scholarly journals Sources of genomic diversity in the self-fertile plant pathogen, Sclerotinia sclerotiorum, and consequences for resistance breeding

2020 ◽  
Author(s):  
Lone Buchwaldt ◽  
Harsh Garg ◽  
Krishna D. Puri ◽  
Jonathan Durkin ◽  
Jennifer Adam ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Point Mutation ◽  
Ssr Markers ◽  
Sclerotinia Sclerotiorum ◽  
Quantitative Resistance ◽  
Life Cycles ◽  
Genomic Diversity ◽  
Western Canada ◽  
Genomic Change ◽  
Over Time

AbstractThe ascomycete, Sclerotinia sclerotiorum, has a broad host range and causes yield loss in dicotyledonous crops world wide. Genomic diversity and aggressiveness were determined in a population of 127 isolates from individual canola (Brassica napus) fields in western Canada. Genotyping with 39 simple sequence repeat (SSR) markers revealed each isolate was an unique haplotype. Analysis of molecular variation showed 97% was due to isolate and 3% to geographical location. Testing of mycelium compatibility identified clones of mutually compatible isolates, and stings of pairwise compatible isolates not seen before. Importantly, mutually compatible isolates had similar SSR haplotype, in contrast to high diversity among incompatible isolates. Isolates from the Province of Manitoba had higher allelic richness and higher mycelium compatibility (61%) than Alberta (35%) and Saskatchewan (39%). All compatible Manitoba isolates were interconnected in clones and strings, which can be explained by wetter growing seasons and more susceptible crops species both favouring more mycelium interaction and life cycles. Analysis of linkage disequilibrium rejected random recombination, consistent with a self-fertile fungus and restricted outcrossing due to mycelium incompatibility, and only one meiosis per lifecycle. More probable sources of genomic diversity is slippage during DNA replication and point mutation affecting single nucleotides, not withstanding the high mutation rate of SSRs compared to genes. It seems accumulation of these polymorphisms lead to increasing mycelium incompatibility in a population over time. A phylogenetic tree grouped isolates into 17 sub-populations. Aggressiveness was tested by inoculating one isolate from each sub-population onto B. napus lines with quantitative resistance. Results were significant for isolate, line, and isolate by line interaction. These isolates represent the genomic and pathogenic diversity in western Canada, and are suitable for resistance screening in canola breeding programs. Since the S. sclerotiorum life cycle is universal, conclusions on sources of genomic diversity extrapolates to populations in other geographical areas and host crops.Author summarySclerotinia sclerotiorum populations from various plant species and geographical areas have been studied extensively using mycelium compatibility tests and genotyping with a shared set of 6-13 SSR markers published in 2001. Most conclude the pathogen is clonally propagated with some degree of outcrossing. In the present study, a population of S. sclerotiorum isolates from 1.5 million km2 area in western Canada were tested for mycelium compatibility, and genotyped with 9 published and 30 newly developed SSR markers targeting all chromosomes in the dikaryot genome (8+8). A new way of visualizing mycelium compatibility results revealed clones of mutual compatible isolates, as well as long and short strings of pairwise compatible isolates. Importantly, clonal isolates had similar SSR haplotype, while incompatible isolates were highly dissimilar; a relationship difficult to discern previously. Analysis of population structure found a lack of linkage disequilibrium ruling out random recombination. Outcrossing, a result of alignment of non-sister chromosomes during meiosis, is unlikely in S. sclerotiorum, since mycelium incompatibility prevents karyogamy, and compatibility only occur between isolates with similar genomic composition. Instead, genomic diversity comprise transfer of nuclei through hyphal anastomosis, allelic modifications during cell division and point mutation. Genomic polymorphisms accumulate over time likely result in gradual divergence of individuals, which seems to resemble the ‘ring-species’ concept. We are currently studying whether nuclei in microconidia might also contribute to diversity. A phylogenetic analysis grouped isolates into 17 sub-populations. One isolate from each sub-population showed different level of aggressiveness when inoculated onto B. napus lines previously determined to have quantitative resistance to a single isolate. Seed of these lines and S. sclerotiorum isolates have been transferred to plant breeders, and can be requested from the corresponding author for breeding purposes. Quantitative resistance is likely to hold up over time, since the rate of genomic change is relatively slow in S. sclerotiorum.

