Elite Soybean Research Articles

Molecular validation of Rpp5 gene linked to soybean rust resistance in Indian genotypes

Soybean is an important oilseed crop which is affected by several diseases. Soybean rust is one of the most important diseases of soybean. The present study was aimed at screening of elite soybean lines with SSR markers for resistance to soybean rust disease. Among the markers used, Satt 275 showed polymorphism for both the parents (EC 241780 and JS 335) as well as other genotypes. The amplified PCR product of genotypes with polymorphic marker Satt 275 was sequenced and most of the sequences scored an E value of 0.031 and an identity of 90 per cent with the mRNA sequence of the Rpp5 gene. The classification results revealed that the sequence of the advanced line DSb 30-2 showed the highest degree of identity with the concerned Rpp5 like disease resistance mRNA sequence.

Transcriptomic analysis of genes in soybean in response to Peronospora manshurica infection

BackgroundSoybean downy mildew (SDM), caused by Peronospora manshurica (Pm), is a major fungal disease in soybean. To date, little is known regarding the defense mechanism at molecular level and how soybean plants response to Pm infection. In this study, differential gene expression in SDM-resistant (HR) and SDM-susceptible (HS) genotype was analyzed by RNA-seq to identify differentially expressed genes (DEGs) following Pm infection.ResultsOf a total of 55,017 genes mapped to the soybean reference genome sequences, 2581 DEGs were identified. Clustering analysis of DEGs revealed that these genes could be grouped into 8 clusters with distinct expression patterns. Functional annotation based on gene ontology (GO) and KEGG analysis indicated they involved in diverse metabolism pathways. Of particular interest were the detected DEGs participating in SA/ROS and JA signalling transduction and plant/pathogen interaction.ConclusionTotally, 52 DEGs with P value < 0.001 and log2 fold change > 2 or < − 2 upon fungal inoculation were identified, suggesting they were SDM defense responsive genes. These findings have paved way in further functional characterization of candidate genes and subsequently can be used in breeding of elite soybean varieties with better SDM-resistance.

Field evaluation of three sources of genetic resistance to sudden death syndrome of soybean.

Despite numerous challenges, field testing of three sources of genetic resistance to sudden death syndrome of soybean provides information to more effectively improve resistance to this disease in cultivars. Sudden death syndrome (SDS) of soybean [Glycine max (L.) Merrill] is a disease that causes yield loss in soybean growing regions across the USA and worldwide. While several quantitative trait loci (QTL) for SDS resistance have been mapped, studies to further evaluate these QTL are limited. The objective of our research was to map SDS resistance QTL and to test the effect of mapped resistance QTL on foliar symptoms when incorporated into elite soybean backgrounds. We mapped a QTL from Ripley to chromosome 10 (CHR10) and a QTL from PI507531 to chromosomes 1 and 18 (CHR1 and 18). Six populations were then developed to test the following QTL: cqSDS-001, with resistance originating from PI567374, CHR10, CHR1, and CHR18. The populations whichsegregated for resistant and susceptible QTL alleles were field tested in multiple environments and evaluated for SDS foliar symptoms. While foliar disease development was variable across environments and populations, a significant effect of each QTL on disease was detected within at least one environment. This includes the detection of cqSDS-001 in three genetic backgrounds. The QTL allele from the resistant parents was associated with greater resistance than the susceptible alleles for all QTL and backgrounds with the exception of the allele for CHR18, where the opposite occurred. This study highlights the importance and difficulties of evaluating QTL and the need for multi-year SDS field testing. The information presented in this study can aid breeders in making decisions to improve resistance to SDS.

