A Novel Approach to CAFO Odor Assessment: Odorant Field Collection by Sorbent Tube / Thermal Reconstitution in the Laboratory

Historically, odor emission monitoring of high density livestock operations has been limited to direct, whole-air assessment utilizing remote site sampling by plastic bags, human sensory panelists and dynamic dilution olfactometry. On-going efforts by these authors are directed at enabling the translation of these sensory ‘only’ monitoring protocols to instrument ‘primarily, with sensory oversight’ alternatives. This current work attempts to address the latter requirement for sensory oversight and the associated need for improved methods of remote site whole-air sample collection. Published works by these authors as well as others places in serious question the appropriateness of the use of plastic bags for the challenge of CAFO odor assessment; especially relative to sample points at increasing downwind distance from the source. Concerns increase due to the associated natural dilution effects relative to priority semi-volatile odorants. This current submission reports on the progress to date in the development and evaluation of alternative whole-air sampling strategies which attempt to address the primary limitation of plastic sampling bags; the adsorption loss-to-wall of high impact semi-volatile odorants such as p-cresol. In this approach the actual field air sampling is carried out utilizing sorbent tubes for on-site collection of the volatiles/odorants from a measured volume of air. These sorbent tube collections are then transported to the laboratory for reconstitution within a heat traced, passivated and piston-displaced vessel prior to composite odor assessment. The sample reconstitution process is accomplished simply by thermally desorbing the collected odorants into a flowing diluent gas stream and making up to final volume to yield a match of the originally sampled environment

Directional Selection from Host Plants Is a Major Force Driving Host Specificity in Magnaporthe Species

One major threat to global food security that requires immediate attention, is the increasing incidence of host shift and host expansion in growing number of pathogenic fungi and emergence of new pathogens. The threat is more alarming because, yield quality and quantity improvement efforts are encouraging the cultivation of uniform plants with low genetic diversity that are increasingly susceptible to emerging pathogens. However, the influence of host genome differentiation on pathogen genome differentiation and its contribution to emergence and adaptability is still obscure. Here, we compared genome sequence of 6 isolates of Magnaporthe species obtained from three different host plants. We demonstrated the evolutionary relationship between Magnaporthe species and the influence of host differentiation on pathogens. Phylogenetic analysis showed that evolution of pathogen directly corresponds with host divergence, suggesting that host-pathogen interaction has led to co-evolution. Furthermore, we identified an asymmetric selection pressure on Magnaporthe species. Oryza sativa-infecting isolates showed higher directional selection from host and subsequently tends to lower the genetic diversity in its genome. We concluded that, frequent gene loss or gain, new transposon acquisition and sequence divergence are host adaptability mechanisms for Magnaporthe species, and this coevolution processes is greatly driven by directional selection from host plants

An updated database of virus circular RNAs provides new insights into the biogenesis mechanism of the molecule

ABSTRACTVirus circular RNAs (circRNA) have been reported to be extensively expressed and play important roles in viral infections. Previously we build the first database of virus circRNAs named VirusCircBase which has been widely used in the field. This study significantly improved the database on both the data quantity and database functionality: the number of virus circRNAs, virus species, host organisms was increased from 46440, 23, 9 to 60859, 43, 22, respectively, and 1902 full-length virus circRNAs were newly added; new functions were added such as visualization of the expression level of virus circRNAs and visualization of virus circRNAs in the Genome Browser. Analysis of the expression of virus circRNAs showed that they had low expression levels in most cells or tissues and showed strong expression heterogeneity. Analysis of the splicing of virus circRNAs showed that they used a much higher proportion of non-canonical back-splicing signals compared to those in animals and plants, and mainly used the A5SS (alternative 5’ splice site) in alternative-splicing. Most virus circRNAs have no more than two isoforms. Finally, human genes associated with the virus circRNA production were investigated and more than 1000 human genes exhibited moderate correlations with the expression of virus circRNAs. Most of them showed negative correlations including 42 genes encoding RNA-binding proteins. They were significantly enriched in biological processes related to cell cycle and RNA processing. Overall, the study provides a valuable resource for further studies of virus circRNAs and also provides new insights into the biogenesis mechanisms of virus circRNAs

