Evolution and Adaptation of Forest and Crop Pathogens in the Anthropocene

2020 ◽  
pp. PHYTO-08-20-035
Author(s):  
Pauline Hessenauer ◽  
Nicolas Feau ◽  
Upinder Gill ◽  
Benjamin Schwessinger ◽  
Gurcharn S. Brar ◽  
...  
Keyword(s):  
Population Genomics ◽  
Production Systems ◽  
Management Strategies ◽  
Forest Trees ◽  
Forest Production ◽  
Population Genomic ◽  
Genomic Studies ◽  
Pathogen Populations ◽  
Different Characteristics ◽  
Global Food

Anthropocene marks the era when human activity is making a significant impact on earth, its ecological and biogeographical systems. The domestication and intensification of agricultural and forest production systems have had a large impact on plant and tree health. Some pathogens benefitted from these human activities and have evolved and adapted in response to the expansion of crop and forest systems, resulting in global outbreaks. Global pathogen genomics data including population genomics and high-quality reference assemblies are crucial for understanding the evolution and adaptation of pathogens. Crops and forest trees have remarkably different characteristics, such as reproductive time and the level of domestication. They also have different production systems for disease management with more intensive management in crops than forest trees. By comparing and contrasting results from pathogen population genomic studies done on widely different agricultural and forest production systems, we can improve our understanding of pathogen evolution and adaptation to different selection pressures. We find that in spite of these differences, similar processes such as hybridization, host jumps, selection, specialization, and clonal expansion are shaping the pathogen populations in both crops and forest trees. We propose some solutions to reduce these impacts and lower the probability of global pathogen outbreaks so that we can envision better management strategies to sustain global food production as well as ecosystem services.

scholarly journals A beginner's guide to low-coverage whole genome sequencing for population genomics

2021 ◽  
Author(s):  
Runyang Nicolas Lou ◽  
Arne Jacobs ◽  
Aryn Wilder ◽  
Nina Overgaard Therkildsen
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Population Genomics ◽  
Cost Effective ◽  
Whole Genome ◽  
Model Species ◽  
Population Genomic ◽  
Genomic Studies ◽  
Lower Depth ◽  
Low Coverage

Low-coverage whole genome sequencing (lcWGS) has emerged as a powerful and cost-effective approach for population genomic studies in both model and non-model species. However, with read depths too low to confidently call individual genotypes, lcWGS requires specialized analysis tools that explicitly account for genotype uncertainty. A growing number of such tools have become available, but it can be difficult to get an overview of what types of analyses can be performed reliably with lcWGS data, and how the distribution of sequencing effort between the number of samples analyzed and per-sample sequencing depths affects inference accuracy. In this introductory guide to lcWGS, we first illustrate how the per-sample cost for lcWGS is now comparable to RAD-seq and Pool-seq in many systems. We then provide an overview of software packages that explicitly account for genotype uncertainty in different types of population genomic inference. Next, we use both simulated and empirical data to assess the accuracy of allele frequency and genetic diversity estimation, detection of population structure, and selection scans under different sequencing strategies. Our results show that spreading a given amount of sequencing effort across more samples with lower depth per sample consistently improves the accuracy of most types of inference, with a few notable exceptions. Finally, we assess the potential for using imputation to bolster inference from lcWGS data in non-model species, and discuss current limitations and future perspectives for lcWGS-based population genomics research. With this overview, we hope to make lcWGS more approachable and stimulate its broader adoption.

scholarly journals A beginner's guide to low-coverage whole genome sequencing for population genomics

2021 ◽  
Author(s):  
Runyang Nicolas Lou ◽  
Arne Jacobs ◽  
Aryn Wilder ◽  
Nina Overgaard Therkildsen
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Population Genomics ◽  
Cost Effective ◽  
Whole Genome ◽  
Model Species ◽  
Population Genomic ◽  
Genomic Studies ◽  
Lower Depth ◽  
Low Coverage

Low-coverage whole genome sequencing (lcWGS) has emerged as a powerful and cost-effective approach for population genomic studies in both model and non-model species. However, with read depths too low to confidently call individual genotypes, lcWGS requires specialized analysis tools that explicitly account for genotype uncertainty. A growing number of such tools have become available, but it can be difficult to get an overview of what types of analyses can be performed reliably with lcWGS data, and how the distribution of sequencing effort between the number of samples analyzed and per-sample sequencing depths affects inference accuracy. In this introductory guide to lcWGS, we first illustrate how the per-sample cost for lcWGS is now comparable to RAD-seq and Pool-seq in many systems. We then provide an overview of software packages that explicitly account for genotype uncertainty in different types of population genomic inference. Next, we use both simulated and empirical data to assess the accuracy of allele frequency and genetic diversity estimation, detection of population structure, and selection scans under different sequencing strategies. Our results show that spreading a given amount of sequencing effort across more samples with lower depth per sample consistently improves the accuracy of most types of inference, with a few notable exceptions. Finally, we assess the potential for using imputation to bolster inference from lcWGS data in non-model species, and discuss current limitations and future perspectives for lcWGS-based population genomics research. With this overview, we hope to make lcWGS more approachable and stimulate its broader adoption.

