumes. A cleaved amplified polymorphic sequences marker tightly linked to Ruv2 was developed to facilitate breeding. This work establishes a basis for map-based cloning of Ruv2 and breeding for rust resistance in cowpea and other legume crops.

A major natural genetic variation associated with root system architecture and plasticity improves waterlogging tolerance and yield in soybean

Natural genetic variations in waterlogging tolerance are controlled by multiple genes mapped as quantitative trait loci (QTLs) in major crops, including soybean (Glycine max L.). In this research, 2 novel QTLs associated with waterlogging tolerance were mapped from an elite/exotic soybean cross. The subsequent research was focused on a major QTL (qWT_Gm03) with the tolerant allele from the exotic parent. This QTL was isolated into near-isogenic backgrounds, and its effects on waterlogging tolerance were validated in multiple environments. Fine mapping narrowed qWT_Gm03 into a genomic region of <380 Kbp excluding Rps1 gene for Phytophthora sojae resistance. The tolerant allele of qWT_Gm03 promotes root growth under nonstress conditions and favourable root plasticity under waterlogging, resulting in improved waterlogging tolerance, yield, and drought tolerance-related traits, possibly through more efficient water/nutrient uptakes. Meanwhile, involvement of auxin pathways was also identified in the regulation of waterlogging tolerance, as the genotypic differences of qWT_Gm03 in waterlogging tolerance and formation of adventitious/aerial roots can be complemented by an exogenous auxin-biosynthesis inhibitor. These findings provided genetic resources to address the urgent demand of improving waterlogging tolerance in soybean and revealed the determinant roles of root architecture and plasticity in the plant adaptation to waterlogging.

Acid phosphatase gene GmHAD1 linked to low phosphorus tolerance in soybean, through fine mapping

KEY MESSAGE

Map-based cloning identified GmHAD1, a gene which encodes a HAD-like acid phosphatase, associated with soybean tolerance to low phosphorus stress. Phosphorus (P) deficiency in soils is a major limiting factor for crop growth worldwide. Plants may adapt to low phosphorus (LP) conditions via changes to root morphology, including the number, length, orientation, and branching of the principal root classes. To elucidate the genetic mechanisms for LP tolerance in soybean, quantitative trait loci (QTL) related to root morphology responses to LP were identified via hydroponic experiments. In total, we identified 14 major loci associated with these traits in a RIL population. The log-likelihood scores ranged from 2.81 to 7.43, explaining 4.23-13.98% of phenotypic variance. A major locus on chromosome 08, named qP8-2, was co-localized with an important P efficiency QTL (qPE8), containing phosphatase genes GmACP1 and GmACP2. Another major locus on chromosome 10 named qP10-2 explained 4.80-13.98% of the total phenotypic variance in root morphology. The qP10-2 contains GmHAD1, a gene which encodes an acid phosphatase. In the transgenic soybean hairy roots, GmHAD1 overexpression increased P efficiency by 8.4-16.5% relative to the control. Transgenic Arabidopsis plants had higher biomass than wild-type plants across both short- and long-term P reduction. These results suggest that GmHAD1, an acid phosphatase gene, improved the utilization of organic phosphate by soybean and Arabidopsis plants.

Evolutionary Divergence of TNL Disease-Resistant Proteins in Soybean (Glycine max) and Common Bean (Phaseolus vulgaris)

Disease-resistant genes (R genes) encode proteins that are involved in protecting plants from their pathogens and pests. Availability of complete genome sequences from soybean and common bean allowed us to perform a genome-wide identification and analysis of the Toll interleukin-1 receptor-like nucleotide-binding site leucine-rich repeat (TNL) proteins. Hidden Markov model (HMM) profiling of all protein sequences resulted in the identification of 117 and 77 regular TNL genes in soybean and common bean, respectively. We also identified TNL gene homologs with unique domains, and signal peptides as well as nuclear localization signals. The TNL genes in soybean formed 28 clusters located on 10 of the 20 chromosomes, with the majority found on chromosome 3, 6 and 16. Similarly, the TNL genes in common bean formed 14 clusters located on five of the 11 chromosomes, with the majority found on chromosome 10. Phylogenetic analyses of the TNL genes from Arabidopsis, soybean and common bean revealed less divergence within legumes relative to the divergence between legumes and Arabidopsis. Syntenic blocks were found between chromosomes Pv10 and Gm03, Pv07 and Gm10, as well as Pv01 and Gm14. The gene expression data revealed basal level expression and tissue specificity, while analysis of available microRNA data showed 37 predicted microRNA families involved in targeting the identified TNL genes in soybean and common bean.

Development of a high-density linkage map and chromosome segment substitution lines for Japanese soybean cultivar Enrei

Using progeny of a cross between Japanese soybean Enrei and Chinese soybean Peking, we developed a high-density linkage map and chromosomal segment substitution lines (CSSLs). The map consists of 2,177 markers with polymorphism information for 32 accessions and provides a detailed genetic framework for these markers. The marker order on the linkage map revealed close agreement with that on the chromosome-scale assembly, Wm82.a2.v1. The differences, especially on Chr. 5 and Chr. 11, in the present map provides information to identify regions in the genome assembly where additional information is required to resolve marker order and assign remaining scaffolds. To cover the entire soybean genome, we used 999 BC3F2 backcross plants and selected 103 CSSLs carrying chromosomal segments from Peking in the genetic background of Enrei. Using these low-genetic-complexity resources, we dissected variation in traits related to flowering, maturity and yield into approximately 50 reproducible quantitative trait loci (QTLs) and evaluated QTLs with small genetic effects as single genetic factors in a uniform genetic background. CSSLs developed in this study may be good starting material for removing the unfavourable characteristics of Peking during pre-breeding and for isolation of genes conferring disease and stress resistance that have not yet been characterized.

