Detection and fine-mapping of SC7 resistance genes via linkage and association analysis in soybean

Identification of soybean mosaic virus strain SC7 resistance loci and candidate genes in soybean [Glycine max (L.) Merr.]

Soybean [Glycine max (L.) Merr.] is an important legume crop worldwide, which provides abundant plant protein and oil for human beings. Soybean mosaic virus (SMV) can cause serious damage to the yield and quality of soybean, but it is difficult to control SMV with chemicals, breeding SMV-resistant varieties has become the most effective way to control the disease. Therefore, it is important to identify SMV resistance genes from soybean resources and apply them to soybean breeding. In this study, the disease rates (DRs) of 219 soybean accessions to SMV strain SC7 in two environments were investigated. A high-density NJAU 355 K SoySNP array was used for genome-wide association study (GWAS) of DR. A 274 kb region on chromosome 15 (1,110,567 bp to 1,384,173 bp) was repeatedly detected in two environments. Six new significant single nucleotide polymorphisms (SNPs) on chromosome 15 were identified. Four of these six SNPs were located within two candidate genes, Glyma.15G015700 and Glyma.15G015800. The elite haplotype Glyma.15G015700Hap I with low DR exhibited strong resistance to SC7. The expression of Glyma.15G015700 in the SMV-resistant accession increased significantly after inoculation with SC7. Furthermore, most of the proteins predicted to interact with Glyma.15G015700 are heat shock proteins, which have been shown to be related to disease resistance. In summary, new SMV resistance loci and a new candidate gene, Glyma.15G015700, were identified and might be utilized in further soybean disease resistance breeding.

Major viral diseases in grain legumes: designing disease resistant legumes from plant breeding and OMICS integration

Grain legumes play a crucial role in human nutrition and as a staple crop for low-income farmers in developing and underdeveloped nations, contributing to overall food security and agroecosystem services. Viral diseases are major biotic stresses that severely challenge global grain legume production. In this review, we discuss how exploring naturally resistant grain legume genotypes within germplasm, landraces, and crop wild relatives could be used as promising, economically viable, and eco-environmentally friendly solution to reduce yield losses. Studies based on Mendelian and classical genetics have enhanced our understanding of key genetic determinants that govern resistance to various viral diseases in grain legumes. Recent advances in molecular marker technology and genomic resources have enabled us to identify genomic regions controlling viral disease resistance in various grain legumes using techniques such as QTL mapping, genome-wide association studies, whole-genome resequencing, pangenome and 'omics' approaches. These comprehensive genomic resources have expedited the adoption of genomics-assisted breeding for developing virus-resistant grain legumes. Concurrently, progress in functional genomics, especially transcriptomics, has helped unravel underlying candidate gene(s) and their roles in viral disease resistance in legumes. This review also examines the progress in genetic engineering-based strategies, including RNA interference, and the potential of synthetic biology techniques, such as synthetic promoters and synthetic transcription factors, for creating viral-resistant grain legumes. It also elaborates on the prospects and limitations of cutting-edge breeding technologies and emerging biotechnological tools (e.g., genomic selection, rapid generation advances, and CRISPR/Cas9-based genome editing tool) in developing virus-disease-resistant grain legumes to ensure global food security.

A novel soybean malectin-like receptor kinase-encoding gene, GmMLRK1, provides resistance to soybean mosaic virus

Soybean mosaic virus (SMV) severely damages soybean [Glycine max (L.) Merr.] yield and seed quality. Moreover, the underlying genetic determinants of resistance to SMV remain largely unknown. Here, we performed a genome-wide association study (GWAS) of SMV resistance in a panel of 219 diverse soybean accessions across four environments and identified a new resistance-related gene, GmMLRK1, at the major resistance locus Rsv4 on chromosome 2. GmMLRK1 encodes a malectin-like receptor kinase (RK) that was induced earlier and to a greater degree in leaves of the SMV-resistant cultivar Kefeng No. 1 than in those of the susceptible cultivar Nannong 1138-2 after inoculation. We demonstrated that soybean plants overexpressing GmMLRK1 show broad-spectrum resistance to both strains SC7 and SC3 on the basis of reduced viral accumulation, increased reactive oxygen species production, and local cell death associated with the hypersensitive response. In contrast, GmMLRK1 knockout mutants were more susceptible to both pathotypes. Haplotype analysis revealed the presence of five haplotypes (H1-H5) within the soybean population, and only H1 provided SMV resistance, which was independent of its tightly linked SMV resistance gene RNase-H at the same locus. These results report a novel gene that adds new understanding of SMV resistance and can be used for breeding resistant soybean accessions.

