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Pythium damping-off and root rot of soybean [Glycine max (L.) Merr.] causes poor stands and consequently reduces yields. Resistance to seedling diseases caused by Pythium spp. was reported in the soybean cultivar Archer and was described to be associated with the Rps1k gene for resistance to Phytophthora sojae. To characterize the inheritance of Pythium damping-off resistance in Archer and to determine if this resistance is linked to Rps1k, the cross of Archer x 'Hutcheson' (susceptible parent) was made and [F.sub.2:4] lines generated. Parents and [F.sub.2:4] lines were screened with Pythium aphanidermatum using a hypocotyl inoculation technique. Five days after inoculation, plant survival was scored. The [F.sub.2:4] lines and parents were also inoculated with race 7 of P. sojae to assess the association of resistance to Pythium spp. with the Rps1k gene. Data from the [F.sub.2:4] lines fit the model for a single dominant gene in Archer that confers resistance to P. aphanidermatum. The genetic linkage test showed that resistance to P. aphanidermatum was independent of the Rps1k gene in Archer. To identify the genomic location of the Pythium resistance gene, F.sub.2:4] lines were screened with simple sequence repeat (SSR) markers from all the soybean molecular linkage groups (MLGs). Two SSR markers, Satt510 and Satt114 on MLG F, which were polymorphic between the parents and the resistant and susceptible bulks, were shown to be associated with Pythium resistance. The Pythium resistance gene; named Rpa1, was located 10.6 cM from Satt510 and 26.6 cM from Satt114.

Charcoal rot of soybean [Glycine max (L.) Merr.], caused by the soilborne fungus Macrophomina phaseolina (Tassi) Goid., has ranked among the most important soybean diseases in the United States. Disease management is typically done in a multifaceted approach through crop rotation, tillage, irrigation, and seed treatments aimed at minimizing damage caused by the pathogen. Development of genetic resistance to charcoal rot appears to be the most efficient strategy to control the disease; however, there are no reports of genetic regions associated with resistance to the disease. The objective of this study was to identify quantitative trait loci (QTLs) governing resistance to charcoal rot in soybean using a biparental population of PI 567562A (resistant) × PI 567437 (susceptible). A total of 140 F2–derived lines were genotyped with 5403 single nucleotide polymorphism (SNP) markers covering 20 chromosomes, of which 2283 were polymorphic. Resistance to charcoal rot was evaluated in the F2:3 lines using the cut‐stem inoculation technique under greenhouse conditions. The QTL mapping analysis indicated one QTL on chromosome 15 explaining 29.4% of phenotypic variation, and two QTLs on chromosome 16 explaining 25.4 and 8.4% of phenotypic variation for resistance to M. phaseliona. To our knowledge, this is the first report of genomic regions harboring resistance to charcoal rot in soybean, and it may facilitate breeding and molecular engineering progress to combat charcoal rot disease in the future. [ABSTRACT FROM AUTHOR]

Charcoal rot, caused by Macrophomina phaseolina, is a widespread drought-associated, soilborne disease of soybean. Generally, disease severity is assessed indirectly as host colonization at the end of the growing season. Few studies have measured the effects of disease during the season. Two moderately charcoal rot resistant cultivars (‘DT 97-4290‘ and ‘Delta Pineland 4546‘), a drought tolerant cultivar (‘R01-1581F’) and a susceptible cultivar (‘LS 980358‘) were planted in microplots filled with uninoculated steam pasteurized soil or pasteurized soil infested with M. phaseolina. Half of the plots were irrigated and half were drought stressed. Stomatal conductance and infrared canopy temperatures were measured 47, 70, 77 and 98 days after planting (DAP) in 2008 and 52, 63, 72 and 84 DAP in 2009. Yields were taken at the end of the season. There were significant differences in stomatal conductance. In 2008, stomatal conductance was significantly lower 47 DAP in the non-irrigated/inoculated plots than the other treatments. At 98 DAP, stomatal conductance was highest in the irrigated/non-inoculated plots. In 2009, stomatal conductance was significantly higher in the non-infested plots than the infested plots of ‘LS 890358‘ and ‘R01-1581F’ across sample times, but not in plots of the resistant cultivars ‘DT 97-4290‘ or ‘DPL 4546‘. These differences were reflected in significantly greater canopy temperatures and lower yields in the infested compared with the non-infested plots of the susceptible, but not the resistant cultivars. These results show that root infection by M. phaseolina can reduce water movement in soybean and reduce yields in susceptible cultivars. [ABSTRACT FROM AUTHOR]