Identification of a major quantitative trait locus underlying salt tolerance in \u2018Jidou 12\u2019 soybean cultivar

BackgroundIdentification of the quantitative trait locus (QTL) underlying salt tolerance is a prerequisite for marker-assisted selection in the salt-tolerant breeding process.MethodsIn this study, the recombinant inbred lines derived from the salt-tolerant elite soybean cultivar ‘Jidou 12’ and the salt-sensitive elite cultivar ‘Ji NF 58’ were used to identify the QTL associated with salt tolerance, using both salt tolerance rating (STR) and leaf chlorophyll content (SPAD) as indicators.ResultsA major salt-tolerant QTL, which was flanked by SSR markers GMABAB and Barcsoyssr_03_1421 on chromosome 3, was identified based on single-marker regression, single trait composite interval mapping, and multiple interval mapping analysis. For STR, the LOD ranged from 19.8 to 20.1; R2 ranged from 44.3 to 44.7%; and the additive effect ranged from 0.876 to 0.885 among the three mapping methods. For SPAD, the LOD ranged from 10.6 to 11.0; R2 ranged from 27.0 to 27.6%; and the additive effect ranged from 1.634 to 1.679 among the three mapping methods.ConclusionsIn this study, a major QTL conditioning salt tolerance on chromosome 3 was identified. The DNA markers closely associated with the QTLs might be useful in marker-assisted selection for soybean salt tolerance improvement in Huanghuaihai, China.

Characterization of a new GmFAD3A allele in Brazilian CS303TNKCA soybean cultivar.

We molecularly characterized a new mutation in the GmFAD3A gene associated with low linolenic content in the Brazilian soybean cultivar CS303TNKCA and developed a molecular marker to select this mutation. Soybean is one of the most important crops cultivated worldwide. Soybean oil has 13% palmitic acid, 4% stearic acid, 20% oleic acid, 55% linoleic acid and 8% linolenic acid. Breeding programs are developing varieties with high oleic and low polyunsaturated fatty acids (linoleic and linolenic) to improve the oil oxidative stability and make the varieties more attractive for the soy industry. The main goal of this study was to characterize the low linoleic acid trait in CS303TNKCA cultivar. We sequenced CS303TNKCA GmFAD3A, GmFAD3B and GmFAD3C genes and identified an adenine point deletion in the GmFAD3A exon 5 (delA). This alteration creates a premature stop codon, leading to a truncated protein with just 207 residues that result in a non-functional enzyme. Analysis of enzymatic activity by heterologous expression in yeast support delA as the cause of low linolenic acid content in CS303TNKCA. Thus, we developed a TaqMan genotyping assay to associate delA with low linolenic acid content in segregating populations. Lines homozygous for delA had a linolenic acid content of 3.3 to 4.4%, and the variation at this locus accounted for 50.83 to 73.70% of the phenotypic variation. This molecular marker is a new tool to introgress the low linolenic acid trait into elite soybean cultivars and can be used to combine with high oleic trait markers to produce soybean with enhanced economic value. The advantage of using CS303TNKCA compared to other lines available in the literature is that this cultivar has good agronomic characteristics and is adapted to Brazilian conditions.

Development of a Simple Hydroponic Assay to Study Vertical and Horizontal Resistance of Soybean and Pathotypes of Phytophthora sojae

Phytophthora root rot, caused by Phytophthora sojae, is one of the most damaging diseases of soybean and the introgression of Rps (Resistance to P. sojae) genes into elite soybean lines is arguably the best way to manage this disease. Current bioassays to phenotype the gene-for-gene relationship are hampered with respect to reproducibility and long-term stability of isolates, and do not accurately predict horizontal resistance individually. The aim of our study was to investigate a new way of phenotyping P. sojae isolates and vertical and horizontal resistance in soybean that relies on zoospores inoculated directly into a hydroponic system. Inoculation of P. sojae isolates against a set of eight differentials accurately and reproducibly identified pathotypes over a period of two years. When applied to test vertical resistance of soybean lines with known and unknown Rps genes, the bioassay relied on plant dry weight to correctly identify all genes. In addition, simultaneous inoculations of three P. sojae isolates, collectively carrying eight major virulence factors against 64 soybean lines with known and unknown levels of horizontal resistance, separated the plants into five distinct groups of root rot, allowing the discrimination of lines with various degrees of partial resistance. Based on those results, this bioassay offers several advantages in facilitating efforts in breeding soybean for P. sojae resistance and in identifying virulence factors in P. sojae.