RSC3 K of soybean cv. Kefeng No.1 confers resistance to soybean mosaic virus by interacting with the viral protein P3

Soybean mosaic virus (SMV) is one of the most devastating viral pathogens of soybean (Glycine max (L.) Merr). In total, 22 Chinese SMV strains (SC1-SC22) have been classified based on the responses of 10 soybean cultivars to these pathogens. However, although several SMV-resistance loci in soybean have been identified, no gene conferring SMV resistance in the resistant soybean cultivar (cv.) Kefeng No.1 has been cloned and verified. Here, using F₂ -derived F₃ (F_2:3 ) and recombinant inbred line (RIL) populations from a cross between Kefeng No.1 and susceptible soybean cv. Nannong 1138-2, we localized the gene in Kefeng No.1 that mediated resistance to SMV-SC3 strain to a 90-kb interval on chromosome 2. To study the functions of candidate genes in this interval, we performed Bean pod mottle virus (BPMV)-induced gene silencing (VIGS). We identified a recombinant gene (which we named R_SC3 K) harboring an internal deletion of a genomic DNA fragment partially flanking the LOC100526921 and LOC100812666 reference genes as the SMV-SC3 resistance gene. By shuffling genes between infectious SMV DNA clones based on the avirulent isolate SC3 and virulent isolate 1129, we determined that the viral protein P3 is the avirulence determinant mediating SMV-SC3 resistance on Kefeng No.1. P3 interacts with RNase proteins encoded by R_SC3 K, LOC100526921, and LOC100812666. The recombinant R_SC3 K conveys much higher anti-SMV activity than LOC100526921 and LOC100812666, although those two genes also encode proteins that inhibit SMV accumulation, as revealed by gene silencing in a susceptible cultivar and by overexpression in Nicotiana benthamiana. These findings demonstrate that R_SC3 K mediates the resistance of Kefeng No.1 to SMV-SC3 and that SMV resistance of soybean is determined by the antiviral activity of RNase proteins.

Transcriptome mapping related genes encoding PR1 protein involved in necrotic symptoms to soybean mosaic virus infection

Necrosis caused by soybean mosaic virus (SMV) has not been specifically distinguished from susceptible symptoms. The molecular mechanism for the occurrence of necrosis is largely overlooked in soybean genetic research. Field evaluation reveals that SMV disease seriously influences soybean production as indicated by decreasing 22.4% ~ 77.0% and 8.8% ~ 17.0% of yield and quality production, respectively. To expand molecular mechanism behind necrotic reactions, transcriptomic data obtained from the asymptomatic, mosaic, and necrotic pools were assessed. Compared between asymptomatic and mosaic plants, 1689 and 1752 up- and down-regulated differentially expressed genes (DEGs) were specifically found in necrotic plants. Interestingly, the top five enriched pathways with up-regulated DEGs were highly related to the process of the stress response, whereas the top three enriched pathways with down-regulated DEGs were highly related to the process of photosynthesis, demonstrating that defense systems are extensively activated, while the photosynthesis systems were severely destroyed. Further, results of the phylogenetic tree based on gene expression pattern and an amino acid sequence and validation experiments discovered three PR1 genes, Glyma.15G062400, Glyma.15G062500, and Glyma.15G062700, which were especially expressed in necrotic leaves. Meanwhile, exogenous salicylic acid (SA) but not methyl jasmonate (MeJA) could induce the three PR1 gene expressions on healthy leaves. Contrastingly, exogenous SA obviously decreased the expression level of Glyma.15G062400, Glyma.15G062500, and concentration of SMV, but increased Glyma.15G062700 expression in necrotic leaves. These results showed that GmPR1 is associated with the development of SMV-induced necrotic symptoms in soybean. Glyma.15G062400, Glyma.15G062500, and Glyma.15G062700 is up-regulated in necrotic leaves at the transcriptional levels, which will greatly facilitate a better understanding of the mechanism behind necrosis caused by SMV disease.

Supplementary information

The online version contains supplementary material available at 10.1007/s11032-022-01351-3.

Digs out and characterization of the resistance gene accountable to soybean mosaic virus in soybean (Glycine max (L.) Merrill)

A putative candidate gene conferring resistance to SMV strain SC1 was identified on chromosome 2, and the linked marker was validated in soybean cultivars Soybean mosaic, caused by the soybean mosaic virus, is the most common disease in soybean and a significant impediment to soybean production in the Huanghuai and Yangtze River regions of China. Kefeng No.1, a soybean cultivar, showed high resistance to soybean mosaic virus strain (SC1) collected from Huanghuai and Yangtze River regions. Genetic analysis based on the Mendelian genic population derived from the cross Kefeng No.1 × Nannong 1138-2 revealed that Kefeng No.1 possesses a single dominant gene. Furthermore, genetic fine-mapping using an F₂ population containing 281 individuals delimited resistant gene to a genomic region of 186 kb flanked by SSR markers BS020610 and BS020620 on chromosome 2. Within this region, there were 14 genes based on the Williams 82 reference genome. According to sequence analysis, six of the 14 genes have amino acid differences, and one of these genes is the Rsv4 allele designated as Rsc1-DR. The functional analysis of candidate genes using the bean pod mottle virus (BPMV)-induced gene silencing (VIGS) system revealed that Rsc1-DR was accountable for Kefeng No.1's resistance to SMV-SC1. Based on the genome sequence of Rsc1-DR, an Insertion/Deletion (InDel) molecular marker, JT0212, was developed and genotyped using 100 soybean cultivars, and the coincidence rate was 89%. The study enriched our understanding of the SMV resistance mechanism. The marker developed in this study could be directly used by the soybean breeders to select the genotypes with favorable alleles for making crosses, and also it will facilitate marker-assisted selection of SMV resistance in soybean breeding.

