Soybean Accession PI Research Articles

The Soybean Rpp3 Gene Encodes a TIR-NBS-LRR Protein that Confers Resistance to Phakopsora pachyrhizi.

Soybean rust is an economically significant disease caused by the fungus Phakopsora pachyrhizi that negatively impacts soybean (Glycine max [L.] Merr.) production throughout the world. Susceptible plants infected by P. pachyrhizi develop tan-colored lesions on the leaf surface that give rise to funnel-shaped uredinia as the disease progresses. While most soybean germplasm is susceptible, seven genetic loci (Rpp1 to Rpp7) that provide race-specific resistance to P. pachyrhizi (Rpp) have been identified. Rpp3 was first discovered and characterized in the soybean accession PI 462312 (Ankur), and it was also determined to be one of two Rpp genes present in PI 506764 (Hyuuga). Genetic crosses with PI 506764 were later used to fine-map the Rpp3 locus to a 371-kb region on chromosome 6. The corresponding region in the susceptible Williams 82 (Wm82) reference genome contains several homologous nucleotide binding site-leucine rich repeat (NBS-LRR) genes. To identify Rpp3, we designed oligonucleotide primers to amplify Rpp3 candidate (Rpp3C) NBS-LRR genes at this locus from PI 462312, PI 506764, and Wm82 using polymerase chain reaction (PCR). Five Rpp3C genes were identified in both Rpp3-resistant soybean lines, and co-silencing these genes compromised resistance to P. pachyrhizi. Gene expression analysis and sequence comparisons of the Rpp3C genes in PI 462312 and PI 506764 suggest that a single candidate gene, Rpp3C3, is responsible for Rpp3-mediated resistance. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2024.

Identification of genomic loci conferring broad-spectrum resistance to multiple nematode species in exotic soybean accession PI 567305.

Genetic analysis identified a unique combination of major QTL for resistance to important soybean nematodes concurrently present in a single soybean accession, which has not been reported earlier. An exotic soybean [Glycine max (L.) Merr.] accession, PI 567305, was reported to be highly resistant to three important nematode species, soybean cyst (SCN), root-knot (RKN), and reniform (RN) nematodes. However, genetic basis controlling broad-spectrum resistance in this germplasm has not been investigated. We report results of genetic analysis to identify genomic loci conferring resistance to these nematode species. A bi-parental population consisting of 242 F8-derived recombinant inbred lines (RILs) was developed from a cross of a nematode susceptible cultivar, Magellan, and resistant accession, PI 567305. The RILs were phenotyped for nematode resistance to three SCN HG types. They were genotyped using the Infinium SoySNP6K BeadChips and genotype-by-sequencing (GBS) methods in an attempt to evaluate the cost-effectiveness and efficiency of these two genotyping platforms. Genetic analysis confirmed the major QTL on chromosomes (Chrs) 10 and 18 with broad-spectrum resistance to the three nematodes present in this germplasm. Haplotype and copy number variation analyses of SCN resistance QTL indicated that PI 567305 has a different haplotype, which is associated with likely a unique SCN resistance mechanism different from Peking- or PI 88788-type resistance. The evaluations of both Infinium Beadchip- and GBS-based genotyping technologies provided comprehensive insights for researchers to choose a cost-effective and efficient platform for QTL mapping and for other genomic studies in soybeans.

Genetic characterization of qSCN10 from an exotic soybean accession PI 567516C reveals a novel source conferring broad-spectrum resistance to soybean cyst nematode.

The qSCN10 locus with broad-spectrum SCN resistance was fine-mapped to a 379-kb region on chromosome 10 in soybean accession PI 567516C. Candidate genes and potential application benefits of this locus were discussed. Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most devastating pests of soybean, causing significant yield losses worldwide every year. Genetic resistance has been the major strategy to control this pest. However, the overuse of the same genetic resistance derived primarily from PI 88788 has led to the genetic shifts in nematode populations and resulted in the reduced effectiveness in soybean resistance to SCN. Therefore, novel genetic resistance resources, especially those with broad-spectrum resistance, are needed to develop new resistant cultivars to cope with the genetic shifts in nematode populations. In this study, a quantitative trait locus (QTL) qSCN10 previously identified from a soybean landrace PI 567516C was confirmed to confer resistance to multiple SCN HG Types. This QTL was further fine-mapped to a 379-kb region. There are 51 genes in this region. Four of them are defense-related and were regulated by SCN infection, suggesting their potential role in mediating resistance to SCN. The phylogenetic and haplotype analyses of qSCN10 as well as other information indicate that this locus is different from other reported resistance QTL or genes. There was no yield drag or other unfavorable traits associated with this QTL when near-isogenic lines with and without qSCN10 were tested in a SCN-free field. Therefore, our study not only provides further insight into the genetic basis of soybean resistance to SCN, but also identifies a novel genetic resistance resource for breeding soybean for durable, broad-spectrum resistance to this pest.