Response and interaction of Bradyrhizobium japonicum and arbuscular mycorrhizal fungi in the soybean rhizosphere

Regulatory response and interaction of Bradyrhizobium and arbuscular mycorrhizal fungi (AMF) play a vital role in rhizospheric soil processes and productivity of soybean (Glycine max L.). Nitrogen (N) and phosphorus (P) are essential nutrients for plant growth and productivity, the synergistic interaction(s) of AMF and Bradyrhizobium along with rhizospheric beneficial microorganisms stimulate soybean growth and development through enhanced mineral nutrient acquisition (N and P) and improved rhizosphere environment. Such interactions are crucial, especially under low-input eco-friendly agricultural cropping systems, which rely on biological processes rather than agrochemicals to maintain soil quality, sustainability, and productivity. Furthermore, enhancement of N-fixation by root nodules along with AMF-mediated synergism improves plant P nutrition and uptake, and proliferation of phosphate-solubilizing fungi. However, the genetic and/or allelic diversity among native strains, their genes/enzymes and many environmental factors (e.g., soil organic matter, fertilizers, light, temperature, soil moisture, and biotic interactors) affect the interactions between AMF and Bradyrhizobium. New information is available regarding the genetic composition of elite soybean inoculant strains in maximizing symbiotic performance, N-fixing capabilities and depending on N and P status the host-mediated regulation of root architecture. Overall, for sustainable soybean production systems, a deeper understanding of the interaction effects of Bradyrhizobium and AMF co-inoculation are expected in the future, so that optimized combinations of microorganisms can be applied as effective soil inoculants for plant growth promotion and fitness. The objective of this review is to offer insights into the mechanistic interactions of AMF and Bradyrhizobium and rhizopheric soil health, and elucidate the role of environmental factors in regulating growth, development and sustainable soybean productivity.

ITRAQ protein profile analysis of developmental dynamics in soybean [Glycine max (L.) Merr.] leaves.

Zao5241 is an elite soybean [Glycine max (L.) Merr.] line and backbone parent. In this study, we employed iTRAQ to analyze the proteomes and protein expression profiles of Zao5241 during leaf development. We identified 1,245 proteins in all experiments, of which only 45 had been previously annotated. Among overlapping proteins between three biological replicates, 598 proteins with 2 unique peptides identified were reliably quantified. The protein datasets were classified into 36 GO functional terms, and the photosynthesis term was most significantly enriched. A total of 113 proteins were defined as being differentially expressed during leaf development; 41 proteins were found to be differently expressed between two and four week old leaves, and 84 proteins were found to be differently expressed between two and six week old leaves, respectively. Cluster analysis of the data revealed dynamic proteomes. Proteins annotated as electron carrier activity were greatly enriched in the peak expression profiles, and photosynthesis proteins were negatively modulated along the whole time course. This dataset will serve as the foundation for a systems biology approach to understanding photosynthetic development.

Agronomic Evaluation of a High Protein Allele from PI407788A on Chromosome 15 across Two Soybean Backgrounds

Soybean [Glycine max (L.) Merr.] protein is a prominent plant‐based protein source worldwide due to its high quality and relatively low cost. A major barrier to the development of high protein cultivars is the negative relationship between seed protein and seed yield. A large effect protein quantitative trait locus (QTL) has been mapped to the same location on chromosome (chr) 15 in several studies and given the designation, cqSeed protein‐001. The objective of this study was to evaluate the effect of the high protein allele from PI407788A at the chr 15 locus on seed composition and agronomic traits. Populations of near isogenic lines (NILs) segregating for the high protein allele on chr 15 were developed by backcrossing this allele into two elite soybean backgrounds, and these NILs were evaluated at four field environments in Illinois. Across the two backgrounds, the PI407788A allele significantly (P &lt; 0.0001) increased seed protein and decreased seed oil compared to the recurrent alleles but had a nonsignificant effect on yield. Information from this study will aid breeders in forming strategies to develop cultivars with increased seed protein and yield to meet the needs of a growing world population.

