Physical mapping integrated with syntenic analysis to characterize the gene space of the long arm of wheat chromosome 1A

Background: Bread wheat (Triticum aestivum L.) is one of the most important crops worldwide and its production faces pressing challenges, the solution of which demands genome information. However, the large, highly repetitive hexaploid wheat genome has been considered intractable to standard sequencing approaches. Therefore the International Wheat Genome Sequencing Consortium (IWGSC) proposes to map and sequence the genome on a chromosome-by-chromosome basis. Methodology/Principal Findings: We have constructed a physical map of the long arm of bread wheat chromosome 1A using chromosome-specific BAC libraries by High Information Content Fingerprinting (HICF). Two alternative methods (FPC and LTC) were used to assemble the fingerprints into a high-resolution physical map of the chromosome arm. A total of 365 molecular markers were added to the map, in addition to 1122 putative unique transcripts that were identified by microarray hybridization. The final map consists of 1180 FPC based or 583 LTC based contigs. Conclusions/Significance: The physical map presented here marks an important step forward in mapping of hexaploid bread wheat. The map is orders of magnitude more detailed than previously available maps of this chromosome, and the assignment of over a thousand putative expressed gene sequences to specific map locations will greatly assist future functional studies. This map will be an essential tool for future sequencing of and positional cloning within chromosome 1A

Supplementary File for Capturing wheat phenotypes at the genome level

Supplementary S1: Yield and related traits in bread wheat. Table S1: Examples of genomic regions, candidate and cloned genes for yield and related traits in bread wheat. Supplementary S2: Drought tolerance. Table S2: Examples of genomic regions and candidate genes for drought tolerance. Supplementary S3: Heat tolerance. Table S3. Examples of genomic regions and candidate genes for heat tolerance. Supplementary S4: salinity tolerance in bread wheat. Table S4. Examples of genomic regions and candidate genes for salinity tolerance in bread wheat. Supplementary S5: Frost tolerance. Supplementary S6: Disease resistance. Table S5. Examples of genomic regions, candidate and cloned genes mapped for disease resistance in wheat species. Supplementary S7 insect and mite resistance. Table S6. Examples of genomic regions and candidate genes mapped for insect and mite resistance. Supplementary S8: Quality traits. Table S7. Examples of genomic regions, candidate and cloned genes for quality traits.Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world’s most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public–private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.Peer reviewe

A rare cardiovascular cause of fever of unknown origin: Infected thoracal aortic aneurysm

Aortitis can cause fever of unknown origin. Those affected patients had presented with sepsis. It is an important consideration that when we could not identify the origin of transthoracic echocardiography. However it is difficult to be revealed of descending aorta by transthoracic echocardiography. Therefore, computed tomography angiography may be kept in mind for diagnosis in patients with aortitis. We report a patient presenting to our hospital with sepsis and detected a saccular aneurysm and periaortic abscess and air collection in thoracal aorta due to Staphylococcus aureus. © 2016 The Czech Society of Cardiolog

In vitro characterisation of probiotic properties of Enterococcus faecium and Enterococcus durans strains isolated from raw milk and traditional dairy products

WOS: 000486322600001In this study, some probiotic characteristics such as antimicrobial activity, vancomycin resistance, growth ability at pH, resistance to bile salts, bile salt deconjugation and hydrophobicity of 30 Enterococcus faecium and Enterococcus durans strains isolated and identified from raw milk and various dairy products were investigated. According to the study results, antimicrobial activity profiling, pH and bile salt resistance and bile salt deconjugation ability of Enterococcus strains varied depending on the species and strains and all the strains showed resistance to the tested bile salt concentrations. It was concluded that the E. faecium and E. durans strains tested showed probiotic characteristics and have the potential to be used in food production.Ege University Scientific Research FundEge University [2011-ZRF-010]The present study was funded by Ege University Scientific Research Fund (Project Number: 2011-ZRF-010) and presented as a poster proceeding at the 'The 2nd International Symposium on "Traditional Foods from Adriatic to the Caucasus"' held between 24 October and 26 October 2013