Fine-mapping and characterization of qSCN18, a novel QTL controlling soybean cyst nematode resistance in PI 567516C.

The qSCN18 QTL from PI 56756C was confirmed and fine-mapped to improve soybean resistance to the SCN population HG Type 2.5.7 using near-isogenic lines carrying recombination crossovers within the QTL region. The QTL underlying resistance was fine-mapped to a 166-Kbp region on chromosome 18, and the candidate genes were selected based on genomic analyses. Soybean cyst nematode (SCN, Heterodera glycines, Ichinohe) is the most devastating pathogen of soybean. Understanding the genetic basis of SCN resistance is crucial for managing this parasite in the field. Two major loci, rhg1 and Rhg4, were previously characterized as valuable resources for SCN resistance. However, their continuous use has caused shifts in the virulence of SCN populations, which can overcome the resistance conferred by these two major loci. Reduced effectiveness became a major concern in the soybean industry due to continuous use of rhg1 for decades. Thus, it is imperative to identify sources of SCN resistance for durable SCN management. A novel QTL qSCN18 was identified in PI567516C. To fine-map qSCN18 and identify resistance genes, a large backcross population was developed. Nineteen near-isogenic lines (NILs) carrying recombination crossovers within the QTL region were identified. The first phase of fine-mapping narrowed the QTL region to 549-Kbp, whereas the second phase confined the region to 166-Kbp containing 23 genes. Two flanking markers, MK-1 and MK-6, were developed and validated to detect the presence of the qSCN18 resistance allele. Haplotype analysis clustered the fine-mapped qSCN18 region from PI 567516C with the cqSCN-007 locus previously mapped in the wild soybean accession PI 468916. The NILs were developed to further characterize the causal gene(s) harbored in this QTL. This study also confirmed the previously identified qSCN18. The results will facilitate marker-assisted selection (MAS) introducing the qSCN18 locus from PI 567516C into high-yielding soybean cultivars with durable resistance to SCN.

Characterizing resistance to soybean cyst nematode in PI 494182, an early maturing soybean accession

AbstractThe soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) generates more damage to soybean [Glycine max (L.) Merr.] than any other parasite in most soybean‐producing countries. The use of SCN‐resistant cultivars remains the most effective method to limit losses caused by SCN. The SCN‐resistant accession PI 88788 has been used almost exclusively to control SCN over the past decades, inducing a shift in nematode virulence to overcome the resistance. Furthermore, PI 88788 and other sources of resistance characterized to date belong to maturity groups (MGs) III and higher, making them less attractive to develop early maturing soybean varieties (MGs 0‐000). In this work, we performed a quantitative trait loci (QTL) analysis of the SCN‐resistant soybean accession PI 494182 (MG 0). A recombinant inbred lines (RILs) population (‘Costaud’ × PI 494182) segregating for SCN resistance was challenged with SCN (H. glycines [HG] type 0) and genotyped via genotyping‐by‐sequencing (GBS) to produce a genetic map. Six resistance QTL were identified, including a potentially new resistance locus on chromosome 07. A subset of the RIL population was confronted to a HG type 2.5.7 SCN population and some of these exhibited resistance toward this type. Whole‐genome sequencing of PI 494182 and Costaud allowed us to determine the alleles and their copy number for three candidate genes: GmSNAP11, GmSNAP18 (Rhg1), and GmSHMT08 (Rhg4). Finally, we determined that selecting for PI 494182 alleles at some SCN‐resistance QTL could entail linkage drag (decrease in protein concentration and 100‐seed weight, increase in oil concentration). This work provides useful markers for introgressing SCN resistance in early maturing soybean varieties.

Rpp1 Encodes a ULP1-NBS-LRR Protein That Controls Immunity to Phakopsora pachyrhizi in Soybean.