Impact of Technology Infusion on System Complexity and Modularity

2015 ◽  
Author(s):  
GwangKi Min ◽  
Eun Suk Suh ◽  
Katja Hölttä-Otto
Keyword(s):  
System Performance ◽  
New Technologies ◽  
Life Cycles ◽  
System Complexity ◽  
Host System ◽  
Technology Infusion ◽  
Long Life ◽  
Impact Of Technology ◽  
The Impact ◽  
Over Time

Complex systems often have long life cycles with requirements that are likely to change over time. Therefore, it is important to be able to adapt the system accordingly over time. This is often accomplished by infusing new technologies into the host system in order to update or improve overall system performance. However, technology infusion often results in a disruption in the host system. This can take the form of a system redesign or a change in the inherent attributes of the system. In this study, we analyzed the impact of technology infusion on system attributes, specifically the complexity and modularity. Two different systems that were infused with new technologies were analyzed for changes in complexity and modularity.

scholarly journals Genomic diversity, life strategies and ecology of marine HTVC010P-type pelagiphages

2021 ◽  
Vol 7 (7) ◽  
Author(s):  
Sen Du ◽  
Fang Qin ◽  
Zefeng Zhang ◽  
Zhen Tian ◽  
Mingyu Yang ◽  
...  
Keyword(s):  
Life Cycles ◽  
Genomic Diversity ◽  
Global Ocean ◽  
Comparative Genomic ◽  
Trna Genes ◽  
Life Strategies ◽  
Phage Group ◽  
Integrase Gene ◽  
Subgroup Ii ◽  
Integration Sites

SAR11 bacteria dominate ocean surface bacterioplankton communities, and play an important role in marine carbon and nutrient cycling. The biology and ecology of SAR11 are impacted by SAR11 phages (pelagiphages) that are highly diverse and abundant in the ocean. Among the currently known pelagiphages, HTVC010P represents an extremely abundant but under-studied phage group in the ocean. In this study, we have isolated seven new HTVC010P-type pelagiphages, and recovered 77 nearly full-length HTVC010P-type metagenomic viral genomes from marine metagenomes. Comparative genomic and phylogenomic analyses showed that HTVC010P-type pelagiphages display genome synteny and can be clustered into two major subgroups, with subgroup I consisting of strictly lytic phages and subgroup II mostly consisting of phages with potential lysogenic life cycles. All but one member of the subgroup II contain an integrase gene. Site-specific integration of subgroup II HTVC010P-type pelagiphage was either verified experimentally or identified by in silico genomic sequence analyses, which revealed that various SAR11 tRNA genes can serve as the integration sites of HTVC010P-type pelagiphages. Moreover, HTVC010P-type pelagiphage integration was confirmed by the detection of several Global Ocean Survey (GOS) fragments that contain hybrid phage–host integration sites. Metagenomic recruitment analysis revealed that these HTVC010P-type phages were globally distributed and most lytic subgroup I members exhibited higher relative abundance. Altogether, this study significantly expands our knowledge about the genetic diversity, life strategies and ecology of HTVC010P-type pelagiphages.

Breeding durum wheat in western Canada: Historical trends in yield and related variables

1995 ◽  
Vol 75 (1) ◽  
pp. 55-60 ◽  
Author(s):  
T. N. McCaig ◽  
J. M. Clarke
Keyword(s):  
Durum Wheat ◽  
Triticum Turgidum ◽  
Kernel Weight ◽  
Western Canada ◽  
Kernel Number ◽  
Historical Trends ◽  
Days To Maturity ◽  
Sink Demand ◽  
Over Time ◽  
Selection Of

