Rsv1 Locus Research Articles

Genome assembly of the popular Korean soybean cultivar Hwangkeum.

Massive resequencing efforts have been undertaken to catalog allelic variants in major crop species including soybean, but the scope of the information for genetic variation often depends on short sequence reads mapped to the extant reference genome. Additional de novo assembled genome sequences provide a unique opportunity to explore a dispensable genome fraction in the pan-genome of a species. Here, we report the de novo assembly and annotation of Hwangkeum, a popular soybean cultivar in Korea. The assembly was constructed using PromethION nanopore sequencing data and two genetic maps and was then error-corrected using Illumina short-reads and PacBio SMRT reads. The 933.12 Mb assembly was annotated as containing 79,870 transcripts for 58,550 genes using RNA-Seq data and the public soybean annotation set. Comparison of the Hwangkeum assembly with the Williams 82 soybean reference genome sequence (Wm82.a2.v1) revealed 1.8 million single-nucleotide polymorphisms, 0.5 million indels, and 25 thousand putative structural variants. However, there was no natural megabase-scale chromosomal rearrangement. Incidentally, by adding two novel subfamilies, we found that soybean contains four clearly separated subfamilies of centromeric satellite repeats. Analyses of satellite repeats and gene content suggested that the Hwangkeum assembly is a high-quality assembly. This was further supported by comparison of the marker arrangement of anthocyanin biosynthesis genes and of gene arrangement at the Rsv3 locus. Therefore, the results indicate that the de novo assembly of Hwangkeum is a valuable additional reference genome resource for characterizing traits for the improvement of this important crop species.

Molecular characterization of NBS-LRR genes in the soybean Rsv3 locus reveals several divergent alleles that likely confer resistance to the soybean mosaic virus.

The divergence patterns of NBS - LRR genes in soybean Rsv3 locus were deciphered and several divergent alleles ( NBS_C, NBS_D and Columbia NBS_E ) were identified as the likely functional candidates of Rsv3. The soybean Rsv3 locus, which confers resistance to the soybean mosaic virus (SMV), has been previously mapped to a region containing five nucleotide binding site-leucine-rich repeats (NBS-LRR) genes (referred to as nbs_A-E) in Williams 82. In resistant cultivars, however, the number of NBS-LRR genes in this region and their divergence from susceptible alleles remain unclear. In the present study, we constructed and screened a bacterial artificial chromosome (BAC) library for an Rsv3-possessing cultivar, Zaoshu 18. Sequencing two positive BAC inserts on the Rsv3 locus revealed that Zaoshu 18 possesses the same gene content and order as Williams 82, but two of the NBS-LRR genes, NBS_C and NBS_D, exhibit distinct features that were not observed in the Williams 82 alleles. Obtaining theseNBS-LRR genes from eight additional cultivars demonstrated that the NBS_A-D genes diverged into two different alleles: the nbs_A-D alleles were associated with the rsv3-type cultivars, whereas the NBS_A-D alleles were associated with the Rsv3-possessing cultivars. For the NBS_E gene, the cultivar Columbia possesses an allele (NBS_E) that differed from that in Zaoshu 18 and rsv3-type cultivars (nbs_E). Exchanged fragments were further detected on alleles of the NBS_C-E genes, suggesting that recombination is a major force responsible for allele divergence. Also, the LRR domains of the NBS_C-E genes exhibited extremely strong signals of positive selection. Overall, the divergence patterns of the NBS-LRR genes in Rsv3 locus elucidated by this study indicate that not only NBS_C but also NBS_D and Columbia NBS_E are likely functional alleles that confer resistance to SMV.

Two Tightly Linked Genes for Soybean Mosaic Virus Resistance in Soybean

Soybean mosaic virus (SMV), a member of the Potyviridae family, is the most common virus negatively affecting yield and seed quality in soybean [Glycine max (L.) Merr.]. Seven SMV strains, G1 through G7, and three independent SMV resistance genes (R‐genes), Rsv1, Rsv3, and Rsv4, have been previously identified. The Rsv1 locus contains at least 10 alleles conferring differential plant reactions to SMV strains, and it was mapped at very complex resistance‐gene‐rich region. In this study, two alleles of the Rsv1 locus were analyzed by crossing PI 96983 (Rsv1) and cultivar York (Rsv1‐y) soybean to evaluate whether Rsv1 and Rsv1‐y belong to the same or different but closely linked loci. To break possible linkage, 3000 F2:3 lines were developed and investigated using infections of the SMV‐G1 strain in a greenhouse. The occurrence of segregating and susceptible lines indicated tight linkage between two genes. The recombination frequency (RF) was estimated using the maximum likelihood (ML) formula concluding that Rsv1 and Rsv1‐y are two tightly linked loci located apart with genetic distance of 2.2 cM on chromosome 13. A new symbol of Rsv5 has been assigned for the resistance gene in York to replace the original Rsv1‐y allele assignment. This research provided the first evidence for existence of two R‐genes on chromosome 13, conferring resistance to different SMV strains. Both loci, Rsv1 and Rsv5, can be easily transferred into susceptible cultivars in a breeding program to provide broad and durable protection against SMV strains.