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.

Identification of Quantitative Trait Locus and Candidate Genes for Drought Tolerance in a Soybean Recombinant Inbred Line Population

With global warming and regional decreases in precipitation, drought has become a problem worldwide. As the number of arid regions in the world is increasing, drought has become a major factor leading to significant crop yield reductions and food crises. Soybean is a crop that is relatively sensitive to drought. It is also a crop that requires more water during growth and development. The aim of this study was to identify the quantitative trait locus (QTL) that affects drought tolerance in soybean by using a recombinant inbred line (RIL) population from a cross between the drought-tolerant cultivar 'Jindou21' and the drought-sensitive cultivar 'Zhongdou33'. Nine agronomic and physiological traits were identified under drought and well-watered conditions. Genetic maps were constructed with 923,420 polymorphic single nucleotide polymorphism (SNP) markers distributed on 20 chromosomes at an average genetic distance of 0.57 centimorgan (cM) between markers. A total of five QTLs with a logarithm of odds (LOD) value of 4.035-8.681 were identified on five chromosomes. Under well-watered conditions and drought-stress conditions, one QTL related to the main stem node number was located on chromosome 16, accounting for 17.177% of the phenotypic variation. Nine candidate genes for drought resistance were screened from this QTL, namely Glyma.16G036700, Glyma.16G036400, Glyma.16G036600, Glyma.16G036800, Glyma.13G312700, Glyma.13G312800, Glyma.16G042900, Glyma.16G043200, and Glyma.15G100700. These genes were annotated as NAC transport factor, GATA transport factor, and BTB/POZ-MATH proteins. This result can be used for molecular marker-assisted selection and provide a reference for breeding for drought tolerance in soybean.

Mapping Locus RSC11K and predicting candidate gene resistant to Soybean mosaic virus strain SC11 through linkage analysis combined with genome resequencing of the parents in soybean

Soybean mosaic virus (SMV) strain SC11 was prevalent in middle China. Its resistance was controlled by a Mendelian single dominant gene RSC11K in soybean Kefeng-1. This study aimed at mapping RSC11K and identifying its candidate gene. RSC11K locus was mapped ~217 kb interval between two SNP-linkage-disequilibrium-blocks (Gm02_BLOCK_11273955_11464884 and Gm02_BLOCK_11486875_11491354) in W82.a1.v1 genome using recombinant inbred lines population derived from Kefeng-1 (Resistant) × NN1138-2 (Susceptible), but inserted with a ~245 kb segment in W82.a2.v1 genome. In the entire 462 kb RSC11K region, 429 SNPs, 142 InDels and 34 putative genes were identified with more SNPs/InDels distributed in non-functional regions. Thereinto, ten genes contained SNP/InDel variants with high and moderate functional impacts on proteins, among which Glyma.02G119700 encoded a typical innate immune receptor-like kinase involving in virus disease process and responded to SMV inoculation, therefore was recognized as RSC11K's candidate gene. The novel RSC11K locus and candidate genes may help developing SMV resistance germplasm.

Decades of Genetic Research on Soybean mosaic virus Resistance in Soybean

This review summarizes the history and current state of the known genetic basis for soybean resistance to Soybean mosaic virus (SMV), and examines how the integration of molecular markers has been utilized in breeding for crop improvement. SVM causes yield loss and seed quality reduction in soybean based on the SMV strain and the host genotype. Understanding the molecular underpinnings of SMV-soybean interactions and the genes conferring resistance to SMV has been a focus of intense research interest for decades. Soybean reactions are classified into three main responses: resistant, necrotic, or susceptible. Significant progress has been achieved that has greatly increased the understanding of soybean germplasm diversity, differential reactions to SMV strains, genotype-strain interactions, genes/alleles conferring specific reactions, and interactions among resistance genes and alleles. Many studies that aimed to uncover the physical position of resistance genes have been published in recent decades, collectively proposing different candidate genes. The studies on SMV resistance loci revealed that the resistance genes are mainly distributed on three chromosomes. Resistance has been pyramided in various combinations for durable resistance to SMV strains. The causative genes are still elusive despite early successes in identifying resistance alleles in soybean; however, a gene at the Rsv4 locus has been well validated.