Canadian durum wheat (Triticum turgidum L.) production is centred in the Brown and Dark Brown soil zones, areas of limited rainfall. For more than 50 yr, lines have been evaluated in the multi-location Durum Cooperative Test. Data from this test, over the period 1947–1992, were analyzed with the objectives of determining the advances that have been made within the Canada Western Amber Durum (CWAD) wheat class and comparing yield-related variables of recently registered cultivars with those of earlier cultivars. Canadian-developed cultivars have increased yields about 0.81% yr−1 relative to Hercules, or approximately 22.6 kg ha−1 yr−1. As kernel weight has remained unchanged, the genetic yield increases have resulted entirely from an increase in the number of kernels produced. Because kernel number is determined prior to, and during, anthesis, further yield increases may depend upon selection of genotypes that produce higher numbers of kernels, thereby increasing sink demand. While plant height and hectolitre weight have been decreasing over time, neither variable was significantly (P < 0.05) correlated with the yield increases that have taken place over the 29-yr period. The selection pressure toward shorter cultivars may have involved other agronomic advantages, such as decreased lodging. Days to maturity did not change significantly over time and was not correlated with yield. Key words:Triticum turgidum, kernel number, kernel weight, height, hectolitre weight

scholarly journals DYNAMICS OF THE LINKAGE DISEQUILIBRIUM FUNCTION UNDER MODELS OF GENE-FREQUENCY HITCHHIKING

Genetics ◽  
1981 ◽  
Vol 99 (2) ◽  
pp. 337-356
Author(s):  
Marjorie A Asmussen ◽  
Michael T Clegg
Keyword(s):  
Linkage Disequilibrium ◽  
Gene Frequency ◽  
Initial Conditions ◽  
Recombination Fraction ◽  
Qualitative Description ◽  
Selection Intensity ◽  
Gene Frequencies ◽  
Dependent Behavior ◽  
Wide Range ◽  
Over Time

ABSTRACT The dynamic behavior of the linkage disequilibrium (D) between a neutral and a selected locus is analyzed for a variety of deterministic selection models. The time-dependent behavior of D is governed by the gene frequency at the selected locus (p) and by the selection (s) and recombination (r) parameters. Thomson (1977) showed numerically that D may increase under certain initial conditions. We give exact conditions for D to increase in time, which require that the selection intensity exceed the recombination fraction (s &gt; r) and that p be near zero or one. We conclude from this result that gene frequency hitchhiking is most likely to be important when a new favorable mutant enters a population. We also show that, for what can be a wide range of gene frequencies, D will decay at a faster rate than the neutral rate. Consequently, the hitchhiking effect may quickly diminish as the selected gene becomes more common.—The method of analysis allows a complete qualitative description of the dynamics of D as a function of s and r. Two major findings concern the range of gene frequencies at the selected locus for which D either increases over time or decays at a faster rate than under neutrality. For all models considered, the region where D increases (i) first enlarges then shrinks as selection intensifies, and (ii) steadily shrinks as r increases. In contrast, the region of accelerated decay constantly enlarges as the selection intensity increases. This region will either shrink or enlarge as r increases, depending upon the form of selection in force.

Acquisition of New In Vivo Genomic Change over Time in Multiple Myeloma.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2481-2481
Author(s):  
Yu-Tzu Tai ◽  
Leutz Buon ◽  
Benjamin King ◽  
Cheng Li Cheng Li ◽  
Peter Burger Peter Burger ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Drug Resistance ◽  
Snp Array ◽  
Genomic Change ◽  
Myeloma Cells ◽  
Genomic Changes ◽  
Time Points ◽  
A Genome ◽  
Over Time

Abstract Multiple myeloma (MM) cells present with significant genetic abnormality. This genetic instability is considered responsible for not only development of malignant phenotype but also progression of myeloma as well as development of drug resistance. We have previously demonstrated that MM cell lines have elevated homologous recombination activity that leads to acquisition of new genomic changes over time and is associated with development of drug resistance (Blood2004; 104: 3409). However, such genomic evolution in patient samples has not been documented. Here, we have performed a genome wide loss of heterozygosity (LOH) assay, using high-density oligonucleotide arrays capable of measuring up to 500K single nucleotide polymorphisms (SNP) loci, and identify areas of amplification and losses to determine ongoing development of new changes that may reflect instability. We have evaluated 17 MM patients with purified myeloma cells obtained at two time points, at least six months apart. CD138–expressing myeloma cells from these patients were purified and their peripheral blood mononuclear cells were also obtained. Genomic DNA from these cells was digested with StyI, PCR amplified and hybridized to 250K SNP array. Results from CD138+ myeloma cells from two time points or more were compared with each other using the dChip software for LOH and copy number analysis. During the LOH analysis, we have adapted a tumor vs. tumor comparison to track all the new SNPs affected. We have observed that myeloma cells acquired new LOH loci in the subsequent samples. These new areas of genetic changes were recurrent; for example on chromosome 13, an average area of recurrent LOH of 87 Mb was found to be present among three patients. We were able to observe recurrence of significant copy changes on several chromosomes with/without LOH. The reproducible area of new acquisition of LOH and/or significant copy changes interestingly involved areas on chromosomes 1p, 1q, 8p, 9q, 13q, 15, 16q, 20p, 21q, and X that may have significant role in the pathogenesis and progression of the disease. We are currently analyzing the gene expression profile from these time points to identify expression changes correlating with the observed genomic changes on follow up samples. In summary we demonstrate continued acquisition of new genomic changes in vivo in MM over time and provide a molecular basis for evolution of more aggressive disease able to escape therapeutic interventions. The mechanism governing such evolution is an important target to not only inhibit progression of the disease but also development of drug resistance.