Impact of seed protein alleles from three soybean sources on seed composition and agronomic traits.

Evaluation of seed protein alleles in soybean populations showed that an increase in protein concentration is generally associated with a decrease in oil concentration and yield. Soybean [Glycine max (L.) Merrill] meal is one of the most important plant-based protein sources in the world. Developing cultivars high in seed protein concentration and seed yield is a difficult task because the traits have an inverse relationship. Over two decades ago, a protein quantitative trait loci (QTL) was mapped on chromosome (chr) 20, and this QTL has been mapped to the same position in several studies and given the confirmed QTL designation cqSeed protein-003. In addition, the wp allele on chr 2, which confers pink flower color, has also been associated with increased protein concentration. The objective of our study was to evaluate the effect of cqSeed protein-003 and the wp locus on seed composition and agronomic traits in elite soybean backgrounds adapted to the Midwestern USA. Segregating populations of isogenic lines were developed to test the wp allele and the chr 20 high protein QTL alleles from Danbaekkong (PI619083) and Glycine soja PI468916 at cqSeed protein-003. An increase in protein concentration and decrease in yield were generally coupled with the high protein alleles at cqSeed protein-003 across populations, whereas the effects of wp on protein concentration and yield were variable. These results not only demonstrate the difficulty in developing cultivars with increased protein and yield but also provide information for breeding programs seeking to improve seed composition and agronomic traits simultaneously.

Genome-wide association study for soybean cyst nematode resistance in Chinese elite soybean cultivars

Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is a highly recalcitrant endoparasite of soybean roots, causing more yield loss than any other pest. To identify quantitative trait loci (QTL) controlling resistance to SCN (HG type 2.5.7, race 1), a genome-wide association study (GWAS) was performed. The association panel, consisting of 120 Chinese soybean cultivars, was genotyped with 7189 single nucleotide polymorphism (SNPs). A total of 6204 SNPs with minor allele frequency >0.05 were used to estimate linkage disequilibrium (LD) and population structure. The mean level of LD measured by r 2 declined very rapidly to half its maximum value (0.51) at 220 kb. The overall population structure was approximately coincident with geographic origin. The GWAS results identified 13 SNPs in 7 different genomic regions significantly associated with SCN resistance. Of these, three SNPs were localized in previously mapped QTL intervals, including rhg1 and Rhg4. The GWAS results also detected 10 SNPs in 5 different genomic regions associated with SCN resistance. The identified loci explained an average of 95.5% of the phenotypic variance. The proportion of phenotypic variance was due to additive genetic variance of the validated SNPs. The present study identified multiple new loci and refined chromosomal regions of known loci associated with SCN resistance. The loci and trait-associated SNPs identified in this study can be used for developing soybean cultivars with durable resistance against SCN.

Corpoica Guayuriba 9: new improved soybean (Glycine max [L] Merril) variety with specific adaptation to the Colombian foothills

Soybean in Colombia is constituted, like corn, as the main raw material for the production of balanced concentrates for animal feeding. The national soybean production satisfies only 7.0% of the demand for poultry-swine chain, with imports in 2014 of 363501 tons of grain and 1018256 tons of soybean meal. Currently, in Colombia, soybean is only produced in the Orinoquia region, mainly in the high plains and foothills and is part of the rice-corn-soy rotation system for the colonization of native savannas. In order to promote cultivation which allows the occupation of 500000 potentially hectares in the foothills with new varieties beyond current and meet domestic demand, Corpoica is responsible for the plant breeding. As a result of a research in plant genetic resources during nine years (2006-2014), the study of a group of elite soybean genotypes on two contrasting regions: high plains and foothills. In addition, main components analysis per genotype-location interaction were determined for L-189 genotype identified with specific adaptation to the foothills and the highest experimental yield of 2660 k.ha-1, superior in more than half a ton to the yield obtained by the control varieties (P-34 and Superior 6); with traits which bring competitive advantages such as a larger number of pods per plant (56) and smaller seeds (15.2g), besides an acquired tolerance to the Cercospora sp. pathogen.