Fine mapping of the Rsv1-h gene in the soybean cultivar Suweon 97 that confers resistance to two Chinese strains of the soybean mosaic virus.

The Rsv1 - h gene in cultivar Suweon 97, which confers resistance to SMVs, was mapped to a 97.5-kb location (29,815,195-29,912,667bp on chromosome 13) in the Rsv1 locus, thereby providing additional insights into the molecular nature underlying variations in resistance alleles in this particular locus. Soybean mosaic virus (SMV) is a well-known devastating pathogen of soybean (Glycine max (L.) Merrill.) causing significant yield losses and seed quality deterioration. A single dominant allele, Rsv1-h, which confers resistance to multiple SMV strains, was previously reported in the cultivar Suweon 97, but its exact location is unknown. In the present study, Suweon 97 was crossed with a SMV-sensitive cultivar, Williams 82. Inoculating 267 F 2 individuals with two Chinese SMV strains (SC6-N and SC7-N) demonstrated that one single dominant gene confers SMV resistance. Another 1,150 F 2 individuals were then screened for two simple sequence repeat (SSR) markers (BARCSOYSSR_13_1103 and BARCSOYSSR_13_1187) that flank the Rsv1 locus. Seventy-four recombinants were identified and 20 additional polymorphic SSR markers within the Rsv1 region were then employed in genotyping these recombinants. F 2:3 and F 3:4 recombinant lines were also inoculated with SC6-N and SC7-N to determine their phenotypes. The final data revealed that in Suweon 97, the Rsv1-h gene that confers resistance to SC6-N and SC7-N was flanked by BARCSOYSSR_13_1114 and BARCSOYSSR_13_1115, two markers that delimit a 97.5-kb region in the reference Williams 82 genome. In such region, eight genes were present, of which two, Glyma13g184800 and Glyma13g184900, encode the characteristic CC-NBS-LRR type of resistance gene and were considered potential candidates for Rsv1-h.

Transfer of the Rsv3 locus from 'Harosoy' for resistance to soybean mosaic virus strains C and D in Japan.

Resistance to soybean mosaic virus (SMV) is imperative for soybean (Glycine max (L.) Merr.) production in the Tohoku region. Molecular markers for SMV resistance were previously reported for U.S. SMV strains, but they cannot be applied because of the differences in strain classification between Japan and the U.S. A U.S. variety ‘Harosoy’ has been used mainly as a donor of resistance to SMV strains C and D in a Japanese breeding program, resulting in resistant varieties such as ‘Fukuibuki.’ Because ‘Harosoy’ harbors the Rsv3 gene conferring resistance to the virulent SMV strain groups, G5 through G7, it appears that the Rsv3 gene confers resistance to strains C and D. In this study, we introduced resistance to the two strains from ‘Fukuibuki’ into a leading variety ‘Ohsuzu’ by recurrent backcrossing with marker-assisted selection. All lines selected with markers near Rsv3 showed resistance to the strains, suggesting that the Rsv3 locus is responsible for the resistance. Three years of trials showed that one of the breeding lines, ‘Tohoku 169,’ was equivalent to ‘Ohsuzu’ with respect to agricultural characteristics such as seed size, maturity date, and seed yield, except for the SMV resistance.

Identification of a New Allele at the Rsv3 Locus for Resistance to Soybean Mosaic Virus in PI 61944 Soybean Accession