Next-generation sequencing to identify candidate genes and develop diagnostic markers for a novel Phytophthora resistance gene, RpsHC18, in soybean

KEY MESSAGE

A novel Phytophthora sojae resistance gene RpsHC18 was identified and finely mapped on soybean chromosome 3. Two NBS-LRR candidate genes were identified and two diagnostic markers of RpsHC18 were developed. Phytophthora root rot caused by Phytophthora sojae is a destructive disease of soybean. The most effective disease-control strategy is to deploy resistant cultivars carrying Phytophthora-resistant Rps genes. The soybean cultivar Huachun 18 has a broad and distinct resistance spectrum to 12 P. sojae isolates. Quantitative trait loci sequencing (QTL-seq), based on the whole-genome resequencing (WGRS) of two extreme resistant and susceptible phenotype bulks from an F2:3 population, was performed, and one 767-kb genomic region with ΔSNP-index ≥ 0.9 on chromosome 3 was identified as the RpsHC18 candidate region in Huachun 18. The candidate region was reduced to a 146-kb region by fine mapping. Nonsynonymous SNP and haplotype analyses were carried out in the 146-kb region among ten soybean genotypes using WGRS. Four specific nonsynonymous SNPs were identified in two nucleotide-binding sites-leucine-rich repeat (NBS-LRR) genes, RpsHC18-NBL1 and RpsHC18-NBL2, which were considered to be the candidate genes. Finally, one specific SNP marker in each candidate gene was successfully developed using a tetra-primer ARMS-PCR assay, and the two markers were verified to be specific for RpsHC18 and to effectively distinguish other known Rps genes. In this study, we applied an integrated genomic-based strategy combining WGRS with traditional genetic mapping to identify RpsHC18 candidate genes and develop diagnostic markers. These results suggest that next-generation sequencing is a precise, rapid and cost-effective way to identify candidate genes and develop diagnostic markers, and it can accelerate Rps gene cloning and marker-assisted selection for breeding of P. sojae-resistant soybean cultivars.

Fine Mapping and Identification of a Novel Phytophthora Root Rot Resistance Locus RpsZS18 on Chromosome 2 in Soybean

Phytophthora root rot (PRR) caused by Phytophthora sojae is a major soybean disease that causes severe economic losses worldwide. Using soybean cultivars carrying a Rps resistance gene is the most effective strategy for controlling this disease. We previously detected a novel Phytophthora resistance gene, RpsZS18, on chromosome 2 of the soybean cultivar Zaoshu18. The aim of the present study was to identify and finely map RpsZS18. We used 232 F2:3 families generated from a cross between Zaoshu18 (resistant) and Williams (susceptible) as the mapping population. Simple sequence repeat (SSR) markers distributed on chromosome 2 were used to map RpsZS18. First, 12 SSR markers linked with RpsZS18 were identified by linkage analyses, including two newly developed SSR markers, ZCSSR33 and ZCSSR46, that flanked the gene at distances of 0.9 and 0.5 cM, respectively. Second, PCR-based InDel markers were developed based on sequence differences between the two parents and used to further narrow down the mapping region of RpsZS18 to 71.3 kb. Third, haplotype analyses were carried out in the RpsZS18 region using 14 soybean genotypes with whole-genome resequencing. We detected six genes with unique haplotype sequences in Zaoshu18. Finally, quantitative real-time PCR assays of the six genes revealed an EF-hand calcium-binding domain containing protein encoding gene (Glyma.02g245700), a pfkB carbohydrate kinase encoding gene (Glyma.02g245800), and a gene with no functional annotation (Glyma.02g246300), are putative candidate PRR resistance genes. This study provides useful information for breeding P. sojae-resistant soybean cultivars.

Large-Scale Investigation of Soybean Gene Functions by Overexpressing a Full-Length Soybean cDNA Library in Arabidopsis

Molecular breeding has become an important approach for crop improvement, and a prerequisite for molecular breeding is elucidation of the functions of genetic loci or genes. Soybean is one of the most important food and oil crops worldwide. However, due to the difficulty of genetic transformation in soybean, studies of its functional genomics lag far behind those of other crops such as rice, which severely impairs the progress of molecular improvement in soybean. Here, we describe an effective large-scale strategy to investigate the functions of soybean genes via overexpression of a full-length soybean cDNA library in Arabidopsis. The overexpression vector pJL12 was modified for use in the construction of a normalized full-length cDNA library. The constructed cDNA library showed good quality; repetitive clones represented approximately 4%, insertion fragments were approximately 2.2 kb, and the full-length rate was approximately 98%. This cDNA library was then overexpressed in Arabidopsis, and approximately 2000 transgenic lines were preliminarily obtained. Phenotypic analyses of the positive T₁ transgenic plants showed that more than 5% of the T₁ transgenic lines displayed abnormal developmental phenotypes, and approximately 1% of the transgenic lines exhibited potentially favorable traits. We randomly amplified 4 genes with obvious phenotypes (enlarged seeds, yellowish leaves, more branches, and dense siliques) and repeated the transgenic analyses in Arabidopsis. Subsequent phenotypic observation demonstrated that these phenotypes were indeed due to the overexpression of soybean genes. We believe our strategy represents an effective large-scale approach to investigate the functions of soybean genes and further reveal genes favorable for molecular improvement in soybean.