scholarly journals Targeted sequence capture array for phylogenetics and population genomics in the Salicaceae

2020 ◽  
Author(s):  
Brian J. Sanderson ◽  
Stephen P. DiFazio ◽  
Quentin C. Cronk ◽  
Tao Ma ◽  
Matthew S. Olson
Keyword(s):  
Population Genomics ◽  
Sequence Data ◽  
Gene Trees ◽  
Base Pairs ◽  
Phylogenetic Information ◽  
Sequence Capture ◽  
Population Genomic ◽  
The Family ◽  
Genomic Studies ◽  
Targeted Sequence Capture

AbstractPremise of the studyThe family Salicaceae has proved taxonomically challenging, especially in the genus Salix, which is speciose and features frequent hybridization and polyploidy. Past efforts to reconstruct the phylogeny with molecular barcodes have failed to resolve the species relationships of many sections of the genus.MethodsWe used the wealth of sequence data in the family to design sequence capture probes to target regions of 300-1200 base pairs of exonic regions of 972 genes.ResultsWe recovered sequence data for nearly all of the targeted genes in three species of Populus and three species of Salix. We present a species tree, discuss concordance among gene trees, as well as some population genomic summary statistics for these loci.ConclusionsOur sequence capture array has extremely high capture efficiency within the genera Populus and Salix, resulting in abundant phylogenetic information. Additionally, these loci show promise for population genomic studies.

Phosphorus: Past History and Contributions to the Global Food Supply

2019 ◽  
Vol 103 (1) ◽  
pp. 6-8 ◽  
Author(s):  
Terry Roberts
Keyword(s):  
Food Security ◽  
Food Supply ◽  
Food Production ◽  
Production Systems ◽  
Past History ◽  
Phosphate Fertilizer ◽  
Global Food ◽  
Global Food Supply

Since its early rudimentary forms, phosphate fertilizer has developed in step with our understanding of successful food production systems. Recognized as essential to life, the responsible use P in agriculture remains key to food security.

scholarly journals Legumes increase grassland productivity with no effect on nitrous oxide emissions

2019 ◽  
Vol 446 (1-2) ◽  
pp. 163-177 ◽  
Author(s):  
Arlete S. Barneze ◽  
Jeanette Whitaker ◽  
Niall P. McNamara ◽  
Nicholas J. Ostle
Keyword(s):  
Management Practices ◽  
Production Systems ◽  
N Uptake ◽  
Relative Proportion ◽  
Management Strategies ◽  
Ghg Emissions ◽  
Chemical Properties ◽  
Nitrous Oxide Emissions ◽  
Mineral N ◽  
Grassland Productivity

Abstract Aims Grasslands are important agricultural production systems, where ecosystem functioning is affected by land management practices. Grass-legume mixtures are commonly cultivated to increase grassland productivity while reducing the need for nitrogen (N) fertiliser. However, little is known about the effect of this increase in productivity on greenhouse gas (GHG) emissions in grass-legume mixtures. The aim of this study was to investigate interactions between the proportion of legumes in grass-legume mixtures and N-fertiliser addition on productivity and GHG emissions. We tested the hypotheses that an increase in the relative proportion of legumes would increase plant productivity and decrease GHG emissions, and the magnitude of these effects would be reduced by N-fertiliser addition. Methods This was tested in a controlled environment mesocosm experiment with one grass and one legume species grown in mixtures in different proportions, with or without N-fertiliser. The effects on N cycling processes were assessed by measurement of above- and below-ground biomass, shoot N uptake, soil physico-chemical properties and GHG emissions. Results Above-ground productivity and shoot N uptake were greater in legume-grass mixtures compared to grass or legume monocultures, in fertilised and unfertilised soils. However, we found no effect of legume proportion on N2O emissions, total soil N or mineral-N in fertilised or unfertilised soils. Conclusions This study shows that the inclusion of legumes in grass-legume mixtures positively affected productivity, however N cycle were in the short-term unaffected and mainly affected by nitrogen fertilisation. Legumes can be used in grassland management strategies to mitigate climate change by reducing crop demand for N-fertilisers.

A model to account for the consequences of host nutrition on the outcome of gastrointestinal parasitism in sheep: model evaluation

Parasitology ◽  
2007 ◽  
Vol 134 (9) ◽  
pp. 1279-1289 ◽  
Author(s):  
D. VAGENAS ◽  
S. C. BISHOP ◽  
I. KYRIAZAKIS
Keyword(s):  
Mathematical Model ◽  
Worm Burden ◽  
Management Strategies ◽  
Sensitivity Analyses ◽  
Sheep Model ◽  
Host Nutrition ◽  
Gastrointestinal Parasitism ◽  
Different Characteristics ◽  
Nutritional Strategies ◽  
Different Levels

SUMMARYThis paper describes sensitivity analyses and expectations obtained from a mathematical model developed to account for the effects of host nutrition on the consequences of gastrointestinal parasitism in sheep. The scenarios explored included different levels of parasitic challenge at different planes of nutrition, for hosts differing only in their characteristics for growth. The model was able to predict the consequences of host nutrition on the outcome of parasitism, in terms of worm burden, number of eggs excreted per gram faeces and animal performance. The model outputs predict that conclusions on the ability of hosts of different characteristics for growth to cope with parasitism (i.e. resistance) depend on the plane of nutrition. Furthermore, differences in the growth rate of sheep, on their own, are not sufficient to account for differences in the observed resistance of animals. The model forms the basis for evaluating the consequences of differing management strategies and environments, such as breeding for certain traits associated with resistance and nutritional strategies, on the consequences of gastrointestinal parasitism on sheep.