ABSTRACTSoybean mosaic virus (SMV) is a prevalent pathogen in soybean [Glycine max, (L.) Merr.]. Several SMV resistance genes have been discovered, but most of them do not provide resistance to all strains of SMV. The objective of this research was to identify new genes or alleles displaying differential reactions to SMV strains in the SMV‐resistant soybean genotype, PI 61944. Cross combinations were made to develop F2 and F2:3 populations, followed by mapping analyses and greenhouse screenings using G1 and G7 virus strains. A resistant parent, PI 61944 (Rsv‐?), was crossed with a susceptible parent, Essex (rsv), and with differential parents, PI 96983 (Rsv1), L29 (Rsv3), V94‐5152 (Rsv4), and PI 507389 (Rsv1‐n), for allelism tests. Results indicated that resistance to SMV in PI 61944 was controlled by a single, dominant gene. This gene did not appear to be allelic to the Rsv1 locus as was previously reported. Allelism test revealed that the resistance allele in PI 61944 is located at the Rsv3 locus. A molecular marker analysis further revealed that the resistance allele in PI 61944 is located at linkage group B2 (chromosome 14). Additionally, PI 61944 exhibited unique SMV reaction patterns when compared with the reported Rsv3 allele in L29. Therefore, we propose that the new allele, Rsv3‐n, be assigned to the SMV resistance locus in PI 61944. The Rsv3 alleles are rare to find among the soybean germplasm, but can confer resistance to aggressive SMV strains; therefore, we expect PI 61944 to be useful in future breeding efforts.

Multiple genes confer resistance to soybean mosaic virus in the soybean cultivar Hwangkeum

Recombinant inbred lines (RILs) generated from a cross between a cultivated species and its wild progenitor species serve as important germplasm for introgressing valuable genes from a wild species to a cultivated species. During this breeding process, it is equally important to prevent the loss of agronomically important genes in the cultivated species. In an effort to establish an efficient selection system for the single Rsv1 gene conferring durable resistance to soybean mosaic virus (SMV) in the soybean cultivar Hwangkeum (also known as Suweon 97), which is a parent of a RIL population from Hwangkeum (cultivated soybean) × IT182932 (wild soybean), in the present study, we unexpectedly identified an additional necrosis-conditioning gene unmasked by a recombination in the middle of the Rsv1-containing nucleotide-binding leucine-rich repeat gene cluster region and the Rsv3 gene in Hwangkeum. Thus, Hwangkeum contains at least three SMV resistance genes consisting of two tightly linked genes at the Rsv1 locus and the Rsv3 locus. The results of this study provide additional important information for use of the Hwangkeum genome in soybean breeding programmes.

Inheritance and Allelic Relationships of Resistance Genes for Soybean mosaic virus in ‘Corsica’ and ‘Beeson’ Soybean

ABSTRACTSoybean mosaic virus (SMV) is an important viral disease of soybean [Glycine max (L.) Merr.] and causes a drastic reduction of seed yield and quality. Soybean mosaic virus isolates can be classified into one of seven strain groups, G1 through G7. Three loci with SMV resistance alleles Rsv1, Rsv3, and Rsv4 have been reported so far. Each locus contains multiple alleles: nine alleles at Rsv1, three alleles at Rsv3, and two alleles at Rsv4. Soybean cultivars Corsica (PI 559931) and Beeson (PI 548510) exhibit different patterns of response to SMV strains than differential cultivars with known genes. The objective of this study was to investigate the inheritance and allelism of resistance genes in Corsica and Beeson. To examine the inheritance of SMV resistance, Corsica and Beeson were crossed with the susceptible cultivar Essex, and the F2 and F3 progenies were inoculated with a G7 isolate. To identify the allelic relationship of genes in Corsica and Beeson with known SMV resistance loci, they were crossed with PI 96983 (Rsv1), ‘L29’ (Rsv3), and V94‐5152 (Rsv4), and their F2 plants and F2:3 lines were inoculated with G7. A serological tissue blotting immunoassay (TBIA) was used to confirm the presence or absence of the virus in the inoculated plants. Molecular markers were used to confirm the phenotypic data. The results showed a monogenic dominant resistance in Corsica, with the resistant gene located at the Rsv1 locus. Beeson also contains a single dominant gene for SMV resistance, but the gene is located at the Rsv4 locus. Both genes in Corsica and Beeson confer a different SMV reaction pattern than other reported alleles at the same loci. Therefore, we propose the new symbols of Rsv1‐c for the resistant gene in Corsica and Rsv4‐b for the resistant gene in Beeson. The results from the genetic study were confirmed by the molecular markers and TBIA. The information from this study can be used for parent selection by breeders in cross breeding and gene pyramiding.

Fitness penalty in susceptible host is associated with virulence of Soybean mosaic virus on Rsv1-genotype soybean: a consequence of perturbation of HC-Pro and not P3.

