Proceedings of the 40th Annual Meeting, Southern Soybean Disease Workers (March 13-14, 2013, Pensacola Beach, Florida)

Contents Southern United States Soybean Disease Loss Estimates for 2012. Compiled by SR Koenning Update on Detection and Management of QoI Fungicide Resistant Cercospora sojina, the Causal Agent of Frogeye Leaf Spot in Soybean. C Bradley, G Zhang, V Chapara, R Ming, F Zeng, H Young Kelly, and M Newman Identification of Soybean Genotypes to Cercopsora sojina by Field Screening and Molecular Markers. A Mengistu and R Mian Soybean Vein Necrosis Virus. D Hershman Single Applications of Triazole Fungicides at R1 for Management of Cercospora Leaf Blight and Rust in Soybean. RW Schneider, CL Robertson, BM Ward, and EC Silva Observations on soybean rust management in Alabama in 2012. EJ Sikora, D Delaney, and M Delaney Graduate student paper competition (Clayton Hollier, moderator) Logical Areas of Collection: A Precision Concept for Management of Rhizoctonia solani AG1-IA. TN Spurlock, CS Rothrock, and WS Monfort Screening of Soybean Recombinant Inbred Lines against Phakopsora pachyrhizi. M Ganiger, DR Walker, and ZY Chen Effects of Minor Element Nutrition on Cercospora Leaf Blight of Soybean. BM Ward, CL Robertson, RW Schneider, and EC Silva Sensitivity of Cercospora kikuchii Populations to Methyl Benzimidazole, Carbamate, Quinone Outside Inhibitor, and Demethylation Inhibitor Fungicides. P Price, MA Purvis, CL Robertson, GB Padgett, and RW Schneider Effect of Foliar Application of Micronutrients on Severity of Rust in Soybean. EC Silva, BM Ward, CL Robertson, and RW Schneider Southern Soybean Disease Workers paper session (Tom Allen, moderator) History of Reniform Nematode in the South. RT Robbins Role of Seed Quality, Planting Date, and Seed Treatment on Soybean Stand and Yield. JC Rupe, R Holland, A Steger, S Goeke, EE Gbur, WJ Ross, M Wyss, J McCoy, and R Cingolani Screening Soybean Germplasm and Commercial Varieties for Resistance to Phomopsis Seed Decay: Results from 2012 Trials. S Li, G Sciumbato, P Chen, S Sun, J Rupe, R Holland, and A Steger A Novel Seed Treatment with Activity against SDS in Soybeans. C Graham Adenosylhomocysteinase (AHCY) is essential for Virulence of Cercospora kikuchii in soybeans. AK Chanda, RW Schneider, and Z-Y Chen Fungicide Timing Strategies: Targeting Yield Enhancement in Mississippi Soybean. TW Allen, D Cook, A Catchot, J Gore, and N Buehring Update from the United Soybean Board. K Whiting Industry Pest Information Platform for Extension and Education (iPiPE). S Isard, R Magarey, J Golod, and J Russo Proceedings of the Southern Soybean Disease Workers are published annually by the Southern Soybean Disease Workers. Text, references, figures, and tables are reproduced as they were submitted by authors. The opinions expressed by the participants at this conference are their own and do not necessarily represent those of the Southern Soybean Workers. Mention of a trademark or proprietary products in this publication does not constitute a guarantee, warranty, or endorsement of that product by the Southern Soybean Disease Workers

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Exploring the mechanisms of endophytic bacteria for suppressing early blight disease in tomato (Solanum lycopersicum L.)

Controlling early blight of tomatoes using endophytic bacteria is an eco-friendly and sustainable approach to manage this common fungal disease caused by Alternaria solani, Alternaria alternata, and Curvularia lunata. Endophytic bacteria are microorganisms that live inside plant tissues without causing harm and can help protect the host plant from pathogens. In this work, twenty endophytic bacterial isolates from tomato healthy plants were tested against pathogenic fungal isolates that caused early blight disease in vitro. Out of the 20 tested isolates, three (B4, B7, and B17) were considered effective isolates against the growth of fungal pathogens. The three isolates were recognized as Enterobacter cloacae HS-6 (B4), Pseudomonas gessardii HS-5 (B 7), and Pseudomonas mediterranea HS-4 (B17) using 16s-rDNA sequencing. Different concentrations of bacterial cultural diltrates at 20, 40, and 60% were tested for their antagonistic effects on the development of pathogenic fungi in vitro. The lowest dry weights of pathogenic isolates in all bacterial culture filtrates were discovered at 60%. In all culture filtrates, phenolic compounds showed the largest peak area. Under greenhouse conditions, the least disease severity of tomato early blight was found for E. cloacae and its culture filtrate compared to other treatments. Real-time PCR was used to examine the expression pattern of the defense response gene β-1.3 glucanase gene in infected tomato plants with pathogenic fungi (control) as well as its relations with efficient biocontrol agent (E. cloacae). The expression of the gene increased substantially and significantly after three days from the inoculation-infected plants with C. lunata and E. cloacae while it reached the maximum after five days from the inoculation with A. alternata, A. solani and E. cloacae. Our study concluded that the endophytic bacterial isolate E. cloacae can be considered a promising biocontrol agent for preventing tomato early blight