BackgroundBi-parental mapping populations have been commonly utilized to identify and characterize quantitative trait loci (QTL) controlling resistance to soybean cyst nematode (SCN, Heterodera glycines Ichinohe). Although this approach successfully mapped a large number of SCN resistance QTL, it captures only limited allelic diversity that exists in parental lines, and it also has limitations for genomic resolution. In this study, a genome-wide association study (GWAS) was performed using a diverse set of 553 soybean plant introductions (PIs) belonging to maturity groups from III to V to detect QTL/genes associated with SCN resistance to HG Type 0.ResultsOver 45,000 single nucleotide polymorphism (SNP) markers generated by the SoySNP50K iSelect BeadChip (http//www.soybase.org) were utilized for analysis. GWAS identified 14 loci distributed over different chromosomes comprising 60 SNPs significantly associated with SCN resistance. Results also confirmed six QTL that were previously mapped using bi-parental populations, including the rhg1 and Rhg4 loci. GWAS identified eight novel QTL, including QTL on chromosome 10, which we have previously mapped by using a bi-parental population. In addition to the known loci for four simple traits, such as seed coat color, flower color, pubescence color, and stem growth habit, two traits, like lodging and pod shattering, having moderately complex inheritance have been confirmed with great precision by GWAS.ConclusionsThe study showed that GWAS can be employed as an effective strategy for identifying complex traits in soybean and for narrowing GWAS-defined genomic regions, which facilitates positional cloning of the causal gene(s).Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1811-y) contains supplementary material, which is available to authorized users.

The potential of association mapping (AM) and genomic selection (GS) has not yet been explored for investigating resistance to soybean cyst nematode (SCN), the most destructive pest affecting soybean. We genotyped 282 representative accessions from the University of Minnesota soybean breeding program using a genome-wide panel of 1536 single nucleotide polymorphism (SNP) markers and evaluated plant responses to SCN HG type 0. After adjusting for population structure, AM detected significant signals at two loci corresponding to rhg1 and FGAM1 plus a third locus located at the opposite end of chromosome 18. Our analysis also identified a discontinuous long-range haplotype of over 600 kb around rhg1 locus associated with resistance to SCN HG type 0. The same phenotypic and genotypic datasets were then used to access GS accuracy for prediction of SCN resistance in the presence of major genes through a sixfold cross-validation study. Genomic selection using the full marker set produced average prediction accuracy ranging from 0.59 to 0.67 for SCN resistance, significantly more accurate than marker-assisted selection (MAS) strategies using two rhg1-associated DNA makers. Reducing the number of markers to 288 SNPs in the GS training population had little effect on genomic prediction accuracy. This study demonstrates that AM can be an effective genomic tool for identifying genes of interest in diverse germplasm. The results also indicate that improved MAS and GS can enhance breeding efficiency for SCN resistance in existing soybean improvement programs.

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is a serious soybean pest. The use of resistant cultivars is an effective approach for preventing yield loss. In this study, 19,652 publicly available soybean accessions that were previously genotyped with the SoySNP50K iSelect BeadChip were used to evaluate the phylogenetic diversity of SCN resistance genes Rhg1 and Rhg4 in an attempt to identify novel sources of resistance. The sequence information of soybean lines was utilized to develop KASPar (KBioscience Competitive Allele-Specific PCR) assays from single nucleotide polymorphisms (SNPs) of Rhg1, Rhg4, and other novel quantitative trait loci (QTL). These markers were used to genotype a diverse set of 95 soybean germplasm lines and three recombinant inbred line (RIL) populations. SNP markers from the Rhg1 gene were able to differentiate copy number variation (CNV), such as resistant-high copy (PI 88788-type), low copy (Peking-type), and susceptible-single copy (Williams 82) numbers. Similarly, markers for the Rhg4 gene were able to detect Peking-type (resistance) genotypes. The phylogenetic information of SCN resistance loci from a large set of soybean accessions and the gene/QTL specific markers that were developed in this study will accelerate SCN resistance breeding programs.