scholarly journals Industry life cycles of a resource town in Finland – the case of Lieksa

2015 ◽  
Vol 7 (1) ◽  
pp. 16-41 ◽  
Author(s):  
Maija Halonen ◽  
Juha Kotilainen ◽  
Markku Tykkyläinen ◽  
Eero Vatanen
Keyword(s):  
Natural Resources ◽  
Life Cycles ◽  
The Political ◽  
Processing Industry ◽  
Long Run ◽  
Service Production ◽  
Absolute Advantage ◽  
Industry Life Cycles ◽  
Over Time

Abstract The article aims to show how local industry life cycles impact the development of Finnish resource-based rural towns. This study reveals five long-term and overlapping industry cycles which were based on natural resources, assembly industries and service production. In general, the cycles have shortened over time. Transitions from cycle to cycle were enabled by the phases of resilience, which were highly dependent on political and economic processes at different scales. However, the political interventions of the last decades were unable to compensate for the disadvantages in competitiveness of this remote area and lay sustainable foundations for new industries. In the long run, the only exception has been the forest-related processing industry which has a capacity to renew its own operations and adapt to changing market situations. The results demonstrate the high significance of absolute advantage in rural development

scholarly journals miR-128-induced LINE-1 restriction is dependent on down-regulation of hnRNPA1

2017 ◽  
Author(s):  
Lianna Fung ◽  
Herlinda Guzman ◽  
Evgueni Sevrioukov ◽  
Adam Idica ◽  
Eddie Park ◽  
...  
Keyword(s):  
Target Genes ◽  
De Novo ◽  
Somatic Cells ◽  
Direct Interaction ◽  
Life Cycles ◽  
Genomic Diversity ◽  
Protein Levels ◽  
Induced Mutagenesis ◽  
Genomic Locations ◽  
Dual Mechanism

ABSTRACTThe majority of the human genome is made of transposable elements, giving rise to interspaced repeats, including Long Interspersed Element-1s (LINE-1s or L1s). L1s are active human DNA parasites involved in genomic diversity and evolution, but can also contribute to genomic instability and diseases. L1s require host factors to complete their life cycles, whereas the host has evolved numerous mechanisms to restrict L1-induced mutagenesis. Restriction mechanisms in somatic cells include methylation of the L1 promoter, anti-viral factors and RNA-mediated processes such as small RNAs. microRNAs (miRNAs or miRs) are small non-coding RNAs that post-transcriptionally repress multiple target genes often found in the same cellular pathways. We have recently established that the interferon-inducible miR-128 function as a novel restriction factor inhibiting L1 mobilization in somatic cells. We have further demonstrated that miR-128 function through a dual mechanism; by directly targeting L1 RNA for degradation and indirectly by inhibiting a cellular co-factor which L1 is dependent on to transpose to new genomic locations (TNPO1). Here we add another piece to the puzzle of the enigmatic L1 life cycle. We show that miR-128 also inhibits another key cellular factor, hnRNPA1, by significantly reducing mRNA and protein levels through direct interaction with the coding sequence (CDS) of hnRNPA1 mRNA. Furthermore, we demonstrate that repression of hnRNPA1 using shRNA significantly decreases de novo L1 retrotransposition and that induced hnRNPA1 expression enhances L1 mobilization. Finally, we determine that hnRNPA1 is a functional target of miR-128 and that induced hnRNPA1 expression in miR-128-overexpressing cells can partly rescue the miR-128-induced repression of L1’s ability to transpose to different genomic locations. Thus, we have identified an additional mechanism by which miR-128 represses L1 retrotransposition and mediate genomic stability.