Genetic mapping and development of co-segregating markers of RpsQ, which provides resistance to Phytophthora sojae in soybean

KEY MESSAGE

The RpsQ Phytophthora resistance locus was finely mapped to a 118-kb region on soybean chromosome 3. A best candidate gene was predicted and three co-segregating gene markers were developed. Phytophthora root rot (PRR), caused by Phytophthora sojae, is a major threat to sustainable soybean production. The use of genetically resistant cultivars is considered the most effective way to control this disease. The Chinese soybean cultivar Qichadou 1 exhibited a broad spectrum resistance, with a distinct resistance phenotype, following inoculation with 36 Chinese P. sojae isolates. Genetic analyses indicated that the disease resistance in Qichadou 1 is controlled by a single dominant gene. This gene locus was designated as RpsQ and mapped to a 118-kb region between BARCSOYSSR_03_0165 and InDel281 on soybean chromosome 3, and co-segregated with Insert11, Insert144 and SNP276. Within this region, there was only one gene Glyma.03g27200 encoding a protein with a typical serine/threonine protein kinase structure, and the expression pattern analysis showed that this gene induced by P. sojae infection, which was suggested as a best candidate gene of RpsQ. Candidate gene specific marker Insert144 was used to distinguish RpsQ from the other known Rps genes on chromosome 3. Identical polymerase chain reaction amplification products were produced for cultivars Qichadou 1 (RpsQ) and Ludou 4 (Rps9). All other cultivars carrying Rps genes on chromosome 3 produced different PCR products, which all lacked a 144-bp fragment present in Qichadou 1 and Ludou 4. The phenotypes of the analyzed cultivars combined with the physical position of the PRR resistance locus, candidate gene analyses, and the candidate gene marker test revealed RpsQ and Rps9 are likely the same gene, and confer resistance to P. sojae.

Fine mapping of a Phytophthora-resistance gene RpsWY in soybean (Glycine max L.) by high-throughput genome-wide sequencing

KEY MESSAGE

Using a combination of phenotypic screening, genetic and statistical analyses, and high-throughput genome-wide sequencing, we have finely mapped a dominant Phytophthora resistance gene in soybean cultivar Wayao. Phytophthora root rot (PRR) caused by Phytophthora sojae is one of the most important soil-borne diseases in many soybean-production regions in the world. Identification of resistant gene(s) and incorporating them into elite varieties are an effective way for breeding to prevent soybean from being harmed by this disease. Two soybean populations of 191 F2 individuals and 196 F7:8 recombinant inbred lines (RILs) were developed to map Rps gene by crossing a susceptible cultivar Huachun 2 with the resistant cultivar Wayao. Genetic analysis of the F2 population indicated that PRR resistance in Wayao was controlled by a single dominant gene, temporarily named RpsWY, which was mapped on chromosome 3. A high-density genetic linkage bin map was constructed using 3469 recombination bins of the RILs to explore the candidate genes by the high-throughput genome-wide sequencing. The results of genotypic analysis showed that the RpsWY gene was located in bin 401 between 4466230 and 4502773 bp on chromosome 3 through line 71 and 100 of the RILs. Four predicted genes (Glyma03g04350, Glyma03g04360, Glyma03g04370, and Glyma03g04380) were found at the narrowed region of 36.5 kb in bin 401. These results suggest that the high-throughput genome-wide resequencing is an effective method to fine map PRR candidate genes.

Fine Mapping of a Resistance Gene RpsHN that Controls Phytophthora sojae Using Recombinant Inbred Lines and Secondary Populations

Phytophthora root rot (PRR), caused by Phytophthora sojae, has negative effects on soybean yield in China and can be controlled by identifying germplasm resources with resistance genes. In this study, the resistance locus RpsHN in the soybean line Meng8206 was mapped using two mapping populations. Initial mapping was realized using two recombinant inbred line (RIL) populations and included 103 F6:8 RILs derived from a cross of Meng8206 × Linhedafenqing, including 2600 bin markers, and 130 F6:8 RILs derived from a cross of Meng8206 × Zhengyang148, including 2267 bin markers. Subsequently, a 159 F2:3 secondary population derived from a cross of Meng8206 × Linmeng6-46, were used to fine map this locus using SSR markers. Finally, the resistance locus from Meng8206 was fine mapped to a 278.7 kb genomic region flanked by SSR markers SSRSOYN-25 and SSRSOYN-44 at a genetic distance of 1.6 and 1.0 cM on chromosome 3 (Chr. 03). Real-time RT-PCR analysis of the possible candidate genes showed that three genes (Glyma.03g04260, Glyma.03g04300, and Glyma.03g04340) are likely involved in PRR resistance. These results will serve as a basis for cloning, transferring of resistant genes and breeding of P. sojae-resistant soybean cultivars through marker-assisted selection.