Phakopsora pachyrhizi is the causal agent of Asian soybean rust. Susceptible soybean plants infected by virulent isolates of P. pachyrhizi are characterized by tan-colored lesions and erumpent uredinia on the leaf surface. Germplasm screening and genetic analyses have led to the identification of seven loci, Rpp1 to Rpp7, that provide varying degrees of resistance to P. pachyrhizi (Rpp). Two genes, Rpp1 and Rpp1b, map to the same region on soybean chromosome 18. Rpp1 is unique among the Rpp genes in that it confers an immune response (IR) to avirulent P. pachyrhizi isolates. The IR is characterized by a lack of visible symptoms, whereas resistance provided by Rpp1b to Rpp7 results in red-brown foliar lesions. Rpp1 maps to a region spanning approximately 150 kb on chromosome 18 between markers Sct_187 and Sat_064 in L85-2378 (Rpp1), an isoline developed from Williams 82 and PI 200492 (Rpp1). To identify Rpp1, we constructed a bacterial artificial chromosome library from soybean accession PI 200492. Sequencing of the Rpp1 locus identified three homologous nucleotide binding site-leucine rich repeat (NBS-LRR) candidate resistance genes between Sct_187 and Sat_064. Each candidate gene is also predicted to encode an N-terminal ubiquitin-like protease 1 (ULP1) domain. Cosilencing of the Rpp1 candidates abrogated the immune response in the Rpp1 resistant soybean accession PI 200492, indicating that Rpp1 is a ULP1-NBS-LRR protein and plays a key role in the IR.

Soybean PI 675847 A as a new source of salt tolerance

AbstractSoil salinity is a major limitation to legume production in many areas of the world. Identification of the genetic source of salt tolerance is critical in soybean breeding for improving soybean production in salt-affected regions. Vietnam has unique sources of soybean germplasm and varieties are grown in the area where exposure to salinity is frequent. However, there is little research on the identification of salt tolerant sources in the Vietnamese gene pool. The present study compared 18 Vietnamese soybean cultivars for their differences in salt tolerance. Under a range of NaCl stress from 0 to 200 mM NaCl, there was a large variation in salt tolerance among the 18 soybean lines evaluated. The soybean accession PI 675847 A (Vietnamese variety DT2008), was identified as a useful source of salt tolerance. During vegetative growth, PI 675847 A had lower leaf scorch scores, higher cell membrane stability, better photosynthesis and biomass accumulation under NaCl stress than the other 17 strains evaluated. In addition, PI 675847 A maintained better growth and seed yield in salt-affected soils compared with the sensitive lines. Analyses of ion contents in plant leaves under saline conditions showed that PI 675847 A was able to limit uptake and transport of Na+ and Cl−. Because of its higher productivity under saline conditions, PI 675847 A will be a useful germplasm source in soybean improvement programs for salt tolerance.

Genetic mapping and haplotype analysis of a locus for quantitative resistance to Fusarium graminearum in soybean accession PI 567516C.

A major novel quantitative disease resistance locus, qRfg_Gm06, for Fusarium graminearum was genetically mapped to chromosome 6. Genomic-assisted haplotype analysis within this region identified three putative candidate genes. Fusarium graminearum causes seed, root rot, and seedling damping-off in soybean which contributes to reduced stands and yield. A cultivar Magellan and PI 567516C were identified with low and high levels of partial resistance to F. graminearum, respectively. Quantitative disease resistance loci (QDRL) were mapped with 241 F7:8 recombinant inbred lines (RILs) derived from a cross of Magellan × PI 567516C. Phenotypic evaluation for resistance to F. graminearum used the rolled towel assay in a randomized incomplete block design. The genetic map was constructed from 927 polymorphic single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers. One major QDRL qRfg_Gm06 was detected and mapped to chromosome 6 with a LOD score of 20.3 explaining 40.2% of the total phenotypic variation. This QDRL was mapped to a ~400kb genomic region of the Williams 82 reference genome. Genome mining of this region identified 14 putative candidate disease resistance genes. Haplotype analysis of this locus using whole genome re-sequencing (WGRS) of 106 diverse soybean lines narrowed the list to three genes. A SNP genotyping Kompetitive allele-specific PCR (KASP) assay was designed for one of the genes and was validated in a subset of the RILs and all 106 diverse lines.