Crop disease detection with remote sensing is a challenging area that can have significant economic and environmental impact on crop disease management. Spectroscopic remote sensing in the visible and near-infrared (NIR) region has the potential to detect crop changes due to diseases. Soybean cyst nematode (SCN) and sudden death syndrome (SDS) are two common soybean diseases that are extremely difficult to detect in the early stages under mild to moderate infestation levels. The objective of this research study was to relate leaf reflectance to disease conditions and to identify wavebands that best discriminated these crop diseases. A microplot experiment was conducted. Data collected included 800 leaf spectra, corresponding leaf chlorophyll content and disease rating of four soybean cultivars grown under different disease conditions. Disease conditions were created by introducing four disease treatments of control (no disease), SCN, SDS, and SCN+SDS. Crop data were collected on a weekly basis over a 10-week period, starting from 71 days after planting (DAP). The correlation between disease rating and selected vegetation indices (VI) were evaluated. Wavebands with the most disease discrimination capability were identified with stepwise linear discriminant analysis (LDA), logistic discriminant analysis (LgDA) and linear correlation analysis of pooled data. The identified band combinations were used to develop a classification function to identify plant disease condition. The best correlation (>0.8) between disease rating and VI occurred during 112 DAP. Both LDA and LgDA identified several bands in the NIR, red, green and blue regions as critical for disease discrimination. The discriminant models were able to detect over 80% of the healthy plants accurately under cross-validation but showed poor accuracy in discriminating individual diseases. A two-class discriminant model was able to identify 97% of the healthy plants and 58% of the infested plants as having some disease from the plant spectra. [ABSTRACT FROM AUTHOR]

Oomycete pathogens are commonly associated with soybean root rot and have been estimated to reduce soybean yields in the United States by 1.5 million tons on an annual basis. Limited information exists regarding the frequency and diversity of oomycete species across the major soybean-producing regions in North America. A survey was conducted across 11 major soybean-producing states in the United States and the province of Ontario, Canada. In 2011, 2,378 oomycete cultures were isolated from soybean seedling roots on a semiselective medium (CMA-PARPB) and were identified by sequencing of the internal transcribed spacer region of rDNA. Sequence results distinguished a total of 51 Pythium spp., three Phytophthora spp., three Phytopythium spp., and one Aphanomyces sp. in 2011, with Pythium sylvaticum (16%) and P. oopapillum (13%) being the most prevalent. In 2012, the survey was repeated, but, due to drought conditions across the sampling area, fewer total isolates (n = 1,038) were collected. Additionally, in 2012, a second semiselective medium (V8-RPBH) was included, which increased the Phytophthora spp. isolated from 0.7 to 7% of the total isolates. In 2012, 54 Pythium spp., seven Phytophthora spp., six Phytopythium spp., and one Pythiogeton sp. were recovered, with P. sylvaticum (14%) and P. heterothallicum (12%) being recovered most frequently. Pathogenicity and virulence were evaluated with representative isolates of each of the 84 species on soybean cv. Sloan. A seed-rot assay identified 13 and 11 pathogenic species, respectively, at 13 and 20°C. A seedling-root assay conducted at 20°C identified 43 species as pathogenic, having a significantly detrimental effect on the seedling roots as compared with the noninoculated control. A total of 15 species were pathogenic in both the seed and seedling assays. This study provides a comprehensive characterization of oomycete species present in soybean seedling roots in the major production areas in the United States and Ontario, Canada and provides a basis for disease management and breeding programs. [ABSTRACT FROM AUTHOR]