Evaluation of Resistance to Phytophthora sojae in Soybean Mini Core Collections Using an Improved Assay System

Stem and root rot disease caused by Phytophthora sojae is devastating to soybean crops worldwide. Developing host resistance to P. sojae, considered the most effective and stable means to control this disease, is partly hampered by limited germplasm resources. In this study, we first modified conventional methods for a P. sojae resistance assay to a simpler and more cost-effective version, in which the P. sojae inoculum was mixed into the soil and the resistance was evaluated by survival rate (%) of soybean seedlings. This rating had significant correlations (P < 0.01) with the reduction in root fresh weight and the visual root rot severity. Applying this method to evaluate P. sojae resistance in soybean mini core collections comprising either 79 accessions originating from Japan (JMC) or 80 accessions collected around the world (WMC) revealed a wide variation in resistance among the individual varieties. In total, 38 accessions from the JMC and 41 from the WMC exhibited resistance or moderate resistance to P. sojae isolate N1 (with virulence to Rps1b, 3c, 4, 5, and 6), with ≥50% survival. Of these, 26 from the JMC and 29 from the WMC showed at least moderate resistance to P. sojae isolate HR1 (vir Rps1a-c, 1k, 2, 3a-c, 4-6, and 8). Additionally, 24 WCS accessions, in contrast to only 6 from the JMC, exhibited 100% survival after being challenged with both the N1 and HR1 isolates, suggesting a biogeographical difference between the two collections. We further verified two JMC varieties, Daizu and Amagi zairai 90D, for their resistance to an additional four P. sojae isolates (60 to 100% survival), which may provide new and valuable genetic sources for P. sojae resistance breeding in soybean.

A Novel Phytophthora sojae Resistance Rps12 Gene Mapped to a Genomic Region That Contains Several Rps Genes

Phytophthora sojae Kaufmann and Gerdemann, which causes Phytophthora root rot, is a widespread pathogen that limits soybean production worldwide. Development of Phytophthora resistant cultivars carrying Phytophthora resistance Rps genes is a cost-effective approach in controlling this disease. For this mapping study of a novel Rps gene, 290 recombinant inbred lines (RILs) (F7 families) were developed by crossing the P. sojae resistant cultivar PI399036 with the P. sojae susceptible AR2 line, and were phenotyped for responses to a mixture of three P. sojae isolates that overcome most of the known Rps genes. Of these 290 RILs, 130 were homozygous resistant, 12 heterzygous and segregating for Phytophthora resistance, and 148 were recessive homozygous and susceptible. From this population, 59 RILs homozygous for Phytophthora sojae resistance and 61 susceptible to a mixture of P. sojae isolates R17 and Val12-11 or P7074 that overcome resistance encoded by known Rps genes mapped to Chromosome 18 were selected for mapping novel Rps gene. A single gene accounted for the 1:1 segregation of resistance and susceptibility among the RILs. The gene encoding the Phytophthora resistance mapped to a 5.8 cM interval between the SSR markers BARCSOYSSR_18_1840 and Sat_064 located in the lower arm of Chromosome 18. The gene is mapped 2.2 cM proximal to the NBSRps4/6-like sequence that was reported to co-segregate with the Phytophthora resistance genes Rps4 and Rps6. The gene is mapped to a highly recombinogenic, gene-rich genomic region carrying several nucleotide binding site-leucine rich repeat (NBS-LRR)-like genes. We named this novel gene as Rps12, which is expected to be an invaluable resource in breeding soybeans for Phytophthora resistance.

Fine mapping and candidate gene analysis of two loci conferring resistance to Phytophthora sojae in soybean

KEY MESSAGE

RpsUN1 and RpsUN2 were fine mapped to two genomic regions harboring disease resistance-like genes. The haplotypes and instability of the regions and candidate genes for the two resistance loci were characterized. Phytophthora root and stem rot caused by Phytophthora sojae, is one of the most destructive diseases of soybean. Deploying soybean cultivars carrying race-specific resistance conferred by Rps genes is the most practical approach to managing this disease. Previously, two Rps genes, RpsUN1 and RpsUN2 were identified in a landrace PI 567139B and mapped to a 6.5 cM region on chromosome 3 and a 3.0 cM region on chromosome 16, corresponding to 1387 and 423 kb of the soybean reference genome sequences. By analyzing recombinants defined by genotypic and phenotypic screening of the 826 F2:3 families derived from two reciprocal crosses between the two parental lines, RpsUN1 and RpsUN2, were further narrowed to a 151 kb region that harbors five genes including three disease resistance (R)-like genes, and a 36 kb region that contains four genes including five R-like genes, respectively, according to the reference genome. Expressional changes of these nine genes before and after inoculation with the pathogen, as revealed by RNA-seq, suggest that Glyma.03g034600 in the RpsUN1 region and Glyma.16g215200 and Glyma.16g214900 in the RpsUN2 region of PI 567139B may be associated with the resistance to P. sojae. It is also suggested that unequal recombination between/among R-like genes may have occurred, resulting in the formation of two recombinants with inconsistent genotypic and phenotypic observations. The haplotype variation of genomic regions where RpsUN1 and RpsUN2 reside in the entire soybean germplasm deposited in the US soybean germplasm collection suggests that RpsUN1 and RpsUN2 are most likely novel genes.