scholarly journals Life Cycle Modeling of Structural Defects via Computational Geometry and Time Series Forecasting

2019 ◽  
Author(s):  
Sara Mohamadi ◽  
David Lattanzi
Keyword(s):  
Convex Hull ◽  
Model Updating ◽  
Predictive Accuracy ◽  
Fatigue Testing ◽  
Point Clouds ◽  
Life Cycles ◽  
Structural Defects ◽  
Stochastic Dynamic ◽  
Dynamical Process ◽  
Over Time

The evaluation of geometric defects is necessary in order to maintain the integrity of structures over time. These assessments are designed to detect damages of structures and ideally help inspectors to estimate the remaining life of structures. Current methodologies for monitoring structural systems, while providing useful information about the current state of a structure, are limited in the monitoring of defects over time and in linking them to predictive simulation. This paper presents a new approach to the predictive modeling of geometric defects. A combination of segmented from point clouds are parametrized using the convex hull algorithm to extract features from detected defects, and a stochastic dynamic model is then adapted to these features to model the evolution of the hull over time. Describing a defect in terms of its parameterized hull enables consistent temporal tracking for predictive purposes, while implicitly reducing data dimensionality and complexity as well. In this study, 2D point clouds analogous to information derived from point clouds were first generated over simulated life-cycles. The evolutions of point cloud hull parameterizations were modeled as stochastic dynamical processes via autoregressive integrated moving average (ARIMA) and vectorized autoregression (VAR) and compared against ground truth. The results indicate that this convex hull approach provides consistent and accurate representations of defect evolution across a range of defect topologies and is reasonably robust to noisy measurements, however assumptions regarding the underlying dynamical process play a significant the role in predictive accuracy. The results were then validated on experimental data from fatigue testing with high accuracy. Longer term, the results of this work will support finite element model updating for predictive analysis of structural capacity.

scholarly journals Broad-scale puma connectivity could restore genomic diversity to fine-scale coastal populations

2021 ◽  
Author(s):  
Kyle D Gustafson ◽  
Roderick B Gagne ◽  
Michael R Buchalski ◽  
T Winston Vickers ◽  
Seth PD Riley ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Puma Concolor ◽  
Genomic Diversity ◽  
Strong Linkage Disequilibrium ◽  
Fine Scale ◽  
High Genetic Diversity ◽  
Population Genomic ◽  
Genome Wide ◽  
Genetic Clusters

Urbanization is decreasing wildlife habitat and connectivity worldwide, including for apex predators, such as the puma (Puma concolor). Puma populations along California's central and southern coastal habitats have experienced rapid fragmentation from development, leading to calls for demographic and genetic management. To address urgent conservation genomic concerns, we used double-digest restriction-site associated DNA (ddRAD) sequencing to analyze 16,285 genome-wide single-nucleotide polymorphisms (SNPs) from 401 broadly sampled pumas. Our analyses indicated support for 4–10 geographically nested, broad- to fine-scale genetic clusters. At the broadest scale, the 4 genetic clusters had high genetic diversity and exhibited low linkage disequilibrium, indicating pumas have retained statewide genomic diversity. However, multiple lines of evidence indicated substructure, including 10 fine-scale genetic clusters, some of which exhibited allelic fixation and linkage disequilibrium. Fragmented populations along the Southern Coast and Central Coast had particularly low genetic diversity and strong linkage disequilibrium, indicating genetic drift and close inbreeding. Our results demonstrate that genetically at-risk populations are typically nested within a broader-scale group of interconnected populations that collectively retains high genetic diversity and heterogeneous fixations. Thus, extant variation at the broader scale has potential to restore diversity to local populations if management actions can enhance vital gene flow and recombine locally sequestered genetic diversity. These state- and genome-wide results are critically important for science-based conservation and management practices. Our broad- and fine-scale population genomic analysis highlights the information that can be gained from population genomic studies aiming to provide guidance for fragmented population conservation management.

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