Relative Distribution and Incidence of Viruses Associated with Disease Outbreaks in Tomato Fields in Trinidad

2006 ◽  
Vol 7 (1) ◽  
pp. 29
Author(s):  
S. N. Rampersad
Keyword(s):  
Production Systems ◽  
Management Strategies ◽  
Disease Outbreaks ◽  
Tobacco Etch Virus ◽  
The Other ◽  
Multiple Infections ◽  
Relative Distribution ◽  
Tomato Production ◽  
Viral Pathogen ◽  
High Incidence

Tomato production in Trinidad has suffered considerable losses in yield and fruit quality due to infections of hitherto surmised etiology. In order to develop strategies for controlling viral diseases in tomato, the relative distribution and incidence of seven viruses that commonly infect tomato were determined. Of the 362 samples tested, Potato yellow mosaic Trinidad virus (PYMTV) was found in every farm except two and was present at relatively high incidence throughout the country. Tobacco mosaic virus (TMV) and Tobacco etch virus (TEV) were found in fewer farms and at lower incidences while the other viruses were absent. Single infections of either virus were more common than double infections and multiple infections were rare but present. The results indicated that PYMTV is the predominant and most important viral pathogen in tomato production systems in Trinidad; however, begomovirus disease management strategies will also have to accommodate controls Accepted for publication 10 January 2006. Published 9 March 2006.

Die Wertstrommethode in der Prozessindustrie*/The Value Stream Method in the process industry - Analysis of its shortcomings and recommendations for adaption

2017 ◽  
Vol 107 (04) ◽  
pp. 231-234
Author(s):  
K. Erlach ◽  
E. Sheehan ◽  
S. Hartleif
Keyword(s):  
Production Systems ◽  
Design Method ◽  
Design Guidelines ◽  
Process Industry ◽  
Joint Production ◽  
Industry Analysis ◽  
Process Industries ◽  
Good Industry ◽  
Value Stream ◽  
Different Characteristics

In der Stückgutindustrie lassen sich die acht Gestaltungsrichtlinien der Wertstrommethode nach Erlach hervorragend anwenden. In der Prozessindustrie weist die Produktion jedoch häufig andere Merkmale (beispielsweise eine Kuppelproduktion) auf, die neue Herausforderungen an die Wertstrommethode stellen. Aufbauend auf den acht Gestaltungsrichtlinien des Wertstromdesigns werden in diesem Fachbeitrag Handlungsempfehlungen für die Anwendung der Wertstrommethode in der Prozessindustrie diskutiert.   The eight design guidelines of Erlach‘s Value Stream Design Method work well in streamlining operations in the piece-good industry. In the process and chemical industries, however, production systems exhibit different characteristics, like joint production, that present challenges for the eight step value stream design method. Building on the eight design guidelines, this article discusses the deficits of this method in the process industries and gives recommendations for its adaptatio.

Identification of waste management strategies and waste generation factors for thermal power plant sector wastes in Turkey

2018 ◽  
Vol 37 (3) ◽  
pp. 210-218
Author(s):  
Cansu Demir ◽  
Ülkü Yetiş ◽  
Kahraman Ünlü
Keyword(s):  
Waste Management ◽  
Power Plants ◽  
Production Systems ◽  
Thermal Power ◽  
Management Strategies ◽  
Bottom Ash ◽  
Thermal Power Plants ◽  
Waste Generation ◽  
Turkish Republic ◽  
Process Modification

Thermal power plants are of great environmental importance in terms of the huge amounts of wastes that they produce. Although there are process-wise differences among these energy production systems, they all depend on the logic of burning out a fuel and obtaining thermal energy to rotate the turbines. Depending on the process modification and the type of fuel burned, the wastes produced in each step of the overall process may change. In this study, the most expected process and non-process wastes stemming from different power generation processes have been identified and given their European Waste Codes. Giving priority to the waste minimization options for the most problematic wastes from thermal power plants, waste management strategies have been defined. In addition, by using the data collected from site visits, from the literature and provided by the Turkish Republic Ministry of Environment and Urbanization, waste generation factor ranges expressed in terms of kilogram of waste per energy produced annually (kg/MWh) have been estimated. As a result, the highest generation was found to be in fly ash (24–63 for imported coal, 200–270 for native coal), bottom ash (1.3–6 for imported coal, 42–87 for native coal) and the desulfurization wastes (7.3–32) produced in coal combustion power plants. The estimated waste generation factors carry an important role in that they aid the authorities to monitor the production wastes declared by the industries.

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