Identifying Quantitative Trait Loci and Candidate Genes Conferring Resistance to Soybean Mosaic Virus SC7 by Quantitative Trait Loci-Sequencing in Soybean

Soybean mosaic virus (SMV) is detrimental to soybean (Glycine max) breeding, seed quality, and yield worldwide. Improving the basic resistance of host plants is the most effective and economical method to reduce damage from SMV. Therefore, it is necessary to identify and clone novel SMV resistance genes. Here, we report the characterization of two soybean cultivars, DN50 and XQD, with different levels of resistance to SMV. Compared with XQD, DN50 exhibits enhanced resistance to the SMV strain SC7. By combining bulked-segregant analysis (BSA)-seq and fine-mapping, we identified a novel resistance locus, R _SMV -11, spanning an approximately 207-kb region on chromosome 11 and containing 25 annotated genes in the reference Williams 82 genome. Of these genes, we identified eleven with non-synonymous single-nucleotide polymorphisms (SNPs) or insertion-deletion mutations (InDels) in their coding regions between two parents. One gene, GmMATE68 (Glyma.11G028900), harbored a frameshift mutation. GmMATE68 encodes a multidrug and toxic compound extrusion (MATE) transporter that is expressed in all soybean tissues and is induced by SC7. Given that MATE transporter families have been reported to be linked with plant disease resistance, we suggest that GmMATE68 is responsible for SC7 resistance in DN50. Our results reveal a novel SMV-resistance locus, improving understanding of the genetics of soybean disease resistance and providing a potential new tool for marker-assisted selection breeding in soybean.

A bean common mosaic virus-resistance gene in the soybean variant V94-5152 was mapped to the Rsv4 locus conferring resistance to soybean mosaic virus

KEY MESSAGE

In the soybean variant V94-5152, a BCMV-resistance gene was mapped near to the region of SMV-resistance Rsv4 locus, raising a possibility that V94-5152 may rely on Rsv4 locus to resist against both SMV and BCMV. Both Soybean mosaic virus (SMV) and Bean common mosaic virus (BCMV) can induce soybean mosaic diseases, but few studies have explored soybean resistance against BCMV so far. In this study, V94-5152, a soybean variant resistant to BCMV and SMV, was crossed with a susceptible cultivar, Williams 82 to map the resistance gene. By inoculating 292 F2 individuals with a BCMV isolate HZZB011, a segregation ratio of 3 resistant: 1 susceptible was observed, suggesting that V94-5152 possesses a single-dominant resistance gene against BCMV-HZZB011. Bulk segregation analysis (BSA) then revealed that the resistance gene is closely linked to BARCSOYSSR_02_0617, a simple sequence repeat (SSR) marker on chromosome 2. Genotyping neighboring SSR markers among the 292 F2 individuals enabled us to draw a genetic linkage map, which indicated that the BCMV-resistance gene is located 0.2 cM downstream of BARCSOYSSR_02_0617. Amplification and sequencing ten candidate genes (Glyma02g121300 to Glyma02g122200) around this marker then revealed four genes containing nonsynonymous changes or indels. Also, this location is near to the recently cloned SMV-resistance Rsv4 locus from the cultivar Peking. By obtaining ten more sequences of Rsv4 locus from cultivated and wild soybean materials, we further investigated the variation and evolutionary patterns of this virus-resistance locus. It was evident that positive selections had been acting on this locus, with one critical amino acid change (R55P) shared by all resistance soybeans tested.

Soybean Resistance to Soybean Mosaic Virus

Soybean mosaic virus (SMV) occurs in all soybean-growing areas in the world and causes huge losses in soybean yields and seed quality. During early viral infection, molecular interactions between SMV effector proteins and the soybean resistance (R) protein, if present, determine the development of resistance/disease in soybean plants. Depending on the interacting strain and cultivar, R-protein in resistant soybean perceives a specific SMV effector, which triggers either the extreme silent resistance or the typical resistance manifested by hypersensitive responses and induction of salicylic acid and reactive oxygen species. In this review, we consider the major advances that have been made in understanding the soybean–SMV arms race. We also focus on dissecting mechanisms SMV employs to establish infection and how soybean perceives and then responds to SMV attack. In addition, progress on soybean R-genes studies, as well as those addressing independent resistance genes, are also addressed.