The multigenic Rsv1 locus in the soybean plant introduction (PI) 'PI96983' confers extreme resistance against the majority of Soybean mosaic virus (SMV) strains, including SMV-N, but not SMV-G7 and SMV-G7d. In contrast, in susceptible soybean cultivars lacking a functional Rsv1 locus, such as 'Williams82' (rsv1), SMV-N induces severe disease symptoms and accumulates to a high level, whereas both SMV-G7 and SMV-G7d induce mild symptoms and accumulate to a significantly lower level. Gain of virulence by SMV-N on Rsv1-genotype soybean requires concurrent mutations in both the helper-component proteinase (HC-Pro) and P3 cistrons. This is because of the presence of at least two resistance (R) genes, probably belonging to the nucleotide-binding leucine-rich repeat (NB-LRR) class, within the Rsv1 locus, independently mediating the recognition of HC-Pro or P3. In this study, we show that the majority of experimentally evolved mutational pathways that disrupt the avirulence functions of SMV-N on Rsv1-genotype soybean also result in mild symptoms and reduced accumulation, relative to parental SMV-N, in Williams82 (rsv1). Furthermore, the evaluation of SMV-N-derived HC-Pro and P3 chimeras, containing homologous sequences from virulent SMV-G7 or SMV-G7d strains, as well as SMV-N-derived variants containing HC-Pro or P3 point mutation(s) associated with gain of virulence, reveals a direct correlation between the perturbation of HC-Pro and a fitness penalty in Williams82 (rsv1). Collectively, these data demonstrate that gain of virulence by SMV on Rsv1-genotype soybean results in fitness loss in a previously susceptible soybean genotype, this being a consequence of mutations in HC-Pro, but not in P3.

The HC-Pro and P3 Cistrons of an Avirulent Soybean mosaic virus Are Recognized by Different Resistance Genes at the Complex Rsv1 Locus

The complex Rsv1 locus in soybean plant introduction (PI) 'PI96983' confers extreme resistance (ER) against Soybean mosaic virus (SMV) strain N but not SMV-G7 and SMV-G7d. Both the SMV helper-component proteinase (HC-Pro) and P3 cistrons can serve as avirulence factors recognized by Rsv1. To understand the genetics underlying recognition of the two cistrons, we have utilized two soybean lines (L800 and L943) derived from crosses between PI96983 (Rsv1) and Lee68 (rsv1) with distinct recombination events within the Rsv1 locus. L800 contains a single PI96983-derived member (3gG2) of an Rsv1-associated subfamily of nucleotide-binding leucine-rich repeat (NB-LRR) genes. In contrast, although L943 lacks 3gG2, it contains a suite of five other NB-LRR genes belonging to the same family. L800 confers ER against SMV-N whereas L943 allows limited replication at the inoculation site. SMV-N-derived chimeras containing HC-Pro from SMV-G7 or SMV-G7d gained virulence on L943 but not on L800 whereas those with P3 replacement gained virulence on L800 but not on L943. In reciprocal experiments, SMV-G7- and SMV-G7d-derived chimeras with HC-Pro replacement from SMV-N lost virulence on L943 but retained virulence on L800 whereas those with P3 replacement lost virulence on L800 while remaining virulent on L943. These data demonstrate that distinct resistance genes at the Rsv1 locus, likely belonging to the NB-LRR class, mediate recognition of HC-Pro and P3.

Two Novel Alleles at the Rsv 3 Locus for Resistance to Soybean Mosaic Virus in PI 399091 and PI 61947 Soybeans

ABSTRACTSoybean mosaic virus (SMV) is one of the most destructive viral diseases in soybean [Glycine max (L.) Merr.] worldwide. Soybean mosaic virus isolates collected in the United States have been classified into seven strain groups (G1 through G7). Three loci (Rsv1, Rsv3, and Rsv4) conferring resistance to SMV have been reported so far. Each locus has several alleles that confer different reactions to isolates from the seven SMV strains. Plant Introduction (PI) 399091 and PI 61947 showed a different pattern in response to SMV compared to differential genotypes with known genes, and was therefore assumed to carry novel genes or unique alleles. This study was conducted to determine the inheritance and allelic relationships of SMV resistance genes in these PIs. PI 399091 and PI 61947 were crossed with ‘Essex’ (Rsv), PI 96983 (Rsv1), L29 (Rsv3), and V94‐5152 (Rsv4), and the F2 populations and F2:3 lines from these crosses were inoculated with a G7 isolate. A serological tissue blotting immunoassay (TBIA) was used to confirm the presence of the virus in the infected plants. Selected simple sequence repeat (SSR) markers were used to screen the parents and their progenies to confirm the phenotypic SMV reactions. The results revealed that PI 399091 and PI 61947 each contain an allele at the Rsv3 locus. The phenotypic data were confirmed by SSR markers and TBIA. Based on their unique reaction patterns as compared to other reported Rsv3 alleles, PI 399091 and PI 61947 each contain a novel allele at the Rsv3 locus. We propose that the new symbols of Rsv3‐c and Rsv3‐h be assigned to the resistance alleles in PI 399091 and PI 61947, respectively. These alleles can be considered as valuable sources of resistance to virulent SMV strains.