New Alleles of FATB1A to Reduce Palmitic Acid Levels in Soybean

In conventional elite soybean [Glycine max (L.) Merr.] varieties palmitic acid typically constitutes 10% of the total seed oil. Palmitic acid is a saturated fat linked to increased cholesterol levels, and reducing levels of saturated fats in soybean oil is a target for soybean improvement. To identify novel and useful variation that could help in reducing palmitic acid levels in soybean, we screened a chemically mutagenized population. Two lines with reduced levels of seed palmitic acid were identified, and each line had a 30% reduction in palmitic acid. Both lines carried distinct mutations in the FATB1A (Glyma.05G012300) gene that co‐segregated with the reduced palmitic acid phenotype. One line carried a single base change that disrupted the splicing of the FATB1A mRNA, and the second contained a missense mutation (aspartic acid substituted for glycine) in a conserved domain of the FATB1 enzyme. Molecular markers were designed that will enable breeders to follow these new FATB1A mutant alleles in plant populations to facilitate gene stacking for oil improvement.

Identification and genetic relationship of elite soybean breeding lines with high seed protein content in Yangtze-Huai River Valleys

Identification and genetic relationship of elite soybean breeding lines with high seed protein content in Yangtze-Huai River Valleys

Registration of Four Near‐Isogenic Soybean Lines of G00‐3213 for Resistance to Asian Soybean Rust

Soybean rust (SBR), caused by an obligate biotrophic basidiomycete fungus, Phakopsora pachyrhizi, arrived in the continental United States in 2004, where it has since proven to be detrimental to southern soybean [Glycine max (L.) Merr.] production due to yield losses, environmental concerns, and expenses caused by reliance on fungicides for control. Resistance to SBR has been developed primarily by introgressing single, dominant resistance gene(s) into an elite soybean cultivar. Here we describe four near‐isogenic lines (NILs) of G00‐3213: G00‐3213Rpp1 (Reg. No. GP‐400, PI 676017), G00‐3213Rpp2 (Reg. No. GP‐401, PI 676018), G00‐3213Rpp3 (Reg. No. GP‐402, PI 676019), and G00‐3213Rpp4 (Reg. No. GP‐403, PI 676020). These NILs were developed by backcrossing rust resistance genes Rpp1, Rpp2, Rpp3, or Rpp4 into G00‐3213, an elite, maturity group VII soybean line. The NILs have tawny pubescence, tan pod walls, and white flowers and had the same general appearance to the recurrent parent G00‐3213 in the field in 2014. Additionally, each NIL exhibits a similar level of resistance to the GA12 P. pachyrhizi bulk isolate as the original resistant sources of the Rpp genes. These NILs will be useful as parents for public and private plant breeders, as well as for extension agents, crop consultants, and plant pathologists in conducting in‐field determinations for Rpp gene effectiveness in the southern United States.

Pyramids of QTLs enhance host-plant resistance and Bt-mediated resistance to leaf-chewing insects in soybean.