Ppe.RPT/SSC‑1: from QTL mapping to a predictive KASP test for ripening time and soluble solids concentration in peach

Genomic regions associated with ripening time (RPT) and soluble solids concentration (SSC) were mapped using a pedigreed population including multiple F1 and F2 families from the Clemson University peach breeding program (CUPBP). RPT and SSC QTLs were consistently identifed in two seasons (2011 and 2012) and the average datasets (average of two seasons). A target region spanning 10,981,971–11,298,736 bp on chromosome 4 of peach reference genome used for haplotype analysis revealed four haplotypes with signifcant diferences in trait values among diferent diplotype combinations. Favorable alleles at the target region for both RPT and SSC were determined and a DNA test for predicting RPT and SSC was developed. Two Kompetitive Allele Specifc PCR (KASP) assays were validated on 84 peach cultivars and 163 seedlings from the CUPBP, with only one assay (Ppe.RPT/SSC‑1) needed to predict between early and late-season ripening cultivars and low and high SSC. These results advance our understanding of the genetic basis of RPT and SSC and facilitate selection of new peach cultivars with the desired RPT and SSCThis work was funded by USDA’s National Institute of Food and Agriculture-Specialty Crop Research Initiative Projects, “RosBREED: Enabling marker-assisted breeding in Rosaceae” (2009-51181-05858) and “RosBREED: Combining disease resistance and horticultural quality in new rosaceous cultivars” (2014-51181-22378).info:eu-repo/semantics/publishedVersio

An updated database of virus circular RNAs provides new insights into the biogenesis mechanism of the molecule

Virus circular RNAs (circRNA) have been reported to be extensively expressed and play important roles in viral infections. Previously we build the first database of virus circRNAs named VirusCircBase which has been widely used in the field. This study significantly improved the database on both the data quantity and database functionality: the number of virus circRNAs, virus species, host organisms was increased from 46440, 23, 9 to 60859, 43, 22, respectively, and 1902 full-length virus circRNAs were newly added; new functions were added such as visualization of the expression level of virus circRNAs and visualization of virus circRNAs in the Genome Browser. Analysis of the expression of virus circRNAs showed that they had low expression levels in most cells or tissues and showed strong expression heterogeneity. Analysis of the splicing of virus circRNAs showed that they used a much higher proportion of non-canonical back-splicing signals compared to those in animals and plants, and mainly used the A5SS (alternative 5’ splice site) in alternative-splicing. Most virus circRNAs have no more than two isoforms. Finally, human genes associated with the virus circRNA production were investigated and more than 1000 human genes exhibited moderate correlations with the expression of virus circRNAs. Most of them showed negative correlations including 42 genes encoding RNA-binding proteins. They were significantly enriched in biological processes related to cell cycle and RNA processing. Overall, the study provides a valuable resource for further studies of virus circRNAs and also provides new insights into the biogenesis mechanisms of virus circRNAs.</p

A Novel Approach to CAFO Odor Assessment: Odorant Field Collection by Sorbent Tube / Thermal Reconstitution in the Laboratory

Historically, odor emission monitoring of high density livestock operations has been limited to direct, whole-air assessment utilizing remote site sampling by plastic bags, human sensory panelists and dynamic dilution olfactometry. On-going efforts by these authors are directed at enabling the translation of these sensory ‘only’ monitoring protocols to instrument ‘primarily, with sensory oversight’ alternatives. This current work attempts to address the latter requirement for sensory oversight and the associated need for improved methods of remote site whole-air sample collection. Published works by these authors as well as others places in serious question the appropriateness of the use of plastic bags for the challenge of CAFO odor assessment; especially relative to sample points at increasing downwind distance from the source. Concerns increase due to the associated natural dilution effects relative to priority semi-volatile odorants. This current submission reports on the progress to date in the development and evaluation of alternative whole-air sampling strategies which attempt to address the primary limitation of plastic sampling bags; the adsorption loss-to-wall of high impact semi-volatile odorants such as p-cresol. In this approach the actual field air sampling is carried out utilizing sorbent tubes for on-site collection of the volatiles/odorants from a measured volume of air. These sorbent tube collections are then transported to the laboratory for reconstitution within a heat traced, passivated and piston-displaced vessel prior to composite odor assessment. The sample reconstitution process is accomplished simply by thermally desorbing the collected odorants into a flowing diluent gas stream and making up to final volume to yield a match of the originally sampled environment.This is an ASABE Meeting Presentation, Paper No. 064154.</p