Reactions of Commercial Soybean Cultivars from the Mid South to Soybean Mosaic Virus

ABSTRACTSoybean mosaic virus (SMV) is one of the most important viral diseases, causing drastic reductions in seed yield and quality. Seven SMV strains, G1 through G7, have been identified, and three resistance loci, Rsv1, Rsv3, and Rsv4, have been reported in the United States. The objectives of this study were to evaluate the reactions of a set of modern soybean [Glycine max (L.) Merr.] cultivars to SMV and to deduce which previously reported genes were involved in resistance. A total of 303 cultivars currently grown in the mid‐southern United States were screened in the greenhouse with six SMV strains (G1, G2, G3, G5, G6, and G7). The results demonstrated that 189 cultivars were susceptible to all six SMV strains. Three cultivars were resistant to G1, G2, G3, G5, and G6 but developed stem‐tip necrosis after infection with G7, so these were presumed to carry the Rsv1 allele. Sixty‐six cultivars were resistant to G1 through G3 but susceptible to G5 through G7 and presumably carry Rsv1‐y. One cultivar was resistant to G1 through G3 but necrotic to G5 through G7 and may carry Rsv1‐k. Two cultivars probably carry Rsv1‐t because they were resistant to G1, G2, G5, and G6 but necrotic to G3 and G7, and another two cultivars may carry Rsv1‐n because they were necrotic to G1, G2, G5, and G6 but susceptible to G2 and G7. Four cultivars were susceptible to G1 through G3 but resistant to G5 through G7, and therefore they may carry Rsv3. Two cultivars were resistant to all six SMV strains, and therefore they may carry Rsv4, Rsv1‐h, or two‐gene combinations. There were 34 cultivars exhibiting unique SMV reaction patterns that may carry novel genes or alleles, including 23 cultivars that may carry novel alleles at the Rsv1 locus and 11 that may carry novel alleles at the Rsv3 locus. The results from this study can be used by breeders to choose resistant cultivars as parents in soybean breeding programs and by producers to select resistant cultivars in areas where SMV is a disease of concern for soybean production.

The Rsv3 Locus Conferring Resistance to Soybean Mosaic Virus is Associated with a Cluster of Coiled‐Coil Nucleotide‐Binding Leucine‐Rich Repeat Genes

The Soybean mosaic virus (SMV) resistance locus, Rsv3, previously mapped between markers A519F/R and M3Satt in the soybean molecular linkage group B2 (chromosome 14), has been characterized by examination of the soybean genome sequence. The 154 kbp interval encompassing Rsv3 contains a family of closely related coiled‐coil nucleotide‐binding leucine‐rich repeat (CC‐NB‐LRR) genes. Tightly linked to this region are additional CC‐NB‐LRR genes and several leucine‐rich repeat receptor‐like kinase (LRR‐RLK) genes, thereby indicating that members of both multigene families constitute a heterogeneous cluster at the Rsv3 chromosomal region. To further confirm the sequence and genetic map concordance, we developed 16 markers from the genomic sequence including predicted CC‐NB‐LRR genes and their flanking sequences. Mapping of the resultant markers in three populations showed parallel alignment between the genetic and sequence maps in the Rsv3‐containing region. Phylogenetic analysis of five CC‐NB‐LRR genes including a pseudogene showed they were highly similar to each other and formed a subclade within a CC‐NB‐LRR gene clade with representatives from several plant families including legume species. These results demonstrate that the Rsv3 locus is associated with this cluster of CC‐NB‐LRR genes, thereby suggesting that the Rsv3 gene most likely encodes a member of this gene family. In addition, information from this study should facilitate marker‐assisted selection and pyramiding of resistance genes.