Key messageQTL-M and QTL-E enhance soybean resistance to insects. Pyramiding these QTLs withcry1Ac increases protection against Bt-tolerant pests, presenting an opportunity to effectively deploy Bt with host–plant resistance genes.Plant resistance to leaf-chewing insects minimizes the need for insecticide applications, reducing crop production costs and pesticide concerns. In soybean [Glycine max (L.) Merr.], resistance to a broad range of leaf-chewing insects is found in PI 229358 and PI 227687. PI 229358’s resistance is conferred by three quantitative trait loci (QTLs): M, G, and H. PI 227687’s resistance is conferred by QTL-E. The letters indicate the soybean Linkage groups (LGs) on which the QTLs are located. This study aimed to determine if pyramiding PI 229358 and PI 227687 QTLs would enhance soybean resistance to leaf-chewing insects, and if pyramiding these QTLs with Bt (cry1Ac) enhances resistance against Bt-tolerant pests. The near-isogenic lines (NILs): BenningME, BenningMGHE, and BenningME+cry1Ac were developed. BenningME and BenningMGHE were evaluated in detached-leaf and greenhouse assays with soybean looper [SBL, Chrysodeixis includens (Walker)], corn earworm [CEW, Helicoverpa zea (Boddie)], fall armyworm [FAW, Spodoptera frugiperda (J.E. Smith)], and velvetbean caterpillar [VBC, Anticarsia gemmatalis (Hübner)]; and in field-cage assays with SBL. BenningME+cry1Ac was tested in detached-leaf assays against SBL, VBC, and Southern armyworm [SAW, Spodoptera eridania (Cramer)]. In the detached-leaf assay, BenningME showed the strongest antibiosis against CEW, FAW, and VBC. In field-cage conditions, BenningME and BenningMGHE suffered 61 % less defoliation than Benning. BenningME+cry1Ac was more resistant than BenningME and Benningcry1Ac against SBL and SAW. Agriculturally relevant levels of resistance in soybean can be achieved with just two loci, QTL-M and QTL-E. ME+cry1Ac could present an opportunity to protect the durability of Bt genes in elite soybean cultivars. These results should assist the development of effective pest management strategies, and sustainable deployment of Bt genes in soybean.

Construction of a high-density mutant library in soybean and development of a mutant retrieval method using amplicon sequencing.

BackgroundFunctions of most genes predicted in the soybean genome have not been clarified. A mutant library with a high mutation density would be helpful for functional studies and for identification of novel alleles useful for breeding. Development of cost-effective and high-throughput protocols using next generation sequencing (NGS) technologies is expected to simplify the retrieval of mutants with mutations in genes of interest.ResultsTo increase the mutation density, seeds of the Japanese elite soybean cultivar Enrei were treated with the chemical mutagen ethyl methanesulfonate (EMS); M2 seeds produced by M1 plants were treated with EMS once again. The resultant library, which consisted of DNA and seeds from 1536 plants, revealed large morphological and physiological variations. Based on whole-genome re-sequencing analysis of 12 mutant lines, the average number of base changes was 12,796 per line. On average, 691 and 35 per line were missense and nonsense mutations, respectively. Two screening strategies for high resolution melting (HRM) analysis and indexed amplicon sequencing were designed to retrieve the mutants; the mutations were confirmed by Sanger sequencing as the final step. In comparison with HRM screening of several genes, indexed amplicon sequencing allows one to scan a longer sequence range and skip screening steps and to know the sequence information of mutation because it uses systematic DNA pooling and the index of NGS reads, which simplifies the discovery of mutants with amino acid substitutions.ConclusionsA soybean mutant library with a high mutation density was developed. A high mutation density (1 mutation/74 kb) was achieved by repeating the EMS treatment. The mutation density of our library is sufficiently high to obtain a plant in which a gene is nonsense mutated. Thus, our mutant library and the indexed amplicon sequencing will be useful for functional studies of soybean genes and have a potential to yield useful mutant alleles for soybean breeding.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2079-y) contains supplementary material, which is available to authorized users.

Evaluation of high yielding soybean germplasm under water limitation.

Limited information is available for soybean root traits and their plasticity under drought stress. To date, no studies have focused on examining diverse soybean germplasm for regulation of shoot and root response under water limited conditions across varying soil types. In this study, 17 genetically diverse soybean germplasm lines were selected to study root response to water limited conditions in clay (trial 1) and sandy soil (trial 2) in two target environments. Physiological data on shoot traits was measured at multiple crop stages ranging from early vegetative to pod filling. The phenotypic root traits, and biomass accumulation data are collected at pod filling stage. In trial 1, the number of lateral roots and forks were positively correlated with plot yield under water limitation and in trial 2, lateral root thickness was positively correlated with the hill plot yield. Plant Introduction (PI) 578477A and 088444 were found to have higher later root number and forks in clay soil with higher yield under water limitation. In sandy soil, PI458020 was found to have a thicker lateral root system and higher yield under water limitation. The genotypes identified in this study could be used to enhance drought tolerance of elite soybean cultivars through improved root traits specific to target environments.