Potassium chloride (KCl) preplant or foliar applied with fungicides to soybean [Glycine max (L.) Merr.] may allow farmers to increase yields when soil K availability is reduced and/or when Septoria brown spot (SBS) (Septoria glycines), frogeye leaf spot (FLS) (Cercospora sojina), or sudden death syndrome (SDS) (Fusarium solani (Mart.) Sacc. f. sp. glycines) are present. Interactions between fertilizer and fungicide management programs have not been examined in the central United States. Our objective was to evaluate the eff ect of preplant-and foliar-applied KCl alone or combined with pyraclostrobin, azoxystrobin, or azoxystrobin plus lambda-cyhalothrin on soybean response and severity of SBS, FLS, and SDS. Experiments were conducted in northeastern (Novelty) and southeastern (Qulin) Missouri in 2006 and 2007 on soils with low to medium K. Leaf K concentrations increased 1.4 to 6.1 g kg −1 following preplant KCl compared to nontreated or foliar KCl. Leaf Cl concentrations increased signifi cantly with preplant KCl at Qulin and foliar KCl at R4 at Qulin and Novelty. At Novelty, preplant KCl reduced the severity of SBS and FLS up to 6%, and increased yield 340 kg ha −1 , while foliar KCl increased yield 110 kg ha −1 . An R4 application of strobilurin fungicides increased yields 230 to 360 kg ha −1 at Novelty. At Qulin, soybean yield increased 390 kg ha −1 with preplant KCl, while there were variable eff ects of fungicides on the severity of SBS, FLS, or SDS, and no yield increase due to fungicides or foliar KCl. Foliar applications of KCl were no substitute for preplant KCl.

Corn (Zea mays L.) response to boron (B) on fine textured soils has had limited research, and no research has evaluated interactions between B and crop protection chemicals such as pyraclostrobin. This research evaluated effects of foliar‐applied B at 0.56 kg ha−1 and pyraclostrobin {carbamic acid, [2,[[[1‐(4‐chlorophenyl)‐1H‐pyrazol‐3‐yl]oxy]methyl]phenyl]methoxy‐, methyl ester} at 0.11 kg ha−1 a.i. on yield, tissue B concentration, severity of disease, and grain quality. Field research was conducted at four locations in Northeast Missouri from 2008 to 2010. Boron was applied at V5–V6, V5–V6 followed by (fb) pyraclostrobin at VT, and with or without pyraclostrobin at VT. Pyraclostrobin was applied alone at VT, and a nontreated control was also included. Over the 12 site‐years, pyraclostrobin alone at VT increased yield 5% and B at V5–V6 fb pyraclostrobin at VT increased yield 6% compared to the nontreated control. A split‐application of B at V5–V6 fb pyraclostrobin at VT increased yield 0.52 Mg ha−1 compared to B plus pyraclostrobin at VT. Pyraclostrobin increased grain moisture 3 to 7 g kg−1, decreased starch 1 to 2 g kg−1, and decreased extractable starch 3 to 4 g kg−1 concentration compared to the nontreated control. However, no difference in the number of barren stalks, grain with diplodia (Stenocarpella maydis) symptoms, oil, or protein concentrations was detected among treatments. Disease severity was reduced most consistently with B at V5–V6 fb pyraclostrobin or pyraclostrobin alone. Boron at 0.56 kg ha−1should be applied before VT to avoid antagonism with pyraclostrobin on fine textured soils.

Eff ective management of soil N fertilizer, including the use of enhanced effi ciency N fertilizer sources and optimal dates of fertilizer application, may increase agronomic performance of double-cropped winter wheat (Triticum aestivum L.) with soybean [Glycine max (L.) Merr.] under no-till (NT) management. In a double-cropping system, ratios and dates of application of polymercoated urea (PCU) may aff ect both wheat and subsequent soybean yields. Th e objectives of this research, conducted over three growing seasons (2008-2010) in northeastern Missouri, were to evaluate urea release over a range of PCU application dates, and to assess the eff ects of the fall to spring application dates of PCU and ratios of PCU with noncoated urea (NCU) compared with ammonium nitrate (AN) and NCU on wheat and double-crop soybean yield. Th e experimental design was a factorial that included two N application rates (84 and 112 kg N ha -1 ), seven application dates (October-April), fi ve N fertilizer source/ratios, and nontreated controls. Urea-N release from PCU fertilizers applied on 15 October was <30% by 15 February in two of the three study years. Wheat yields were signifi cantly (P ≤ 0.05) aff ected by the three-way interactions of year × N source × N rate and year × N source × application date. In two of the three study years, yields were 450 to 500 kg ha -1 greater with an October application of 100% PCU compared to 100% NCU. Double-crop soybean yields were not aff ected by preceding winter wheat N management.