Cooperative functioning between phenylalanine ammonia lyase and isochorismate synthase activities contributes to salicylic acid biosynthesis in soybean

Salicylic acid (SA), an essential regulator of plant defense, is derived from chorismate via either the phenylalanine ammonia lyase (PAL) or the isochorismate synthase (ICS) catalyzed steps. The ICS pathway is thought to be the primary contributor of defense-related SA, at least in Arabidopsis. We investigated the relative contributions of PAL and ICS to defense-related SA accumulation in soybean (Glycine max). Soybean plants silenced for five PAL isoforms or two ICS isoforms were analyzed for SA concentrations and SA-derived defense responses to the hemibiotrophic pathogens Pseudomonas syringae and Phytophthora sojae. We show that, unlike in Arabidopsis, PAL and ICS pathways are equally important for pathogen-induced SA biosynthesis in soybean. Knock-down of either pathway shuts down SA biosynthesis and abrogates pathogen resistance. Moreover, unlike in Arabidopsis, pathogen infection is associated with the suppression of ICS gene expression. Pathogen-induced biosynthesis of SA via the PAL pathway correlates inversely with phenylalanine concentrations. Although infections with either virulent or avirulent strains of the pathogens increase SA concentrations, resistance protein-mediated response to avirulent P. sojae strains may function in an SA-independent manner. These results show that PAL- and ICS-catalyzed reactions function cooperatively in soybean defense and highlight the importance of PAL in pathogen-induced SA biosynthesis.

Molecular Soybean-Pathogen Interactions

Soybean hosts a wide variety of pathogens that cause significant yield losses. The importance of soybean as a major oilseed crop has led to research focused on its interactions with pathogens, such as Soybean mosaic virus, Pseudomonas syringae, Phytophthora sojae, Phakopsora pachyrhizi, and Heterodera glycines. Pioneering work on soybean's interactions with these organisms, which represent the five major pathogen groups (viruses, bacteria, oomycetes, fungi, and nematodes), has contributed to our understanding of the molecular mechanisms underlying virulence and immunity. These mechanisms involve conserved and unique features that validate the need for research in both soybean and homologous model systems. In this review, we discuss identification of effectors and their functions as well as resistance gene-mediated recognition and signaling. We also point out areas in which model systems and recent advances in resources and tools have provided opportunities to gain deeper insights into soybean-pathogen interactions.

Phenotypic evaluation and genetic dissection of resistance to Phytophthora sojae in the Chinese soybean mini core collection

BACKGROUND

Phytophthora root and stem rot (PRR) caused by Phytophthora sojae is one of the most serious diseases affecting soybean (Glycine max (L.) Merr.) production all over the world. The most economical and environmentally-friendly way to control the disease is the exploration and utilization of resistant varieties.

RESULTS

We screened a soybean mini core collection composed of 224 germplasm accessions for resistance against eleven P. sojae isolates. Soybean accessions from the Southern and Huanghuai regions, especially the Hubei, Jiangsu, Sichuan and Fujian provinces, had the most varied and broadest spectrum of resistance. Based on gene postulation, Rps1b, Rps1c, Rps4, Rps7 and novel resistance genes were identified in resistant accessions. Consequently, association mapping of resistance to each isolate was performed with 1,645 single nucleotide polymorphism (SNP) markers. A total of 14 marker-trait associations for Phytophthora resistance were identified. Among them, four were located in known PRR resistance loci intervals, five were located in other disease resistance quantitative trait locus (QTL) regions, and five associations unmasked novel loci for PRR resistance. In addition, we also identified candidate genes related to resistance.

CONCLUSION

This is the first P. sojae resistance evaluation conducted using the Chinese soybean mini core collection, which is a representative sample of Chinese soybean cultivars. The resistance reaction analyses provided an excellent database of resistant resources and genetic variations for future breeding programs. The SNP markers associated with resistance will facilitate marker-assisted selection (MAS) in breeding programs for resistance to PRR, and the candidate genes may be useful for exploring the mechanism underlying P. sojae resistance.

Loci and candidate gene identification for resistance to Phytophthora sojae via association analysis in soybean [Glycine max (L.) Merr]

Phytophthora sojae is an oomycete soil-borne plant pathogen that causes the serious disease Phytophthora root rot in soybean, leading to great loss of soybean production every year. Understanding the genetic basis of this plant-pathogen interaction is important to improve soybean disease resistance. To discover genes or QTLs underlying naturally occurring variations in soybean P.sojae resistance, we performed a genome-wide association study using 59,845 single-nucleotide polymorphisms identified from re-sequencing of 279 accessions from Yangtze-Huai soybean breeding germplasm. We used two models for association analysis. The same strong peak was detected by both two models on chromosome 13. Within the 500-kb flanking regions, three candidate genes (Glyma13g32980, Glyma13g33900, Glyma13g33512) had SNPs in their exon regions. Four other genes were located in this region, two of which contained a leucine-rich repeat domain, which is an important characteristic of R genes in plants. These candidate genes could be potentially useful for improving the resistance of cultivated soybean to P.sojae in future soybean breeding.