Cercospora sojina causes frogeye leaf spot of soybean, which can cause serious economic losses in the United States. In this study, 132 C. sojina isolates were collected from six fields (from two counties, Cross and Crawford) in Arkansas. To determine mating type, a multiplex polymerase chain reaction assay was developed with primers specific for C. sojina. Of the 132 isolates, 68 isolates had the MAT1-1-1 idiomorph and 64 isolates had the MAT1-2 idiomorph; no isolates possessed both idiomorphs. Both mating types were present in a variety of spatial scales, including separate lesions on individual leaves. Clone-corrected data from eight microsatellites indicated that mating-type loci were present in approximately equal proportions in all populations analyzed, which suggests that Arkansas populations of C. sojina are undergoing cryptic sexual reproduction. All six populations evaluated had high genotypic diversity of 26 to 79%. In addition, among strains isolated from a single leaf, multiple and distinct haplotypes were associated with both mating types, supporting the hypothesis that sexual reproduction occurs within the populations. Most populations showed significant gametic disequilibrium but levels of disequilibrium were relatively low, particularly in populations from Crawford County. A low differentiation index (GST) was observed for all simple-sequence repeat markers across all populations. Furthermore, the value of G statistics between populations suggests that significant genetic exchange exists among the populations. Taken together, these results demonstrate that C. sojina populations from Arkansas are genetically diverse and most likely undergoing sexual reproduction. [ABSTRACT FROM AUTHOR]

The primary controls for charcoal rot in soybean, caused by the fungal pathogen Macrophomina phaseolina , are to avoid drought stress and to plant a moderately resistant cultivar. The effects of irrigation and cultivar were determined in 2011 and 2013 at the Lon Mann Cotton Research Station, Marianna, AR. Four soybean cultivars (Hutcheson, Osage, Ozark, and R01581F) were planted in plots with or without added M . phaseolina inoculum and subjected to three furrow irrigation regimes: full-season irrigation (Full), irrigation terminated at R5 (CutR5), and nonirrigated (NonIrr). Normalized difference vegetation index (NDVI) was measured at R3 and R6. At harvest, plants and yields were collected. Roots and stems were split and the extent of visible colonization by M. phaseolina microsclerotia was assessed in the roots with a 1 to 5 scale (RSS) and the percent plant height stem discoloration measured. Precipitation in September and October was 54 and 65% below the 30-year average in 2011 and 2013, respectively. The CutR5 irrigation treatment resulted in one less irrigation than Full each year, but CutR5 NDVIs at R6 and yields were significantly lower than those with Full and not significantly different from those of NonIrr. The CutR5 RSS ratings were greater than either Full or NonIrr. Plant colonization by M. phaseolina was negatively correlated to yield in 2011 but not in 2013. No premature plant death caused by charcoal rot was observed in either year. These results indicated that late-season drought stress may be more important to charcoal rot development than drought stress throughout the season, but other factors are needed to trigger early plant death and subsequent yield losses observed in grower fields., Competing Interests: The author(s) declare no conflict of interest.

Cercospora leaf blight (CLB) of soybean, caused by Cercospora cf. flagellaris , C. kikuchii , and C. cf. sigesbeckiae , is an economically important disease in the southern United States. Cultivar resistance to CLB is inconsistent; therefore, fungicides in the quinone outside inhibitor (QoI) class have been relied on to manage the disease. Approximately 620 isolates from plants exhibiting CLB were collected between 2018 and 2021 from 19 locations in eight southern states. A novel polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay based on two genes, calmodulin and histone h3 , was developed to differentiate between the dominant species of Cercospora , C. cf. flagellaris , and C. cf. sigesbeckiae . A multilocus phylogenetic analysis of actin, calmodulin, histone h3, ITS rDNA, and transcription elongation factor 1-α was used to confirm PCR-RFLP results and identify remaining isolates. Approximately 80% of the isolates collected were identified as C. cf. flagellaris , while 15% classified as C. cf. sigesbeckiae , 2% as C. kikuchii , and 3% as previously unreported Cercospora species associated with CLB in the United States. PCR-RFLP of cytochrome b ( cytb ) identified QoI-resistance conferred by the G143A substitution. Approximately 64 to 83% of isolates were determined to be QoI-resistant, and all contained the G143A substitution. Results of discriminatory dose assays using azoxystrobin (1 ppm) were 100% consistent with PCR-RFLP results. To our knowledge, this constitutes the first report of QoI resistance in CLB pathogen populations from Alabama, Arkansas, Kentucky, Mississippi, Missouri, Tennessee, and Texas. In areas where high frequencies of resistance have been identified, QoI fungicides should be avoided, and fungicide products with alternative modes-of-action should be utilized in the absence of CLB-resistant soybean cultivars., Competing Interests: The author(s) declare no conflict of interest.