S11-20124C' (Reg. No. CV-532, PI 689118) is a high-yielding semi-determinate early maturity group V (5.1) conventional soybean [Glycine max (L.) Merr.] cultivar developed and released in 2017 by the University of Missouri-Fisher Delta Research Center Soybean Breeding program. It was developed through conventional breeding from a cross between 'S05-11482' × 'S06-4649RR'. The development of high-yielding conventional soybean became advantageous due to premium prices ofered for non-genetically modiied soybean products, as well as lower seed costs compared with herbicidetolerant cultivars. Additionally, early maturity group V (5.1) soybeans are highly desirable for early planting and after wheat (Triticum aestivum L.) in double cropping systems. S11-20124C was evaluated in 113 environments from 2012 to 2016 in Missouri and other southern states. It is demonstrated to be well adapted through its consistent superior or equivalent performance to the commercial checks with similar maturity. S11-20124C has a wide disease resistance package, including moderate resistance to soybean cyst nematode races 1, 2, 3, 5, and 14 (HG Type 2.5.7, Type 1.2.5.7, Type 7, Type 2.5.7, Type 1.3.6.7 respectively) and resistance to southern root-knot nematode and reniform nematode . Seed averages 416 g kg −1 protein and 245 g kg −1 oil. High yield potential, resistance to multiple diseases, and broad adaptation make S11-20124C a good choice for soybean growers across US southern states.

Key messageWe performed QTL analysis for SCN resistance in PI 437655 in two mapping populations, characterized CNV ofRhg1through whole-genome resequencing and evaluated the effects of QTL pyramiding to enhance resistance.AbstractSoybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most serious pests of soybean worldwide. PI 437655 has broader resistance to SCN HG types than PI 88788. The objectives of this study were to identify quantitative trait loci (QTL) underlying SCN resistance in PI 437655, and to evaluate the QTL for their contribution to SCN resistance. Two F6:7 recombinant inbred line populations, derived from cv. Williams 82 × PI 437655 and cv. Hutcheson × PI 437655 crosses, were evaluated for resistance to SCN HG types 1.2.5.7 (PA2), 0 (PA3), 1.3.5.6.7 (PA14), and 1.2.3.4.5.6.7 (LY2). The 1,536 SNP array was used to genotype the mapping populations and construct genetic linkage maps. Two significant QTL were consistently mapped on chromosomes (Chr.) 18 and 20 in these two populations. One QTL on Chr. 18, which corresponds to the known Rhg1 locus, contributed resistance to SCN HG types 1.2.5.7, 0, 1.3.5.6.7, and 1.2.3.4.5.6.7 (PA2, PA3, PA14, and LY2, respectively). Copy number variation (CNV) analysis by whole-genome resequencing showed that PI 437655 and PI 88788 had similar CNV at the Rhg1 locus. The QTL on Chr. 20 contributed resistance to SCN HG types 1.3.5.6.7 (PA14) and 1.2.3.4.5.6.7 (LY2). Evaluation of both QTL showed that pyramiding of Rhg1 and the QTL on Chr. 20 significantly improved the resistance to SCN HG types 1.3.5.6.7 (PA14) and 1.2.3.4.5.6.7 (LY2) in both populations. Our studies provided useful information for deploying PI 437655 as a donor for SCN resistance in soybean breeding through marker-assisted selection.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-014-2409-5) contains supplementary material, which is available to authorized users.