Genetic Analysis of Resistance to Soybean Mosaic Virus in PI 438307 Soybean Accession

Soybean mosaic virus (SMV) is the most prevalent viral pathogen and economic threat to soybean production worldwide. Three independent genes harboring SMV resistance have been identified: Rsv1, Rsv3, and Rsv4. Although the resistance genes (R‐genes) have been found in some germplasm, usually they provide protection to some, but not all, viral strains. The objective of this research was to identify a new source of SMV resistance in Korean soybean accession PI 438307. The soybean genotype PI 438307 was crossed with susceptible parent ‘Essex’ (rsv), and differential parents PI 96983 (Rsv1), L29 (Rsv3), and V94‐5152 (Rsv4). F2 plants and F2:3 lines derived from all four cross combinations were screened with SMV‐G7 strain. Additionally, F2 plants obtainSed from PI 438307 (R) × Essex (S) were genotyped with two simple sequence repeat (SSR) markers on chromosome 2 (MLG D1b). Inheritance and allelic studies revealed that resistance to SMV in PI 438307 is controlled by a single dominant gene allelic to the Rsv4 locus. PI 438307 exhibited unique symptomology when compared to reported Rsv4 alleles in V94‐5152, PI 88788 and Beeson. PI 438307 was resistant to SMV‐G1 through G6 and resistant at seedling stages to SMV‐G7. Therefore, it was proposed that the new allele Rsv4‐v might be assigned to the SMV resistance in this soybean accession. Soybean sources carrying Rsv4 alleles are rare among the soybean germplasm and confer resistance to all or most SMV strains; therefore, this allele may be a good choice for breeding programs in the future.

Suitability of Soybean Meal from Insect-Resistant Soybeans for Broiler Chickens.

Benning(M) and Benning(MGH) are near-isogenic lines (NILs) of the soybean cultivar Benning, which contain insect-resistance quantitative trait loci (QTLs) from the soybean accession PI 229358. Benning(M) contains QTL-M, which confers antibiosis and antixenosis. In addition to QTL-M, Benning(MGH) contains QTL-G, which confers antibiosis, and QTL-H, which confers antixenosis. Soybean meal was produced from Benning and the NILs. Nutritional composition, digestible amino acid content, and nitrogen-corrected true metabolizable energy (TMEN) were equivalent among soybean meals. A 21-day broiler feeding trial was carried out to determine if the QTLs affect soybean meal quality. Weight gain and feed-to-gain ratio were evaluated. No biologically significant differences were detected for broilers fed Benning, Benning(M), and Benning(MGH). This demonstrates that soybean meal produced from the insect-resistant NILs is equivalent to soybean meal produced from their non-insect-resistant parent cultivar for broiler weight gain.

Identification and mapping of resistance genes to Phakopsora pachyrhizi in soybean (Glycine max L.) accession PI 594767-A

The goal of this study was to study resistance inheritance in the soybean (Glycine max L.) accession PI 594767-A to the Phakopsora pachyrhizi isolate PPUFV02, and map the resistance gene(s) identified using microsatellite markers. Crosses between PI 594767-A and the susceptible cultivar 'Conquista' gave rise to the segregating subpopulations 26C-2 and 26C-5, which in the F2 generation were evaluated for their reactions to PPUFV02. In addition, analyses with microsatellite markers linked to the Rpp1-Rpp5 loci were also performed. The segregation pattern obtained in 26C-2 revealed that resistance was governed by a recessive gene; a 1:2:1 segregation pattern was observed in 26C-5, indicating control by a gene with partial dominance. This variability may have been caused because environmental conditions, particularly temperature, when 26C-5 was assessed were unfavorable for pathogen development, allowing the phenotypic expression of heterozygous alleles in PI 594767-A. A resistance gene was located in the soybean linkage group G, in the genomic region between Sct_187r2 and Sat_064 that contains the Rpp1 locus. Resistance in PI 594767-A is probably conferred by a new Rpp1 gene allele, because this accession has a haplotype for Sct_187r2 and Sat_064, which differs from haplotypes of accessions that also contain resistance alleles that map the Rpp1 locus. The use of Sct_187r2 and Sat_064 will facilitate the introgression of the resistance allele from PI 594767-A and its pyramiding with other resistance genes into genotypes with superior agronomic characteristics, in order to obtain cultivars with broad-spectrum resistance to P. pachyrhizi.

Resistance to Phakopsora pachyrhizi in Soybean PI 587905 Maps to the Rpp1 Locus and Exhibits Variable Dominance Associated with Plant Ontogeny

Soybean rust, caused by Phakopsora pachyrhizi Sydow, results in significant soybean (Glycine max (L.) Merr.) yield losses worldwide. The purpose of this research was to confirm the inheritance, gene action, and genomic location of resistance to P. pachyrhizi in soybean accession PI 587905. Two independent populations (F2-derived F3 lines and F2 plants) were inoculated with P. pachyrhizi in a greenhouse and assayed in a field, respectively, in southeastern Paraguay. Both the field F2 and the greenhouse F2-inferred segregation ratios fit the 1:2:1 ratio expected for segregation of a single gene (P > 0.05). Unlike previous studies, gene action differed according to ontogeny. Among seedlings in the greenhouse, gene action was dominant, but in the field assay among adult plants, the gene exhibited incomplete dominance. Molecular markers were used to map the resistance gene in PI 587905 to the Rpp1 locus. This information should be useful to plant breeders for developing and selecting resistant cultivars.