Mapping and characterization QTLs for phenological traits in seven pedigree-connected peach families

Background: Environmental adaptation and expanding harvest seasons are primary goals of most peach [Prunus persica (L.) Batsch] breeding programs. Breeding perennial crops is a challenging task due to their long breeding cycles and large tree size. Pedigree-based analysis using pedigreed families followed by haplotype construction creates a platform for QTL and marker identification, validation, and the use of marker-assisted selection in breeding programs. Results: Phenotypic data of seven F1 low to medium chill full-sib families were collected over 2 years at two locations and genotyped using the 9 K SNP Illumina array. Three QTLs were discovered for bloom date (BD) and mapped on linkage group 1 (LG1) (172–182 cM), LG4 (48–54 cM), and LG7 (62–70 cM), explaining 17–54%, 11–55%, and 11–18% of the phenotypic variance, respectively. The QTL for ripening date (RD) and fruit development period (FDP) on LG4 was co-localized at the central part of LG4 (40–46 cM) and explained between 40 and 75% of the phenotypic variance. Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles and the presence of multiple functional alleles with different effects for a single locus for RD and FDP. Conclusions: A multiple pedigree-linked families approach validated major QTLs for the three key phenological traits which were reported in previous studies across diverse materials, geographical distributions, and QTL mapping methods. Haplotype characterization of these genomic regions differentiates this study from the previous QTL studies. Our results will provide the peach breeder with the haplotypes for three BD QTLs and one RD/FDP QTL to create predictive DNA-based molecular marker tests to select parents and/or seedlings that have desired QTL alleles and cull unwanted genotypes in early seedling stages.</p

Identification and characterization of QTLs for fruit quality traits in peach through a multi-family approach

Background: Fruit quality traits have a significant effect on consumer acceptance and subsequently on peach (Prunus persica (L.) Batsch) consumption. Determining the genetic bases of key fruit quality traits is essential for the industry to improve fruit quality and increase consumption. Pedigree-based analysis across multiple peach pedigrees can identify the genomic basis of complex traits for direct implementation in marker-assisted selection. This strategy provides breeders with better-informed decisions and improves selection efficiency and, subsequently, saves resources and time. Results: Phenotypic data of seven F1 low to medium chill full-sib families were collected over 2 years at two locations and genotyped using the 9 K SNP Illumina array. One major QTL for fruit blush was found on linkage group 4 (LG4) at 40-46 cM that explained from 20 to 32% of the total phenotypic variance and showed three QTL alleles of different effects. For soluble solids concentration (SSC), one QTL was mapped on LG5 at 60-72 cM and explained from 17 to 39% of the phenotypic variance. A major QTL for titratable acidity (TA) co-localized with the major locus for low-acid fruit (D-locus). It was mapped at the proximal end of LG5 and explained 35 to 80% of the phenotypic variance. The new QTL for TA on the distal end of LG5 explained 14 to 22% of the phenotypic variance. This QTL co-localized with the QTL for SSC and affected TA only when the first QTL is homozygous for high acidity (epistasis). Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles. Conclusions: A multi-family-based QTL discovery approach enhanced the ability to discover a new TA QTL at the distal end of LG5 and validated other QTLs which were reported in previous studies. Haplotype characterization of the mapped QTLs distinguishes this work from the previous QTL studies. Identified predictive SNPs and their original sources will facilitate the selection of parents and/or seedlings that have desired QTL alleles. Our findings will help peach breeders develop new predictive, DNA-based molecular marker tests for routine use in marker-assisted breeding.</p