Molecular mapping of the gene(s) conferring resistance to Soybean mosaic virus and Bean common mosaic virus in the soybean cultivar Raiden

KEY MESSAGE

In the soybean cultivar Raiden, both a SMV-resistance gene and a BCMV-resistance gene were fine-mapped to a common region within the Rsv1 complex locus on chromosome 13, in which two CC-NBS-LRR resistance genes (Glyma.13g184800 and Glyma.13g184900) exhibited significant divergence between resistant and susceptible cultivars and were subjected to positive selection. Both Soybean mosaic virus (SMV) and Bean common mosaic virus (BCMV) can induce soybean mosaic diseases. To date, few studies have explored soybean resistance against these two viruses simultaneously. In this work, Raiden, a cultivar resistant to both SMV and BCMV, was crossed with a susceptible cultivar, Williams 82, to fine-map the resistance genes. After inoculating ~ 200 F2 individuals with either SMV (SC6-N) or BCMV (HZZB011), a segregation ratio of 3 resistant:1 susceptible was observed, indicating that for either virus, a single dominant gene confers resistance. Bulk segregation analysis (BSA) revealed that the BCMV-resistance gene is also linked to the SMV-resistance Rsv1 complex locus. Genotyping the F2 individuals with 12 simple sequence repeat (SSR) markers across the Rsv1 complex locus then preliminarily mapped the SMV-resistance gene, Rsv1-r, between SSR markers BARCSOYSSR_13_1075 and BARCSOYSSR_13_1161 and the BCMV-resistance gene between BARCSOYSSR_13_1084 and BARCSOYSSR_13_1115. Furthermore, a population of 1009 F2 individuals was screened with markers BARCSOYSSR_13_1075 and BARCSOYSSR_13_1161, and 32 recombinant F2 individuals were identified. By determining the genotypes of these F2 individuals on multiple internal SSR and single nucleotide polymorphism (SNP) markers and assaying the phenotypes of selected recombinant F2:3 lines, both the SMV- and BCMV-resistance genes were fine-mapped to a common region ( ~ 154.5 kb) between two SNP markers: SNP-38 and SNP-50. Within the mapped region, two CC-NBS-LRR genes exhibited significant divergence between Raiden and Williams 82, and their evolution has been affected by positive selection.

Over-expression of GmKR3, a TIR-NBS-LRR type R gene, confers resistance to multiple viruses in soybean

KEY MESSAGE

That overexpression of GmKR3 enhances innate virus resistance by stimulating. Soybean mosaic virus (SMV) is found in many soybean production areas, and SMV infection is one of the prevalent viral diseases that can cause significant yield losses in soybean. In plants, resistance (R) genes are involved in pathogen reorganization and innate immune response activation. Most R proteins have nucleotide-binding site and leucine-rich repeat (NBS-LRR) domains, and some of the NBS-LRR type R proteins in dicots have Toll/Interleukin-1 Receptor (TIR) motifs. We report here the analysis of the over-expression of GmKR3, a soybean TIR-NBS-LRR type R gene on virus resistance in soybean. When over-expressed in soybean, GmKR3 enhanced the plant's resistance to several strains of SMV, the closely related potyviruses bean common mosaic virus (BCMV) and watermelon mosaic virus (WMV), and the secovirus bean pod mottle virus (BPMV). Importantly, over-expression of GmKR3 did not affect plant growth and development, including yield and qualities of the seeds. HPLC analysis showed that abscisic acid (ABA) content increased in the 35S:GmKR3 transgenic plants, and in both wild-type and 35S:GmKR3 transgenic plants in response to virus inoculation. Consistent with this observation, we found that the expression of two ABA catabolism genes was down-regulated in 35S:GmKR3 transgenic plants. We also found that the expression of Gm04.3, an ABA responsive gene encoding BURP domain-containing protein, was up-regulated in 35S:GmKR3 transgenic plants. Taken together, our results suggest that overexpression of GmKR3 enhanced virus resistance in soybean, which was achieved at least in part via ABA signaling.

Soybean mosaic virus: a successful potyvirus with a wide distribution but restricted natural host range

TAXONOMY

Soybean mosaic virus (SMV) is a species within the genus Potyvirus, family Potyviridae, which includes almost one-quarter of all known plant RNA viruses affecting agriculturally important plants. The Potyvirus genus is the largest of all genera of plant RNA viruses with 160 species.

PARTICLE

The filamentous particles of SMV, typical of potyviruses, are about 7500 Å long and 120 Å in diameter with a central hole of about 15 Å in diameter. Coat protein residues are arranged in helices of about 34 Å pitch having slightly less than nine subunits per turn.

GENOME

The SMV genome consists of a single-stranded, positive-sense, polyadenylated RNA of approximately 9.6 kb with a virus-encoded protein (VPg) linked at the 5' terminus. The genomic RNA contains a single large open reading frame (ORF). The polypeptide produced from the large ORF is processed proteolytically by three viral-encoded proteinases to yield about 10 functional proteins. A small ORF, partially overlapping the P3 cistron, pipo, is encoded as a fusion protein in the N-terminus of P3 (P3N + PIPO).

BIOLOGICAL PROPERTIES

SMV's host range is restricted mostly to two plant species of a single genus: Glycine max (cultivated soybean) and G. soja (wild soybean). SMV is transmitted by aphids non-persistently and by seeds. The variability of SMV is recognized by reactions on cultivars with dominant resistance (R) genes. Recessive resistance genes are not known.