Physiological properties of a drought-resistant wild soybean genotype: Transpiration control with soil drying and expression of root morphology

Aims Wild soybean accession PI 468917 [Glycine soja (Sieb. and Zucc.)] was examined for traits that could potentially be beneficial for development of drought resistant soybean cultivars.

Soybean Germplasm Resistant to Pythium irregulare and Molecular Mapping of Resistance Quantitative Trait Loci derived from the Soybean Accession PI 424354

ABSTRACTPythium irregulare Buisman is an important seed and seedling pathogen of many hosts including soybean [Glycine max (L.) Merr.] and has been increasingly linked to reports of stand losses. The objectives of this research were to identify sources of resistance to P. irregulare, characterize the type of resistance identified, and genetically map the resistance. Sixty‐five soybean genotypes were evaluated for resistance to two isolates of P. irregulare, and approximately one‐third had moderate to high levels of resistance. The PI 424354 had the highest levels of resistance to P. irregulare, and resistance was mapped in two three‐way cross populations: ‘OHS 303’ (moderately susceptible) × (‘Williams’ (moderately susceptible) × PI 424354) and ‘Dennison’ (moderately susceptible) × (Williams × PI 424354). Resistance quantitative trait loci (QTL) with alleles from PI 424354 were mapped on chromosomes 1 and 6 in OHS 303 × (Williams × PI 424354) using composite interval mapping (CIM) for root weights and root rot scores. Resistance QTL from PI 424354 were also mapped on chromosomes 8 and 11 with CIM for root weight data in the Dennison × (Williams × PI 424354) population and chromosome 13 using root rot scores. Each QTL explained 7.9 to 17.8% of the phenotypic variation. These are the first reported putative QTL for resistance to P. irregulare in soybean.

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.

Map Location of the Rpp1 Locus That Confers Resistance to Soybean Rust in Soybean

ABSTRACTSoybean rust (SBR), caused by Phakopsora pachyrhizi, was first discovered in North America in 2004 and has the potential to become a major soybean [Glycine max (L.) Merr.] disease in the USA. Currently, four SBR resistance genes have been identified but not mapped on the soybean genetic linkage map. One of these resistance genes is the Rpp1 gene, which is present in the soybean accession PI 200492 The availability of molecular markers associated with Rpp1 will permit marker‐assisted selection and expedite the incorporation of this gene into U.S. cultivars. We compared simple sequence repeat (SSR) markers between ‘Williams 82’ and the BC5 Williams 82 isoline L85‐2378, which contains the Rpp1 resistance allele from the soybean accession PI 200492, for candidate regions that might contain Rpp1 One candidate region was found with the SSR marker BARC_Sct_187 on linkage group G. A population of BC6F2:3 lines segregating for the Rpp1 resistance locus was genotyped in this region on linkage group G followed by inoculation with the P. pachyrhizi isolate India 73‐1 in the USDA‐ARS Biosafety Level 3 Plant Pathogen Containment Facility at Ft. Detrick, MD. The Rpp1 gene was mapped between SSR markers BARC_Sct_187 and BARC_Sat_064 on linkage group G.

Anastomosis groups of Rhizoctonia solani associated with soybean root and hypocotyl rot in Ontario and resistance of accession PI 442031 to different anastomosis groups

Rhizoctonia solani is a complex species and causes soybean root and hypocotyl rot worldwide. Identifying anastomosis groups (AGs) prevalent in a region and growing cultivars with resistance specific to those AGs is a potential means to minimize economic losses from this disease. The main objectives of this study were (i) to identify the predominant AGs of R. solani associated with soybean root and hypocotyl rot in Ontario using both anastomosis grouping and polymerase chain reaction with AG-specific primers; and (ii) to determine the resistance of the soybean accession PI 442031 to different AGs. In 2 years, 278 R. solani isolates were recovered from diseased soybean plants across Ontario and classified into AG-2-2 IIIB (86.0%), AG-4 (1.4%), and AG-5 (12.6%). In general, isolates of AG-2- 2 IIIB were more aggressive than isolates of AG-4 and AG-5. PI 442031 was moderately resistant to all isolates of AG-4 and AG-5, but was highly susceptible to most AG-2-2 IIIB isolates