Genetic Analysis of “8101” Soybean Containing Three Genes for Resistance to Soybean Mosaic Virus

ABSTRACTSoybean mosaic virus (SMV) occurs in most soybean [Glycine max (L.) Merr.] growing areas around the world. The use of soybean cultivars with resistance to SMV is the most effective way of controlling this disease. Three independent genetic loci (Rsv1, Rsv3, and Rsv4) with multiple alleles for SMV resistance have been identified. The objective of this study was to evaluate the genetic composition of a Chinese soybean line 8101 for SMV resistance. In this study, 8101 was crossed with susceptible cultivars Lee 68, Essex, and Hefeng No. 25. The genotype 8101 was also crossed with resistant lines PI 96983, L29, and V94‐5152 carrying Rsv1, Rsv3, and Rsv4, respectively, to examine the allelic relationship between the genes in 8101 and the previously reported genes at these three loci. The results indicated that 8101 carries three independent dominant genes for resistance to SMV. One of them is at the Rsv1 locus but carries a different allele than the Rsv1 in PI 96983. This new allele confers resistance to SMV G1 but a susceptible reaction to SMV G7. The second gene is at the Rsv3 locus conferring resistance to SMV G7 but a susceptible reaction to SMV G1. The third gene is at the Rsv4 locus and confers resistance to both SMV G1 and G7. The presence of these three genes in 8101 confers resistance to SMV strains G1 through G3 and G5 through G7. The line 8101 is the first genotype identified as carrying all three SMV resistance genes, Rsv1, Rsv3, and Rsv4 Research is underway to further characterize the three resistance genes in 8101.

Experimental adaptation of an RNA virus mimics natural evolution.

Identification of virulence determinants of viruses is of critical importance in virology. In search of such determinants, virologists traditionally utilize comparative genomics between a virulent and an avirulent virus strain and construct chimeras to map their locations. Subsequent comparison reveals sequence differences, and through analyses of site-directed mutants, key residues are identified. In the absence of a naturally occurring virulent strain, an avirulent strain can be functionally converted to a virulent variant via an experimental evolutionary approach. However, the concern remains whether experimentally evolved virulence determinants mimic those that have evolved naturally. To provide a direct comparison, we exploited a plant RNA virus, soybean mosaic virus (SMV), and its natural host, soybean. Through a serial in vivo passage experiment, the molecularly cloned genome of an avirulent SMV strain was converted to virulent variants on functionally immune soybean genotypes harboring resistance factor(s) from the complex Rsv1 locus. Several of the experimentally evolved virulence determinants were identical to those discovered through a comparative genomic approach with a naturally evolved virulent strain. Thus, our observations validate an experimental evolutionary approach to identify relevant virulence determinants of an RNA virus.

Multiplex single nucleotide polymorphism (SNP) assay for detection of soybean mosaic virus resistance genes in soybean

Soybean mosaic virus (SMV) is one of the most destructive viral diseases in soybean (Glycine max). Three independent loci for SMV resistance have been identified in soybean germplasm. The use of genetic resistance is the most effective method of controlling this disease. Marker assisted selection (MAS) has become very important and useful in the effort of selecting genes for SMV resistance. Single nucleotide polymorphism (SNP), because of its abundance and high-throughput potential, is a powerful tool in genome mapping, association studies, diversity analysis, and tagging of important genes in plant genomics. In this study, a 10 SNPs plus one insert/deletion (InDel) multiplex assay was developed for SMV resistance: two SNPs were developed from the candidate gene 3gG2 at Rsv1 locus, two SNPs selected from the clone N11PF linked to Rsv1, one 'BARC' SNP screened from soybean chromosome 13 [linkage group (LG) F] near Rsv1, two 'BARC' SNPs from probe A519 linked to Rsv3, one 'BARC' SNP from chromosome 14 (LG B2) near Rsv3, and two 'BARC' SNPs from chromosome 2 (LG D1b) near Rsv4, plus one InDel marker from expressed sequence tag (EST) AW307114 linked to Rsv4. This 11 SNP/InDel multiplex assay showed polymorphism among 47 diverse soybean germplasm, indicating this assay can be used to investigate the mode of inheritance in a SMV resistant soybean line carrying Rsv1, Rsv3, and/or Rsv4 through a segregating population with phenotypic data, and to select a specific gene or pyramid two or three genes for SMV resistance through MAS in soybean breeding program. The presence of two SMV resistance genes (Rsv1 and Rsv3) in J05 soybean was confirmed by the SNP assay.