Humidity assay for studying plant-pathogen interactions in miniature controlled discrete humidity environments with good throughput

This paper reports a highly economical and accessible approach to generate different discrete relative humidity conditions in spatially separated wells of a modified multi-well plate for humidity assay of plant-pathogen interactions with good throughput. We demonstrated that a discrete humidity gradient could be formed within a few minutes and maintained over a period of a few days inside the device. The device consisted of a freeway channel in the top layer, multiple compartmented wells in the bottom layer, a water source, and a drying agent source. The combinational effects of evaporation, diffusion, and convection were synergized to establish the stable discrete humidity gradient. The device was employed to study visible and molecular disease phenotypes of soybean in responses to infection by Phytophthora sojae, an oomycete pathogen, under a set of humidity conditions, with two near-isogenic soybean lines, Williams and Williams 82, that differ for a Phytophthora resistance gene (Rps1-k). Our result showed that at 63% relative humidity, the transcript level of the defense gene GmPR1 was at minimum in the susceptible soybean line Williams and at maximal level in the resistant line Williams 82 following P. sojae CC5C infection. In addition, we investigated the effects of environmental temperature, dimensional and geometrical parameters, and other configurational factors on the ability of the device to generate miniature humidity environments. This work represents an exploratory effort to economically and efficiently manipulate humidity environments in a space-limited device and shows a great potential to facilitate humidity assay of plant seed germination and development, pathogen growth, and plant-pathogen interactions. Since the proposed device can be easily made, modified, and operated, it is believed that this present humidity manipulation technology will benefit many laboratories in the area of seed science, plant pathology, and plant-microbe biology, where humidity is an important factor that influences plant disease infection, establishment, and development.

Recent Progress in RXLR Effector Research

Some of the most devastating oomycete pathogens deploy effector proteins, with the signature amino acid motif RXLR, that enter plant cells to promote virulence. Research on the function and evolution of RXLR effectors has been very active over the decade that has transpired since their discovery. Comparative genomics indicate that RXLR genes play a major role in virulence for Phytophthora and downy mildew species. Importantly, gene-for-gene resistance against these oomycete lineages is based on recognition of RXLR proteins. Comparative genomics have revealed several mechanisms through which this resistance can be broken, most notably involving epigenetic control of RXLR gene expression. Structural studies have revealed a core fold that is present in the majority of RXLR proteins, providing a foundation for detailed mechanistic understanding of virulence and avirulence functions. Finally, functional studies have demonstrated that suppression of host immunity is a major function for RXLR proteins. Host protein targets are being identified in a variety of plant cell compartments. Some targets comprise hubs that are also manipulated by bacteria and fungi, thereby revealing key points of vulnerability in the plant immune network.

GmSGT1 is differently required for soybean Rps genes-mediated and basal resistance to Phytophthora sojae

KEY MESSAGE

Using RNAi approach, we demonstrate that GmSGT1 is an essential component in soybean against Phytophthora sojae, but not required for Rps 2 or Rps 3a-mediated resistance. Utilization of disease resistance in soybean is a major approach to combat root and stem rot disease, which is caused by Phytophthora sojae and poses a growing threat to soybean safety production. The SGT1 protein is essential for disease resistance in many plant species. Here, we analyzed and characterized functions of GmSGT1 gene family in R protein-mediated resistance and basal defense in this important crop. Five candidate genes of GmSGT1 were identified and they were grouped into three clades. Transcriptional levels of all the tested genes were highly induced upon P. sojae infection in four soybean cultivars that confer different resistant levels. Using a gene silencing system in soybean cotyledons, we demonstrated that silencing GmSGT1 genes comprised race-specific resistance in soybean lines carrying genes at the following loci for race-specific resistance to P. sojae: Rps1a, Rps1c, Rps1d, Rps1k, and Rps8. In contrast, the resistance mediated by Rps2 or Rps3a was not affected. Silencing GmSGT1 genes in cotyledons also reduced resistance to this pathogen in a moderately partial resistant cultivar. We further showed that transient overexpression of GmSGT1-1 in Nicotiana benthamiana could enhance the resistance to P. capsici. These results suggest that GmSGT1 is an essential component for soybean in resisting the pathogen and pathways of Rps-mediated disease resistance are diverse in soybean.

Genetic analysis and fine mapping of RpsJS, a novel resistance gene to Phytophthora sojae in soybean [Glycine max (L.) Merr]

KEY MESSAGE

We finely map a novel resistance gene ( RpsJS ) to Phytophthora sojae in soybean. RpsJS was mapped in 138.9 kb region, including three NBS-LRR type predicted genes, on chromosome 18. Phytophthora root rot (PRR) caused by Phytophthora sojae (P. sojae) has been reported in most soybean-growing regions throughout the world. Development of PRR resistance varieties is the most economical and environmentally safe method for controlling this disease. Chinese soybean line Nannong 10-1 is resistant to many P. sojae isolates, and shows different reaction types to P. sojae isolates as compared with those with known Rps (Resistance to P. sojae) genes, which suggests that the line may carry novel Rps genes or alleles. A mapping population of 231 F(2) individuals from the cross of Nannong 10-1 (Resistant, R) and 06-070583 (Susceptible, S) was used to map the Rps gene. The segregation fits a ratio of 3R:1S within F(2) plants, indicating that resistance in Nannong 10-1 is controlled by a single dominant gene (designated as RpsJS). The results showed that RpsJS was mapped on soybean chromosome 18 (molecular linkage group G, MLG G) flanked by SSR (simple repeat sequences) markers BARCSOYSSR_18_1859 and SSRG60752K at a distance of 0.9 and 0.4 cm, respectively. Among the 14 genes annotated in this 138.9 kb region between the two markers, three genes (Glyma18g51930, Glyma18g51950 and Glyma18g51960) are the nucleotide-binding site and a leucine-rich repeat (NBS-LRR) type gene, which may be involved in recognizing the presence of pathogens and ultimately conferring resistance. Based on marker-assisted resistance spectrum analyses of RpsJS and the mapping results, we inferred that RpsJS was a novel gene or a new allele at the Rps4, Rps5 or Rps6 loci.