GEOGRAPHICAL DISTRIBUTION AND ECONOMIC IMPORTANCE

As a consequence of its seed transmissibility, SMV is present in all soybean-growing areas of the world. SMV infections can reduce significantly seed quantity and quality (e.g. mottled seed coats, reduced seed size and viability, and altered chemical composition).

CONTROL

The most effective means of managing losses from SMV are the planting of virus-free seeds and cultivars containing single or multiple R genes.

KEY ATTRACTIONS

The interactions of SMV with soybean genotypes containing different dominant R genes and an understanding of the functional role(s) of SMV-encoded proteins in virulence, transmission and pathogenicity have been investigated intensively. The SMV-soybean pathosystem has become an excellent model for the examination of the genetics and genomics of a uniquely complex gene-for-gene resistance model in a crop of worldwide importance.

Fine-mapping and identifying candidate genes conferring resistance to Soybean mosaic virus strain SC20 in soybean

KEY MESSAGE

The Mendelian gene conferring resistance to Soybean mosaic virus Strain SC20 in soybean was fine-mapped onto a 79-kb segment on Chr.13 where two closely linked candidate genes were identified and qRT-PCR verified. Soybean mosaic virus (SMV) threatens the world soybean production, particularly in China. A country-wide SMV strain system composed of 22 strains was established in China, among which SC20 is a dominant strain in five provinces in Southern China. Resistance to SC20 was evaluated in parents, F1, F2 and the F2:7 RIL (recombinant inbred line) population derived from a cross between Qihuang-1 (resistant) and NN1138-2 (susceptible). The segregation ratio of resistant to susceptible in the populations suggested a single dominant gene involved in the resistance to SC20 in Qihuang-1. A "partial genome mapping strategy" was used to map the resistance gene on Chromosome 13. Linkage analysis between 178 RILs and genetic markers showed that the SC20-resistance gene located at 3.9 and 3.8 cM to the flanking markers BARCSOYSSR_13_1099 and BARCSOYSSR_13_1185 on Chromosome 13. Subsequently, a residual heterozygote segregating population with 346 individuals was developed by selfing four plants heterozygous at markers adjacent to the tentative SC20-resistance gene; then, the candidate region was delimited to a genomic interval of approximately 79 kb flanked by the new markers gm-ssr_13-14 and gm-indel_13-3. Among the seven annotated candidate genes in this region, two genes, Glyma.13G194700 and Glyma.13G195100, encoding Toll Interleukin Receptor-nucleotide-binding-leucine-rich repeat resistance proteins were identified as candidate resistance genes by quantitative real-time polymerase chain reaction and sequence analysis. The two closely linked genes work together to cause the phenotypic segregation as a single Mendelian gene. These results will facilitate marker-assisted selection, gene cloning and breeding for the resistance to SC20.

Salicylic acid and broad spectrum of NBS-LRR family genes are involved in SMV-soybean interactions

Soybean mosaic virus (SMV) is a severe pathogen reducing crop yield and seed quality of soybean. Although several resistance gene loci including Rsv1, Rsv3 and Rsv4 are identified in some soybean varieties, most of the soybean genes related to SMV infection are still not characterized. In order to reveal genome-wide gene expression profiles in response to SMV infection, we used transcriptome analysis to determine SMV-responsive genes in susceptible variety Hefeng25. Time course RNA-seq analysis at 1, 5 and 10 dpi identified many deregulated pathways and gene families. "Plant-pathogen interaction" pathway with KEGG No. of KO04626 was highly enriched and dozens of NBS-LRR family genes were significantly down-regulated at 5 dpi. qRT-PCR analyses were performed to verify expression patterns of these genes and most were in accordance with the RNA-seq data. As NBS-LRR family proteins are broadly involved in plant immunity responses, our results indicated the importance of this time point (5 dpi) for SMV-soybean interaction. Consistent with it, SMV titer was increased from 1 dpi to 10 dpi and peaked at 5 dpi. Expression of SA (salicylic acid) marker gene PR-1 was induced by SMV infection. Application of exogenous MeSA, an active form of SA, primed the plant resistant to virus infection and reduced SMV accumulation in soybean. Interestingly, MeSA treatment also significantly upregulated expressions of SMV-responsive NBS-LRR genes. Compared with susceptible line Hefeng25, endogenous SA level was higher and was consistently induced by SMV infection in resistant variety RV8143. Moreover, expressions of NBS-LRR family genes were up-regulated by SMV infection in RV8143, while they were down-regulated by SMV infection in Hefeng25. Our results implied that SA and NBS-LRR family genes were involved in SMV-soybean interaction. SMV could compromise soybean defense responses by repression of NBS-LRR family genes in Hefeng25, and SA was implicated in this interaction process.