New sources of resistance to Soybean mosaic virus in soybean

Soybean mosaic virus (SMV) is one of the most prevalent viral diseases in all major soybean-growing areas worldwide. Seven strain groups of SMV (G1-G7) and three resistance loci (Rsv1, Rsv3, and Rsv4) have been identified in soybean (Glycine max). In our initial study, 209 soybean genotypes were screened for reactions to G1 and G7, 129 of which were resistant to one or two strains. The objective of this research was to screen 127 genotypes with six SMV strains and differentiate specific alleles for resistance in these genotypes. The results demonstrated that 84 genotypes carry alleles at the Rsv1 locus: 42 with Rsv1-y, 5 with Rsv1, 19 with Rsv1-k, 8 with Rsv1-t, 8 with Rsv1-r, 1 with Rsv1-n, and 1 with Rsv1-h. Sixteen genotypes were identified to presumably carry new alleles for SMV resistance at Rsv1, Rsv3, or Rsv4. Nine of these 16 genotypes ('Kosuzu', 'Suzumaru', PI 398877, 'Jitsuka', 'Clifford', and 'Tousan 65', 'Corsica', PI 61944, and PI 61947) may carry new alleles at the Rsv1 locus based on the comparison of their differential reaction patterns against the nine reported Rsv1 alleles. Two genotypes (PI 339870 and PI 399091) may carry new resistance alleles at the Rsv3 locus. Five genotypes (KAERI-GNT-220-7, PI 398593, PI 438307, 'Rhosa', and 'Beeson') may carry new alleles at the Rsv4 locus. In addition, 18 genotypes were resistant to all six strains tested and may carry Rsv1-h, Rsv4, Rsv1Rsv3, Rsv1Rsv4, or Rsv3Rsv4. Research is underway to confirm the new SMV resistance alleles through genetic and molecular approaches. Key words: Glycine max, virus reaction, resistance genes, germplasm, Soybean mosaic virus. Le virus de la mosaïque du soja (VMS) est une des maladies virales les plus répandues dans toutes les principales régions productrices de soja (Glycine max), et ce, à l'échelle de la planète. Sept groupes de souches du VMS (G1-G7) et 3 locus de résistance (Rsv1, Rsv3 et Rsv4) ont été identifiés chez le soja. Au cours de notre étude initiale, 209 génotypes de soja ont été criblés pour évaluer leurs réactions à G1 et G7. Parmi ceux-ci, 129 se sont montrés réfractaires à une souche ou aux deux. Le but de cette recherche était de cribler 127 génotypes avec 6 souches de VMS et d'y différencier les allèles spécifiques de la résistance. Les résultats ont démontré que 84 génotypes portent des allèles au niveau du locus Rsv1 : 42 au Rsv1-y, 5 au Rsv1, 19 au Rsv1-k, 8 au Rsv1-t, 8 au Rsv1-r, 1 au Rsv1-n et 1 au Rsv1-h. Seize génotypes ont été identifiés en tant que porteurs probables de nouveaux allèles de résistance au VMS au niveau des locus Rsv1, Rsv3 ou Rsv4. Si l'on compare leurs schémas différentiels de réaction à ceux des 9 allèles Rsv1 visés, 9 de ces seize génotypes ('Kosuzu', 'Suzumaru', PI 398877, 'Jitsuka', 'Clifford', 'Tousan 65', 'Corsica', PI 61944 et PI 61947) peuvent porter de nouveaux allèles au niveau du locus Rsv1 ; deux génotypes (PI 339870 et PI 399091) peuvent porter de nouveaux allèles au niveau du locus Rsv3 ; et cinq génotypes (KAERI-GNT-220-7, PI 398593, PI 438307, 'Rhosa' et 'Beeson') peuvent porter de nouveaux allèles au niveau du locus Rsv4. De plus, 18 génotypes étaient réfractaires aux 6 souches testées et pourraient porter les locus Rsv1-h, Rsv4, Rsv1Rsv3, Rsv1Rsv4 ou Rsv3Rsv4. Des recherches faisant appel à des protocoles génétiques et moléculaires sont en cours de réalisation afin de confirmer la présence des nouveaux allèles de résistance au VMS. Mots-clés : Glycine max, réaction aux virus, gènes de résistance, plasma germinal, virus de la mosaïque du soja.