Effectors as tools in disease resistance breeding against biotrophic, hemibiotrophic, and necrotrophic plant pathogens

One of most important challenges in plant breeding is improving resistance to the plethora of pathogens that threaten our crops. The ever-growing world population, changing pathogen populations, and fungicide resistance issues have increased the urgency of this task. In addition to a vital inflow of novel resistance sources into breeding programs, the functional characterization and deployment of resistance also needs improvement. Therefore, plant breeders need to adopt new strategies and techniques. In modern resistance breeding, effectors are emerging as tools to accelerate and improve the identification, functional characterization, and deployment of resistance genes. Since genome-wide catalogues of effectors have become available for various pathogens, including biotrophs as well as necrotrophs, effector-assisted breeding has been shown to be successful for various crops. "Effectoromics" has contributed to classical resistance breeding as well as for genetically modified approaches. Here, we present an overview of how effector-assisted breeding and deployment is being exploited for various pathosystems.

Genome re-sequencing and functional analysis places the Phytophthora sojae avirulence genes Avr1c and Avr1a in a tandem repeat at a single locus

The aim of this work was to map and identify the Phytophthora sojae Avr1c gene. Progeny from a cross of P. sojae strains ACR10×P7076 were tested for virulence on plants carrying Rps1c. Results indicate that avirulence segregates as a dominant trait. We mapped the Avr1c locus by performing whole genome re-sequencing of composite libraries created from pooled samples. Sequence reads from avirulent (Pool1) and virulent (Pool2) samples were aligned to the reference genome and single nucleotide polymorphisms (SNP) were identified for each pool. High quality SNPs were filtered to select for positions where SNP frequency was close to expected values for each pool. Only three SNP positions fit all requirements, and these occurred in close proximity. Additional DNA markers were developed and scored in the F₂ progeny, producing a fine genetic map that places Avr1c within the Avr1a gene cluster. Transient expression of Avr1c or Avr1a triggers cell death on Rps1c plants, but Avr1c does not trigger cell death on Rps1a plants. Sequence comparisons show that the RXLR effector genes Avr1c and Avr1a are closely related paralogs. Gain of virulence on Rps1c in P. sojae strain P7076 is achieved by gene deletion, but in most other strains this is accomplished by gene silencing. This work provides practical tools for crop breeding and diagnostics, as the Rps1c gene is widely deployed in commercial soybean cultivars.

Recent achievement in gene cloning and functional genomics in soybean

Soybean is a model plant for photoperiodism as well as for symbiotic nitrogen fixation. However, a rather low efficiency in soybean transformation hampers functional analysis of genes isolated from soybean. In comparison, rapid development and progress in flowering time and photoperiodic response have been achieved in Arabidopsis and rice. As the soybean genomic information has been released since 2008, gene cloning and functional genomic studies have been revived as indicated by successfully characterizing genes involved in maturity and nematode resistance. Here, we review some major achievements in the cloning of some important genes and some specific features at genetic or genomic levels revealed by the analysis of functional genomics of soybean.

Molecular mapping of two genes conferring resistance to Phytophthora sojae in a soybean landrace PI 567139B

Phytophthora root and stem rot (PRR), caused by the soil-borne oomycete pathogen Phytophthora sojae, is one of the most destructive diseases of soybean. PRR can be effectively controlled by race-specific genes conferring resistance to P. sojae (Rps). However, the Rps genes are usually non-durable, as populations of P. sojae are highly diverse and quick to adapt, and can be overcome 8-15 years after deployment. Thus, it is important to identify novel Rps genes for development of resistant soybean cultivars. PI 567139B is a soybean landrace carrying excellent resistance to nearly all predominant P. sojae races in Indiana. A mapping population consisting of 245 F2 individuals and 403 F2:3 families was developed from a cross between PI 567139B and the susceptible cultivar 'Williams', and used to dissect the resistance carried by PI 567139B. We found that the resistance in PI 567139B was conferred by two independent Rps genes, designated RpsUN1 and RpsUN2. The former was mapped to a 6.5 cM region between SSR markers Satt159 and BARCSOYSSR_03_0250 that spans the Rps1 locus on chromosome 3, while the latter was mapped to a 3.0 cM region between BARCSOYSSR_16_1275 and Sat_144, approximately 3.0-3.4 cM upstream of Rps2 on chromosome 16. According to the 'Williams 82' reference genome sequence, both regions are highly enriched with NBS-LRR genes. Marker assisted resistance spectrum analyses of these genes with 16 isolates of P. sojae, in combination with the mapping results, suggested that RpsUN1 was likely to be a novel allele at the Rps1 locus, while RpsUN2 was more likely to be a novel Rps gene.