Isolation and validation of a candidate Rsv3 gene from a soybean genotype that confers strain-specific resistance to soybean mosaic virus

Soybean mosaic virus (SMV), a member of the genus Potyvirus, significantly reduces soybean production worldwide. Rsv3, which confers strain-specific resistance to SMV, was previously mapped between the markers A519F/R and M3Satt in chromosome 14 of the soybean [Glycine max (L.) Merr.] genotype L29. Analysis of the soybean genome database revealed that five different NBS-LRR sequences exist between the flanking markers. Among these candidate Rsv3 genes, the full-length cDNA of the Glyma.14g204700 was successfully cloned from L29. Over-expression of Glyma.14g204700 in leaves inoculated with SMV inhibited viral infection in a soybean genotype lacking Rsv3. In addition, the transient silencing of the candidate gene caused a high accumulation of an avirulent strain in L29 carrying Rsv3. Our results therefore provide additional line of evidence to support that Glyma.14g204700 is likely Rsv3 gene that confers strain-specific resistance to SMV.

Fine-mapping and identification of a novel locus Rsc15 underlying soybean resistance to Soybean mosaic virus

KEY MESSAGE

Rsc15, a novel locus underlying soybean resistance to SMV, was fine mapped to a 95-kb region on chromosome 6. The Rsc15- mediated resistance is likely attributed to the gene GmPEX14 , the relative expression of which was highly correlated with the accumulation of H 2 O 2 along with the activities of POD and CAT during the early stages of SMV infection in RN-9. Soybean mosaic virus (SMV) causes severe yield losses and seed quality deterioration in soybean [Glycine max (L.) Merr.] worldwide. A series of single dominant SMV resistance genes have been identified on respective soybean chromosomes 2, 13 and 14, while one novel locus, Rsc15, underlying resistance to the virulent SMV strain SC15 from soybean cultivar RN-9 has been recently mapped to a 14.6-cM region on chromosome 6. However, candidate gene has not yet been identified within this region. In the present study, we aimed to fine map the Rsc15 region and identify candidate gene(s) for this invaluable locus. High-resolution fine-mapping revealed that the Rsc15 gene was located in a 95-kb genomic region which was flanked by the two simple sequence repeat (SSR) markers SSR_06_17 and BARCSOYSSR_06_0835. Allelic sequence comparison and expression profile analysis of candidate genes inferred that the gene Glyma.06g182600 (designated as GmPEX14) was the best candidate gene attributing for the resistance of Rsc15, and that genes encoding receptor-like kinase (RLK) (i.e., Glyma.06g175100 and Glyma.06g184400) and serine/threonine kinase (STK) (i.e., Glyma.06g182900 and Glyma.06g183500) were also potential candidates. High correlations were established between the relative expression level of GmPEX14 and the hydrogen peroxide (H2O2) concentration and activities of catalase (CAT) and peroxidase (POD) during the early stages of SMV-SC15 infection in RN-9. The results of the present study will be useful in marker-assisted breeding for SMV resistance and will lead to further understanding of the molecular mechanisms of host resistance against SMV.

Genome-Wide Association Study Reveals Novel Loci for SC7 Resistance in a Soybean Mutant Panel

Soybean mosaic virus (SMV) is a member of Potyvirus genus that causes severe yield loss and destroys seed quality in soybean [Glycine max (L.) Merr.]. It is important to explore new resistance sources and discover new resistance loci to SMV, which will provide insights to improve breeding strategies for SMV resistance. Here, a genome-wide association study was conducted to accelerate molecular breeding for the improvement of resistance to SMV in soybean. A population of 165 soybean mutants derived from two soybean parents was used in this study. There were 104 SNPs identified significantly associated with resistance to SC7, some of which were located within previous reported quantitative trait loci. Three putative genes on chromosome 1, 9, and 12 were homologous to WRKY72, eEF1Bβ, and RLP9, which were involved in defense response to insect and disease in Arabidopsis. Moreover, the expression levels of these three genes changed in resistance and susceptible soybean accessions after SMV infection. These three putative genes may involve in the resistance to SC7 and be worthy to further research. Collectively, markers significantly associated with resistance to SC7 will be helpful in molecular marker-assisted selection for breeding resistant soybean accessions to SMV, and the candidate genes identified would advance the functional study of resistance to SMV in soybean.

