Dataset Information

Integration of expert knowledge in the definition of Swiss pear core collection.

ABSTRACT: Core collections (CCs) constitute a key tool for the characterization and management of genetic resources (GR). When the institutions involved in GR preservation decide to define a CC, they frequently prefer to select accessions based not only on strictly objective criteria, but also to add others following expert knowledge considerations (popularity, prestige, role in breeding history, or presence of phenotypic features of interest). The aim of this study was to evaluate the implications of approaches that combine formal analytical procedures and expert knowledge on the efficiency of CC definition through a case study to establish a pear CC from the Swiss National Pear Inventory. The CC had to represent a maximum of the genetic diversity, not to exceed 150 accessions, and required to include a priority set (SPPS) with 86 genotypes selected based on expert knowledge. In total, nine strategies were evaluated, resulting of combining compositions of the dataset sampled, sampling sizes and methods. The CCs sampled by mixed approaches provided similar scores, irrespective of the approach considered, and obtained similar efficiency in optimizing the genetic diversity retained. Therefore, mixed approaches can be an appropriate choice for applications involving genetic conservation in tree germplasm collections.

SUBMITTER: Urrestarazu J

PROVIDER: S-EPMC6586639 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

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Integration of expert knowledge in the definition of Swiss pear core collection.

Urrestarazu J J Kägi C C Bühlmann A A Gassmann J J Santesteban L G LG Frey J E JE Kellerhals M M Miranda C C

Scientific reports 20190620 1

Core collections (CCs) constitute a key tool for the characterization and management of genetic resources (GR). When the institutions involved in GR preservation decide to define a CC, they frequently prefer to select accessions based not only on strictly objective criteria, but also to add others following expert knowledge considerations (popularity, prestige, role in breeding history, or presence of phenotypic features of interest). The aim of this study was to evaluate the implications of app ...[more]

PMID: 31221983

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Project description:BackgroundFew methicillin-resistant Staphylococcus aureus (MRSA) from the early years of its global emergence have been sequenced. Knowledge about evolutionary factors promoting the success of specific MRSA multi-locus sequence types (MLSTs) remains scarce. We aimed to characterize a legacy MRSA collection isolated from 1965 to 1987 and compare it against publicly available international and local genomes.MethodsWe accessed 451 historic (1965-1987) MRSA isolates stored in the Culture Collection of Switzerland, mostly collected from the Zurich region. We determined phenotypic antimicrobial resistance (AMR) and performed whole genome sequencing (WGS) using Illumina short-read sequencing on all isolates and long-read sequencing on a selection with Oxford Nanopore Technology. For context, we included 103 publicly available international assemblies from 1960 to 1992 and sequenced 1207 modern Swiss MRSA isolates from 2007 to 2022. We analyzed the core genome (cg)MLST and predicted SCCmec cassette types, AMR, and virulence genes.ResultsAmong the 451 historic Swiss MRSA isolates, we found 17 sequence types (STs) of which 11 have been previously described. Two STs were novel combinations of known loci and six isolates carried previously unsubmitted MLST alleles, representing five new STs (ST7843, ST7844, ST7837, ST7839, and ST7842). Most isolates (83% 376/451) represented ST247-MRSA-I isolated in the 1960s, followed by ST7844 (6% 25/451), a novel single locus variant (SLV) of ST239. Analysis by cgMLST indicated that isolates belonging to ST7844-MRSA-III cluster within the diversity of ST239-MRSA-III. Early MRSA were predominantly from clonal complex (CC)8. From 1980 to the end of the twentieth century, we observed that CC22 and CC5 as well as CC8 were present, both locally and internationally.ConclusionsThe combined analysis of 1761 historic and contemporary MRSA isolates across more than 50 years uncovered novel STs and allowed us a glimpse into the lineage flux between Swiss-German and international MRSA across time.

Project description:The modern biomedical research and healthcare delivery domains have seen an unparalleled increase in the rate of innovation and novel technologies over the past several decades. Catalyzed by paradigm-shifting public and private programs focusing upon the formation and delivery of genomic and personalized medicine, the need for high-throughput and integrative approaches to the collection, management, and analysis of heterogeneous data sets has become imperative. This need is particularly pressing in the translational bioinformatics domain, where many fundamental research questions require the integration of large scale, multi-dimensional clinical phenotype and bio-molecular data sets. Modern biomedical informatics theory and practice has demonstrated the distinct benefits associated with the use of knowledge-based systems in such contexts. A knowledge-based system can be defined as an intelligent agent that employs a computationally tractable knowledge base or repository in order to reason upon data in a targeted domain and reproduce expert performance relative to such reasoning operations. The ultimate goal of the design and use of such agents is to increase the reproducibility, scalability, and accessibility of complex reasoning tasks. Examples of the application of knowledge-based systems in biomedicine span a broad spectrum, from the execution of clinical decision support, to epidemiologic surveillance of public data sets for the purposes of detecting emerging infectious diseases, to the discovery of novel hypotheses in large-scale research data sets. In this chapter, we will review the basic theoretical frameworks that define core knowledge types and reasoning operations with particular emphasis on the applicability of such conceptual models within the biomedical domain, and then go on to introduce a number of prototypical data integration requirements and patterns relevant to the conduct of translational bioinformatics that can be addressed via the design and use of knowledge-based systems.

Project description:BACKGROUND: Sesame (Sesamum indicum L.) is one of the four major oil crops in China. A sesame core collection (CC) was established in China in 2000, but no complete study on its genetic diversity has been carried out at either the phenotypic or molecular level. To provide technical guidance, a theoretical basis for further collection, effective protection, reasonable application, and a complete analysis of sesame genetic resources, a genetic diversity assessment of the sesame CC in China was conducted using phenotypic and molecular data and by extracting a sesame mini-core collection (MC). RESULTS: Results from a genetic diversity assessment of sesame CC in China were significantly inconsistent at the phenotypic and molecular levels. A Mantel test revealed the insignificant correlation between phenotype and molecular marker information (r = 0.0043, t = 0.1320, P = 0.5525). The Shannon-Weaver diversity index (I) and Nei genetic diversity index (h) were higher (I = 0.9537, h = 0.5490) when calculated using phenotypic data from the CC than when using molecular data (I = 0.3467, h = 0.2218). A mini-core collection (MC) containing 184 accessions was extracted based on both phenotypic and molecular data, with a low mean difference percentage (MD, 1.64%), low variance difference percentage (VD, 22.58%), large variable rate of coefficient of variance (VR, 114.86%), and large coincidence rate of range (CR, 95.76%). For molecular data, the diversity indices and the polymorphism information content (PIC) for the MC were significantly higher than for the CC. Compared to an alternative random sampling strategy, the advantages of capturing genetic diversity and validation by extracting a MC using an advanced maximization strategy were proven. CONCLUSIONS: This study provides a comprehensive characterization of the phenotypic and molecular genetic diversities of the sesame CC in China. A MC was extracted using both phenotypic and molecular data. Low MD% and VD%, and large VR% and CR% suggested that the MC provides a good representation of the genetic diversity of the original CC. The MC was more genetically diverse with higher diversity indices and a higher PIC value than the CC. A MC may aid in reasonably and efficiently selecting materials for sesame breeding and for genotypic biological studies, and may also be used as a population for association mapping in sesame.

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Integration of expert knowledge in the definition of Swiss pear core collection.

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Integration of expert knowledge in the definition of Swiss pear core collection.

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