Identification and candidate gene analysis of a novel phytophthora resistance gene Rps10 in a Chinese soybean cultivar

Resistance to Phytophthora sojae isolate PsMC1 was evaluated in 102 F2∶3 families derived from a cross between the resistant soybean cultivar Wandou 15 and the susceptible cultivar Williams and genotyped using simple sequence repeat (SSR) markers. The segregation ratio of resistant, segregating, and susceptible phenotypes in the population suggested that the resistance in Wandou 15 was dominant and monogenic. Twenty-six polymorphic SSR markers were identified on soybean chromosome 17 (Molecular linkage group D2; MLG D2), which were linked to the resistance gene based on bulked segregation analysis (BSA). Markers Sattwd15-24/25 and Sattwd15-47 flanked the resistance gene at a distance of 0.5 cM and 0.8 cM, respectively. Two cosegregating markers, Sattwd15-28 and Sattwd15-32, were also screened in this region. This is the first Rps resistance gene mapped on chromosome 17, which is designated as Rps10. Eight putative genes were found in the mapped region between markers Sattwd15-24/25 and Sattwd15-47. Among them, two candidate genes encoding serine/threonine (Ser/Thr) protein kinases in Wandou 15 and Williams were identified and sequenced. And the differences in genomic sequence and the putative amino acid sequence, respectively, were identified within each candidate gene between Wandou 15 and Williams. This novel gene Rps10 and the linked markers should be useful in developing soybean cultivars with durable resistance to P. sojae.

Two RxLR avirulence genes in Phytophthora sojae determine soybean Rps1k-mediated disease resistance

Resistance to Phytophthora sojae (Rps) genes have been widely used in soybean against root and stem rot diseases caused by this oomycete. Among 15 known soybean Rps genes, Rps1k has been the most widely used in the past four decades. Here, we show that the products of two distinct but closely linked RxLR effector genes are detected by Rps1k-containing plants, resulting in disease resistance. One of the genes is Avr1b-1, that confers avirulence in the presence of Rps1b. Three lines of evidence, including overexpression and gene silencing of Avr1b-1 in stable P. sojae transformants, as well as transient expression of this gene in soybean, indicated that Avr1b could trigger an Rps1k-mediated defense response. Some isolates of P. sojae that do not express Avr1b are nevertheless unable to infect Rps1k plants. In those isolates, we identified a second RxLR effector gene (designated Avr1k), located 5 kb away from Avr1b-1. Silencing or overexpression of Avr1k in P. sojae stable transformants resulted in the loss or gain, respectively, of the avirulence phenotype in the presence of Rps1k. Only isolates of P. sojae with mutant alleles of both Avr1b-1 and Avr1k could evade perception by the soybean plants carrying Rps1k.

Genetic characterization and fine mapping of the novel Phytophthora resistance gene in a Chinese soybean cultivar

Phytophthora root rot (PRR), caused by Phytophthora sojae Kaufmann & Gerdemann, is one of the most destructive diseases of soybean [Glycine max (L.) Merr.]. Deployment of resistance genes is the most economical and effective way of controlling the disease. The soybean cultivar 'Yudou 29' is resistant to many P. sojae isolates in China. The genetic basis of the resistance in 'Yudou 29' was elucidated through an inheritance study and molecular mapping. In response to 25 P. sojae isolates, 'Yudou 29' displayed a new resistance reaction pattern distinct from those of differentials carrying known Rps genes. A population of 214 F2:3 families from a cross between 'Jikedou 2' (PRR susceptible) and 'Yudou 29' was used for Rps gene mapping. The segregation fit a ratio of 1:2:1 for resistance:segregation:susceptibility within this population, indicating that resistance in 'Yudou 29' is controlled by a single dominant gene. This gene was temporarily named RpsYD29 and mapped on soybean chromosome 03 (molecular linkage group N; MLG N) flanked by SSR markers SattWM82-50 and Satt1k4b at a genetic distance of 0.5 and 0.2 cM, respectively. Two nucleotide binding site-leucine rich repeat (NBS-LRR) type genes were detected in the 204.8 kb region between SattWM82-50 and Satt1k4b. These two genes showed high similarity to Rps1k in amino acid sequence and could be candidate genes for PRR resistance. Based on the phenotype reactions and the physical position on soybean chromosome 03, RpsYD29 might be a novel allele at, or a novel gene tightly linked to, the Rps1 locus.

Identification of a new soybean rust resistance gene in PI 567102B

Soybean rust (SBR) caused by Phakopsora pachyrhizi Syd. and P. Syd. is one of the most economically important diseases of soybean (Glycine max (L.) Merr.). Durable resistance to P. pachyrhizi is the most effective long-term strategy to control SBR. The objective of this study was to investigate the genetics of resistance to P. pachyrhizi in soybean accession PI 567102B. This accession was previously identified as resistant to SBR in Paraguay and to P. pachyrhizi isolates from seven states in the USA (Alabama, Florida, Georgia, Louisiana, Mississippi, South Carolina, and Texas). Analysis of two independent populations, one in which F(2) phenotypes were inferred from F(2)-derived F(3) (F(2:3)) families and the other in which F(2) plants had phenotypes measured directly, showed that the resistance in PI 567102B was controlled by a single dominant gene. Two different isolates (MS06-1 and LA04-1) at different locations (Stoneville, MS and Ft. Detrick, MD) were used to independently assay the two populations. Linkage analysis of both populations indicated that the resistance locus was located on chromosome 18 (formerly linkage group G), but at a different location than either Rpp1 or Rpp4, which were previously mapped to this linkage group. Therefore, the SBR resistance in PI 567102B appeared to be conditioned by a previously unreported locus, with an underlying single dominant gene inferred. We propose this gene to be designated Rpp6. Incorporating Rpp6 into improved soybean cultivars may have wide benefits as PI 567102B has been shown to provide resistance to P. pachyrhizi isolates from Paraguay and the US.