Inheritance, fine-mapping, and candidate gene analyses of resistance to soybean mosaic virus strain SC5 in soybean

Soybean mosaic virus (SMV) is one of the most devastating pathogens for soybeans in China. Among the country-wide 22 strains, SC5 dominates in Huang-Huai and Changjiang valleys. For controlling its damage, the resistance gene was searched through Mendelian inheritance study, gene fine-mapping, and candidate gene analysis combined with qRT-PCR (quantitative real-time polymerase chain reaction) analysis. The parents F1, F2, and RILs (recombinant inbred lines) of the cross Kefeng-1 (Resistance, R) × NN1138-2 (Susceptible, S) were used to examine the inheritance of SC5-resistance. The F1 was resistant and the F2 and RILs segregated in a 3R:1S and 1R:1S ratio, respectively, indicating a single dominant gene conferring the Kefeng-1 resistance. Subsequently, the genomic region conferring the resistance was found in "Bin 352-Bin353 with 500 kb" on Chromosome 2 using the phenotyping data of the 427 RILs and a high-density genetic map with 4703 bin markers. In the 500 kb genomic region, 38 putative genes are contained. The association analysis between the SNPs in a putative gene and the resistance phenotype for the 427 RILs prioritized 11 candidate genes using Chi-square criterion. The expression levels of these genes were tested by qRT-PCR. On infection with SC5, 7 out of the 11 genes had differential expression in Kefeng-1 and NN1138-2. Furthermore, integrating SNP-phenotype association analysis with qRT-PCR expression profiling analysis, Glyma02g13495 was found the most possible candidate gene for SC5-resistance. This finding can facilitate the breeding for SC5-resistance through marker-assisted selection and provide a platform to gain a better understanding of SMV-resistance gene system in soybean.

The Current Status of the Soybean-Soybean Mosaic Virus (SMV) Pathosystem

Soybean mosaic virus (SMV) is one of the most devastating pathogens that cost huge economic losses in soybean production worldwide. Due to the duplicated genome, clustered and highly homologous nature of R genes, as well as recalcitrant to transformation, soybean disease resistance studies is largely lagging compared with other diploid crops. In this review, we focus on the major advances that have been made in identifying both the virulence/avirulence factors of SMV and mapping of SMV resistant genes in soybean. In addition, we review the progress in dissecting the SMV resistant signaling pathways in soybean, with a special focus on the studies using virus-induced gene silencing. The soybean genome has been fully sequenced, and the increasingly saturated SNP markers have been identified. With these resources available together with the newly developed genome editing tools, and more efficient soybean transformation system, cloning SMV resistant genes, and ultimately generating cultivars with a broader spectrum resistance to SMV are becoming more realistic than ever.

Quantitative Trait Loci (QTL) Mapping for Glycinin and β-Conglycinin Contents in Soybean (Glycine max L. Merr.)

Compared to β-conglycinin, glycinin contains 3-4 times the methionine and cysteine (sulfur-containing amino acids), accounting for approximately 40 and 30%, respectively, of the total storage protein in soybean. Increasing the soybean storage protein content while improving the ratio of glycinin to β-conglycinin is of great significance for soybean breeding and soy food products. The objective of this study is to analyze the genetic mechanism regulating the glycinin and β-conglycinin contents of soybean by using a recombinant inbred line (RIL) population derived from a cross between Kefeng No. 1 and Nannong 1138-2. Two hundred and twenty-one markers were used to map quantitative trait loci (QTLs) for glycinin (11S) and β-conglycinin (7S) contents, the ratio of glycinin to β-conglycinin (RGC), and the sum of glycinin and β-conglycinin (SGC). A total of 35 QTLs, 3 pairs of epistatic QTLs, and 5 major regions encompassing multiple QTLs were detected. Genes encoding the subunits of β-conglycinin were localized to marker intervals sat_418-satt650 and sat_196-sat_303, which are linked to RGC and SGC; marker sat_318, associated with 11S, 7S, and SGC, was located near Glyma10g04280 (Gy4), which encodes a subunit of glycinin. These results, which take epistatic interactions into account, will improve our understanding of the genetic basis of 11S and 7S contents and will lay a foundation for marker-assisted selection (MAS) breeding of soybean and improving the quality of soybean products.

Association analysis for detecting significant single nucleotide polymorphisms for phosphorus-deficiency tolerance at the seedling stage in soybean [Glycine max (L) Merr]

Tolerance to low-phosphorus soil is a desirable trait in soybean cultivars. Previous quantitative trait locus (QTL) studies for phosphorus-deficiency tolerance were mainly derived from bi-parental segregating populations and few reports from natural population. The objective of this study was to detect QTLs that regulate phosphorus-deficiency tolerance in soybean using association mapping approach. Phosphorus-deficiency tolerance was evaluated according to five traits (plant shoot height, shoot dry weight, phosphorus concentration, phosphorus acquisition efficiency and use efficiency) comprising a conditional phenotype at the seedling stage. Association mapping of the conditional phenotype detected 19 SNPs including 13 SNPs that were significantly associated with the five traits across two years. A novel cluster of SNPs, including three SNPs that consistently showed significant effects over two years, that associated with more than one trait was detected on chromosome 3. All favorable alleles, which were determined based on the mean of conditional phenotypic values of each trait over the two years, could be pyramided into one cultivar through parental cross combination. The best three cross combinations were predicted with the aim of simultaneously improving phosphorus acquisition efficiency and use efficiency. These results will provide a thorough understanding of the genetic basis of phosphorus deficiency tolerance in soybean.