Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity

How standing genetic variation within a pathogen contributes to diversity in host/pathogen interactions is poorly understood, partly because most studied pathogens are host-specific, clonally reproducing organisms which complicates genetic analysis. In contrast, Botrytis cinerea is a sexually reproducing, true haploid ascomycete that can infect a wide range of diverse plant hosts. While previous work had shown significant genomic variation between two isolates, we proceeded to assess the level and frequency of standing variation in a population of B. cinerea. To begin measuring standing genetic variation in B. cinerea, we re-sequenced the genomes of 13 different isolates and aligned them to the previously sequenced T4 reference genome. In addition one of these isolates was resequenced from four independently repeated cultures. A high level of genetic diversity was found within the 13 isolates. Within this variation, we could identify clusters of genes with major effect polymorphisms, i.e., polymorphisms that lead to a predicted functional knockout, that surrounded genes involved in controlling vegetative incompatibility. The genotype at these loci was able to partially predict the interaction of these isolates in vegetative fusion assays showing that these loci control vegetative incompatibility. This suggests that the vegetative incompatibility loci within B. cinerea are associated with regions of increased genetic diversity. The genome re-sequencing of four clones from the one isolate (Grape) that had been independently propagated over 10 years showed no detectable spontaneous mutation. This suggests that B. cinerea does not display an elevated spontaneous mutation rate. Future work will allow us to test if, and how, this diversity may be contributing to the pathogen's broad host range

Parallel loss-of-function at the RPM1 bacterial resistance locus in Arabidopsis thaliana

Dimorphism at the Resistance to Pseudomonas syringae pv. maculicola 1 (RPM1) locus is well documented in natural populations of Arabidopsis thaliana and has been portrayed as a long-term balanced polymorphism. The haplotype from resistant plants contains the RPM1 gene, which enables these plants to recognize at least two structurally unrelated bacterial effector proteins (AvrB and AvrRpm1) from bacterial crop pathogens. A complete deletion of the RPM1 coding sequence has been interpreted as a single event resulting in susceptibility in these individuals. Consequently, the ability to revert to resistance or for alternative R-gene specificities to evolve at this locus has also been lost in these individuals. Our survey of variation at the RPM1 locus in a large species-wide sample of A. thaliana has revealed four new loss-of-function alleles that contain most of the intervening sequence of the RPM1 open reading frame. Multiple loss-of-function alleles may have originated due to the reported intrinsic cost to plants expressing the RPM1 protein. The frequency and geographic distribution of rpm1 alleles observed in our survey indicate the parallel origin and maintenance of these loss-of-function mutations and reveal a more complex history of natural selection at this locus than previously thought

"Missing" G x E Variation Controls Flowering Time in Arabidopsis thaliana.

Understanding how genetic variation interacts with the environment is essential for understanding adaptation. In particular, the life cycle of plants is tightly coordinated with local environmental signals through complex interactions with the genetic variation (G x E). The mechanistic basis for G x E is almost completely unknown. We collected flowering time data for 173 natural inbred lines of Arabidopsis thaliana from Sweden under two growth temperatures (10°C and 16°C), and observed massive G x E variation. To identify the genetic polymorphisms underlying this variation, we conducted genome-wide scans using both SNPs and local variance components. The SNP-based scan identified several variants that had common effects in both environments, but found no trace of G x E effects, whereas the scan using local variance components found both. Furthermore, the G x E effects appears to be concentrated in a small fraction of the genome (0.5%). Our conclusion is that G x E effects in this study are mostly due to large numbers of allele or haplotypes at a small number of loci, many of which correspond to previously identified flowering time genes

Meta-analysis of metabolome QTLs in Arabidopsis: trying to estimate the network size controlling genetic variation of the metabolome.

A central goal of systems biology is to develop models that are both predictive and accurately describe the biological system. One complexity to this endeavor is that it is possible to develop models that appear predictive even if they use far fewer components than the biological system itself uses for the same process. This problem also occurs in quantitative genetics where it is often possible to describe the variation in a system using fewer genes than are actually variable due to the complications of linkage between causal polymorphisms and population structure. Thus, there is a crucial need to begin an empirical investigation into the true number of components that are used by biological systems to determine a phenotypic outcome. In this study, we use a meta-analysis of directly comparable metabolomics quantitative studies using quantitative trait locus mapping and genome wide association mapping to show that it is currently not possible to estimate how many genetic loci are truly polymorphic within Arabidopsis thaliana. Our analysis shows that it would require the analysis of at least a 1000 line bi-parental population to begin to estimate how many polymorphic loci control metabolic variation within Arabidopsis. Understanding the base number of loci that are actually involved in determining variation in metabolic systems is fundamental to developing systems models that are truly reflective of how metabolism is modulated within a living organism

Pathogen Genetic Control of Transcriptome Variation in the Arabidopsis thaliana - Botrytis cinerea Pathosystem

In plant-pathogen relations, disease symptoms arise from the interaction of the host and pathogen genomes. Host-pathogen functional gene interactions are well described, whereas little is known about how the pathogen genetic variation modulates both organisms' transcriptomes. To model and generate hypotheses on a generalist pathogen control of gene expression regulation, we used the Arabidopsis thaliana-Botrytis cinerea pathosystem and the genetic diversity of a collection of 96 B. cinerea isolates. We performed expression-based genome-wide association (eGWA) for each of 23,947 measurable transcripts in Arabidopsis (host), and 9267 measurable transcripts in B. cinerea (pathogen). Unlike other eGWA studies, we detected a relative absence of locally acting expression quantitative trait loci (cis-eQTL), partly caused by structural variants and allelic heterogeneity hindering their identification. This study identified several distantly acting trans-eQTL linked to eQTL hotspots dispersed across Botrytis genome that altered only Botrytis transcripts, only Arabidopsis transcripts, or transcripts from both species. Gene membership in the trans-eQTL hotspots suggests links between gene expression regulation and both known and novel virulence mechanisms in this pathosystem. Genes annotated to these hotspots provide potential targets for blocking manipulation of the host response by this ubiquitous generalist necrotrophic pathogen

The Question of Withdrawal of Russian Army in Latvian Press (1991-1994)

Bakalaura darba „Krievijas armijas izvešanas jautājums latviešu presē 1991.-1994 ” mērķis ir analizēt un konstatēt latviešu preses vērtējumu Krievijas armijas izvešanas jautājumu, analizējot karaspēka izvešanas gaitu, starpvalstu sarunās starp Baltijas un Krievijas delegācijām un problemātiku cilvēktiesību jautājumā (izmantojot laikrakstus „Diena”, „Tēvzemes Avīze”, „Neatkarīgā cīņa”, „Atmoda atpūtai”, „Nacionālā neatkarība”.) Bakalaura darbā tiek aplūkoti latviešu preses un mūsdienu autoru viedokļi par Krievijas armijas izvešanas jautājumu, tādejādi salīdzinot 90.gadu preses objektivitāti.Bachelor work’s „The Question of Withdrawal of Russian Army in Latvian Press (1991-1994)” investigation goal is to analyse Latvian press evaluation in question of withdrawal of Russian army, by analyzing the disengagemnet process, cross –border negotiations between the Baltic and Russian delegations, and human rights issues ( using newspapers „Diena”, „Tēvzemes Avīze” and „Neatkarīgā cīņa” ”, „Atmoda atpūtai”, „Nacionālā neatkarība”) In Bachelor work one of the goales is to compare Latvian press and nowday’s authors opinion about Russian army withdrawal