Genetic characteristics of soybean resistance to HG type 0 and HG type 1.2.3.5.7 of the cyst nematode analyzed by genome-wide association mapping.

BackgroundSoybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most fatal pests of soybean (Glycine max (L.) Merr.) worldwide and causes huge loss of soybean yield each year. Multiple sources of resistance are urgently needed for effective management of SCN via the development of resistant cultivars. The aim of the present study was to investigate the genetic architecture of resistance to SCN HG Type 0 (race 3) and HG Type 1.2.3.5.7 (race 4) in landraces and released elite soybean cultivars mostly from China.ResultsA total of 440 diverse soybean landraces and elite cultivars were screened for resistance to SCN HG Type 0 and HG Type 1.2.3.5.7. Exactly 131 new sources of SCN resistance were identified. Lines were genotyped by SNP markers detected by the Specific Locus Amplified Fragment Sequencing (SLAF-seq) approach. A total of 36,976 SNPs were identified with minor allele frequencies (MAF) > 4 % that were present in 97 % of all the genotypes. Genome-wide association mapping showed that a total of 19 association signals were significantly related to the resistance for the two HG Types. Of the 19 association signals, eight signals overlapped with reported QTL including Rhg1 and Rhg4 genes. Another eight were located in the linked regions encompassing known QTL. Three QTL were found that were not previously reported. The average value of female index (FI) of soybean accessions with resistant alleles was significantly lower than those with susceptible alleles for each peak SNP. Disease resistance proteins with leucine rich regions, cytochrome P450s, protein kinases, zinc finger domain proteins, RING domain proteins, MYB and WRKY transcription activation families were identified. Such proteins may participate in the resistant reaction to SCN and were frequently found in the tightly linked genomic regions of the peak SNPs.ConclusionsGWAS extended understanding of the genetic architecture of SCN resistance in multiple genetic backgrounds. Nineteen association signals were obtained for the resistance to the two Hg Types of SCN. The multiple beneficial alleles from resistant germplasm sources will be useful for the breeding of cultivars with improved resistance to SCN. Analysis of genes near association signals may facilitate the recognition of the causal gene(s) underlying SCN resistances.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1800-1) contains supplementary material, which is available to authorized users.

Genome-wide association mapping of quantitative resistance to sudden death syndrome in soybean.

BackgroundSudden death syndrome (SDS) is a serious threat to soybean production that can be managed with host plant resistance. To dissect the genetic architecture of quantitative resistance to the disease in soybean, two independent association panels of elite soybean cultivars, consisting of 392 and 300 unique accessions, respectively, were evaluated for SDS resistance in multiple environments and years. The two association panels were genotyped with 52,041 and 5,361 single nucleotide polymorphisms (SNPs), respectively. Genome-wide association mapping was carried out using a mixed linear model that accounted for population structure and cryptic relatedness.ResultA total of 20 loci underlying SDS resistance were identified in the two independent studies, including 7 loci localized in previously mapped QTL intervals and 13 novel loci. One strong peak of association on chromosome 18, associated with all disease assessment criteria across the two panels, spanned a physical region of 1.2 Mb around a previously cloned SDS resistance gene (GmRLK18-1) in locus Rfs2. An additional variant independently associated with SDS resistance was also found in this genomic region. Other peaks were within, or close to, sequences annotated as homologous to genes previously shown to be involved in plant disease resistance. The identified loci explained an average of 54.5% of the phenotypic variance measured by different disease assessment criteria.ConclusionsThis study identified multiple novel loci and refined the map locations of known loci related to SDS resistance. These insights into the genetic basis of SDS resistance can now be used to further enhance durable resistance to SDS in soybean. Additionally, the associations identified here provide a basis for further efforts to pinpoint causal variants and to clarify how the implicated genes affect SDS resistance in soybean.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-809) contains supplementary material, which is available to authorized users.