A PCR‐based Marker for the Rsv1 Locus Conferring Resistance to Soybean Mosaic Virus

Soybean mosaic virus (SMV) is a highly destructive viral disease. Three loci with 12 alleles conferring SMV resistance have been identified in soybean [Glycine max (L.) Merr.]. The objective of this study was to develop polymerase chain reaction–based markers for detecting the candidate gene 3gG2 at the Rsv1 locus for SMV resistance in diverse soybean germplasm. A pair of DNA primers, Rsv1‐f/r, was developed from the 3gG2 sequence. This primer pair produced a 341‐bp DNA fragment specific for soybean cultivars containing Rsv1 The same fragment was confirmed in genotypes containing Rsv1 alleles including ‘Kwanggyo’ (Rsv1‐k), ‘Marshall’ (Rsv1‐m), ‘Ogden’ (Rsv1‐t), PI 96983 (Rsv1), PI 507389 (Rsv1‐n), ‘Raiden’ (Rsv1‐r), and ‘Suweon 97’ (Rsv1‐s). The Rsv1‐f/r fragment was also amplified in genotypes with two‐gene combinations (Rsv1Rsv3 and Rsv1Rsv4) but not in genotypes containing only Rsv3 or Rsv4 or in the susceptible genotypes. The primer pair was used to screen for Rsv1 alleles in 97 SMV resistant genotypes. Results showed that 55 genotypes contained the 3gG2 gene, while 17 genotypes carrying the Rsv1‐y allele and additional 25 SMV‐resistant genotypes carrying Rsv3 or Rsv4 were not amplified a product using the 3gG2 primer pair. Analysis of an F2 population derived from J05 (Rsv1Rsv3) × ‘Essex’ (rsv1rsv3) showed a cosegregation between the marker Rsv1‐f/r and the Rsv1 allele. Rsv1‐f/r was also shown to be linked to simple sequence repeat marker Satt114 on soybean molecular linkage group F with a distance of 5.42 cM. This marker will give breeders a tool for marker‐assisted selection and gene pyramiding in soybean breeding for SMV resistance.

Genetic Analysis of Resistance to Soybean Mosaic Virus in J05 Soybean

Soybean cultivar J05 was identified to be resistant to the most virulent strain of soybean mosaic virus (SMV) in northeastern China. However, the reaction of J05 to SMV strains in the United States of America is unknown, and genetic information is needed to utilize this germplasm in a breeding program. The objectives of this study were to determine the reaction of J05 to all US strains of SMV (G1-G7), the inheritance of SMV resistance in J05, and the allelic relationship of resistance genes in J05 with other reported resistance genes. J05 was crossed with susceptible cultivar Essex (rsv) to study the inheritance of SMV resistance. J05 was also crossed with PI 96983 (Rsv1), L29 (Rsv3), and V94-5152 (Rsv4) to test the allelism of resistance genes. F(2) populations and F(2:3) lines from these crosses were inoculated with G1 or G7 in the greenhouse. Inheritance and allelism studies indicate that J05 possesses 2 independent dominant genes for SMV resistance, one at the Rsv1 locus conferring resistance to G1 and necrosis to G7 and the other at the Rsv3 locus conditioning resistance to G7 but susceptibility to G1. The presence of both genes in J05 provides resistance to G1 and G7. J05 is unique from the previous sources that carry 2 genes of Rsv1Rsv3 and will be useful in breeding for SMV resistance.

Characterization of Resistance to Soybean mosaic virus in Diverse Soybean Germplasm

Soybean mosaic virus (SMV) causes one of the most destructive viral diseases in soybean [Glycine max (L.) Merr.] worldwide. Ninety‐eight SMV isolates identified in the USA have been classified into seven strain groups (G1–G7). Three independent loci (Rsv1, Rsv3, and Rsv4) have been identified for SMV resistance. Multiple resistance alleles have been reported for the Rsv1 and Rsv3 locus. The objective of this research was to group diverse soybean genotypes on the basis of their differential reactions to SMV strains. SMV strains G1 and G7 were used to characterize the reactions of 212 soybean genotypes to SMV. Fifty‐five genotypes were resistant to G1 but susceptible to G7, and virus was detected in G7‐inoculated plants. Thirty‐one genotypes were resistant to G1 but exhibited stem‐tip necrosis following G7 inoculation. These 86 soybean genotypes presumably carry alleles at the Rsv1 locus. Thirty‐seven genotypes were resistant to G1 and G7, and SMV was not detected by ELISA, indicating that they probably carry Rsv4, Rsv1‐r, or Rsv1‐h or a combination of two resistance genes Rsv1Rsv3, Rsv1Rsv4, or Rsv3Rsv4. Seven genotypes were susceptible to G1 but resistant to G7 and may carry alleles at the Rsv3 locus. PI 507389 and PI 61944 developed stem‐tip necrosis after inoculation with G1 and a mosaic symptom when inoculated with G7, indicating that PI 61944 may carry the same Rsv1‐n gene as PI 507389. Eighty soybean accessions developed mosaic symptoms when inoculated with G1 or G7 because of the lack of SMV resistance genes. The information from this research will be helpful in selecting SMV‐resistant parents for crossing in a breeding program.