Anthracnose (Colletotrichum dematium) is an important disease in spinach (Spinacia oleracea). Sources of resistance must be identified, and molecular tools must be developed to expedite cultivar development. In this study, a diverse collection of 276 spinach accessions was scored for anthracnose disease severity. We then evaluated marker identification approaches by testing how well haplotype‐based trait modelling compares to single markers in identifying strong association signals. Alleles in linkage disequilibrium were tagged in haplotype blocks, and anthracnose‐associated molecular markers were identified using single‐SNP (sSNP), pairwise haplotype (htP) and multi‐marker haplotype (htM) SNP tagging approaches. We identified 49 significantly associated markers distributed on several spinach chromosomes using all methods. The sSNP approach identified 13 markers, while htP identified 24 (~63% more) and htM 34 (~162% more). Of these markers, four were uniquely identified by the sSNP approach, nine by htP and nineteen by htM. The results indicate that resistance to anthracnose is polygenic and that haplotype‐based analysis may have more power than sSNP. Using a combination of these methods can improve the identification of molecular markers for spinach breeding.
A Gram positive, aerobic, and non-spore-forming bacterial strain, 20TX0166 T , was isolated from a diseased onion bulb in Texas, USA. Upon testing its pathogenicity on onion bulb, it produced pathogenic response which makes it rst species of pathogen belonging to the phylum actinobacteria detected in onion. Phylogenetic analysis of the 16S rRNA gene sequence revealed that the strain belonged to the genus Curtobacterium and was most similar to Curtobacterium accumfaciens LMG 3645 T (100%), C. pusillum DSM 20527 T (99.5%), and C. oceanosedimentum ATCC 31317 T (99.5%). The orthologous ANI (orthoANIu), ANI based on blast (ANIb), and dDDH values between the novel strain and the closest relative, C. accumfaciens LMG 3645 T , were 95.7%, 95.4%, and 63.3%, respectively. These values were below the recommended species cut-off threshold of 96% (ANI) and 70% (dDDH), suggesting the strain may be a novel species. The estimated genome size of the novel species was 3.98 Mbp with a G + C content of 70.8%. Physiologic and phenotypic characters of this novel strain were also unique when compared with the closely related species. The major cellular fatty acids of this strain were C 15:0 anteiso and C 17:0 anteiso. Using a polyphasic approach based on phenotypic and genotypic analyses, strain 20TX0166 T represents a novel species of the genus Curtobacterium, and the name Curtobacterium allii sp. nov.
The effects of cultivar and foliar fungicide application on soybean seed germination, vigor, microflora, and yield after delayed harvest were determined at the University of Arkansas Vegetable Research Station in Kibler, AR, from 2008 to 2010. Seven cultivars with varying levels of resistance to Diaporthe spp. or Cercospora spp. were treated or not treated with a foliar application of azoxystrobin at the R5 growth stage. Plots were harvested three weeks after the plants had reached harvest maturity. Yields were recorded, samples of seed were collected, and standard germination (SG) and accelerated aging (AA) were assessed. Seeds were also assayed for infection by fungi on modified potato dextrose agar and by bacteria on nutrient agar. Seed vigor was significantly reduced by infection with Diaporthe spp., Fusarium spp., and Bacillus subtilis, but not with Cercospora spp. Cultivar had a significant impact on yield, seed vigor, and seed infection levels. The cultivar Osage consistently had high seed vigor and low overall seed infection incidence throughout the study. MO/PSD-0259, AG 4403 and UA 4805 also had relatively high seed vigor and low seed infection incidence. PI 80837 had low incidence of seed infection by Diaporthe spp. and Fusarium spp. in 2008 and 2010, but high levels in 2009 when environmental conditions were especially favorable for these pathogens. AP 350 and Suweon97 generally had relatively high seed infection incidences, particularly of Diaporthe spp. and Fusarium spp., and relatively low seed vigor. Application of the foliar fungicide azoxystrobin at the R5 growth stage significantly increased AA across years and cultivars and increased seed infection by Diaporthe spp. in 2009 across cultivars. There were significant negative correlations between yield and seed infection by Diaporthe spp. and Bacillus subtilis in one year and with Fusarium spp. in all three years. Overall, resistance to seed infection can persist even when harvest is delayed and in addition to Diaporthe spp., other seedborne pathogens may reduce seed vigor and yield.
A Gram-stain-negative, aerobic and non-spore-forming bacterial strain, designated 20TX0172T, was isolated from a rotting onion bulb in Texas, USA. The results of phylogenetic analysis based on the 16S rRNA sequence indicated that the novel strain represented a member of the genus Pseudomonas and had the greatest sequence similarities with Pseudomonas kilonensis 520-20T (99.3 %), Pseudomonas corrugata CFBP 2431T (99.2 %), and Pseudomonas viciae 11K1T (99.2 %) but the 16S rRNA phylogenetic tree displayed a monophyletic clade with Pseudomonas mediterranea CFBP 5447T. In the phylogenetic trees based on sequences of four housekeeping genes (gap1, gltA, gyrB and rpoD), the novel strain formed a separate branch, indicating that the strain was distinct phylogenetically from known species of the genus Pseudomonas . The genome-sequence-derived average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the novel isolate and P. mediterranea DSM 16733T were 86.7 and 32.7 %, respectively. These values were below the accepted species cutoff threshold of 96 % ANI and 70 % dDDH, affirming that the strain represented a novel species. The genome size of the novel species was 5.98 Mbp with a DNA G+C content of 60.8 mol%. On the basis of phenotypic and genotypic characteristics, strain 20TX0172T represents a novel species of the genus Pseudomonas . The name Pseudomonas uvaldensis sp. nov. is proposed. The type strain is 20TX0172T (=NCIMB 15426T=CIP 112022T).
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