The Use and Limitations of Exome Capture to Detect Novel Variation in the Hexaploid Wheat Genome.

The bread wheat (Triticum aestivum) pangenome is a patchwork of variable regions, including translocations and introgressions from progenitors and wild relatives. Although a large number of these have been documented, it is likely that many more remain unknown. To map these variable regions and make them more traceable in breeding programs, wheat accessions need to be genotyped or sequenced. The wheat genome is large and complex and consequently, sequencing efforts are often targeted through exome capture. In this study, we employed exome capture prior to sequencing 12 wheat varieties; 10 elite T. aestivum cultivars and two T. aestivum landrace accessions. Sequence coverage across chromosomes was greater toward distal regions of chromosome arms and lower in centromeric regions, reflecting the capture probe distribution which itself is determined by the known telomere to centromere gene gradient. Superimposed on this general pattern, numerous drops in sequence coverage were observed. Several of these corresponded with reported introgressions. Other drops in coverage could not be readily explained and may point to introgressions that have not, to date, been documented.

A Taxon-Wise Insight Into Rock Weathering and Nitrogen Fixation Functional Profiles of Proglacial Systems.

The Arctic environment is particularly affected by global warming, and a clear trend of the ice retreat is observed worldwide. In proglacial systems, the newly exposed terrain represents different environmental and nutrient conditions compared to later soil stages. Therefore, proglacial systems show several environmental gradients along the soil succession where microorganisms are active protagonists of the soil and carbon pool formation through nitrogen fixation and rock weathering. We studied the microbial succession of three Arctic proglacial systems located in Svalbard (Midtre Lovénbreen), Sweden (Storglaciären), and Greenland (foreland close to Kangerlussuaq). We analyzed 65 whole shotgun metagenomic soil samples for a total of more than 400 Gb of sequencing data. Microbial succession showed common trends typical of proglacial systems with increasing diversity observed along the forefield chronosequence. Microbial trends were explained by the distance from the ice edge in the Midtre Lovénbreen and Storglaciären forefields and by total nitrogen (TN) and total organic carbon (TOC) in the Greenland proglacial system. Furthermore, we focused specifically on genes associated with nitrogen fixation and biotic rock weathering processes, such as nitrogenase genes, obcA genes, and genes involved in cyanide and siderophore synthesis and transport. Whereas we confirmed the presence of these genes in known nitrogen-fixing and/or rock weathering organisms (e.g., Nostoc, Burkholderia), in this study, we also detected organisms that, even if often found in soil and proglacial systems, have never been related to nitrogen-fixing or rock weathering processes before (e.g., Fimbriiglobus, Streptomyces). The different genera showed different gene trends within and among the studied systems, indicating a community constituted by a plurality of organisms involved in nitrogen fixation and biotic rock weathering, and where the latter were driven by different organisms at different soil succession stages.

The role of gene flow and chromosomal instability in shaping the bread wheat genome.

Bread wheat (Triticum aestivum) is one of the world's most important crops; however, a low level of genetic diversity within commercial breeding accessions can significantly limit breeding potential. In contrast, wheat relatives exhibit considerable genetic variation and so potentially provide a valuable source of novel alleles for use in breeding new cultivars. Historically, gene flow between wheat and its relatives may have contributed novel alleles to the bread wheat pangenome. To assess the contribution made by wheat relatives to genetic diversity in bread wheat, we used markers based on single nucleotide polymorphisms to compare bread wheat accessions, created in the past 150 years, with 45 related species. We show that many bread wheat accessions share near-identical haplotype blocks with close relatives of wheat's diploid and tetraploid progenitors, while some show evidence of introgressions from more distant species and structural variation between accessions. Hence, introgressions and chromosomal rearrangements appear to have made a major contribution to genetic diversity in cultivar collections. As gene flow from relatives to bread wheat is an ongoing process, we assess the impact that introgressions might have on future breeding strategies.

Practice patterns of corneal transplantation in Europe: first report by the European Cornea and Cell Transplantation Registry.

PURPOSE: To report practice patterns of corneal transplantation in Europe. SETTING: Corneal clinics in 10 European member states (MS), the United Kingdom, and Switzerland. DESIGN: Multinational registry study. METHODS: Corneal transplant procedures registered in the European Cornea and Cell Transplantation Registry were identified. Preoperative donor and recipient characteristics, indication and reason for transplantation, and surgical techniques were analyzed. RESULTS: A total of 12 913 corneal transplants were identified from 10 European Union MS, the United Kingdom, and Switzerland. Most countries were self-sufficient with regard to donor tissue. Fuchs endothelial corneal dystrophy was the most common indication (41%, n = 5325), followed by regraft (16%, n = 2108), pseudophakic bullous keratopathy (12%, n = 1594), and keratoconus (12%, n = 1506). Descemet stripping automated endothelial keratoplasty (DSAEK, 46%, n = 5918) was the most commonly performed technique, followed by penetrating keratoplasty (30%, n = 3886) and Descemet membrane endothelial keratoplasty (9%, n = 1838). Vision improvement was the main reason for corneal transplantation (90%, n = 11 591). Surgical technique and reason for transplantation differed between indications. CONCLUSIONS: This report provides the most comprehensive overview of corneal transplantation practice patterns in Europe to date. Fuchs endothelial dystrophy is the most common indication, vision improvement the leading reason, and DSAEK the predominant technique for corneal transplantation.

Ultrastructural Analysis of Rehydrated Human Donor Corneas After Air-Drying and Dissection by Femtosecond Laser.

Purpose: To evaluate the efficiency of femtosecond laser (FSL) incision of rehydrated human donor corneas after air-drying and its effects on corneal structure. Methods: We compared the rehydrated and fresh-preserved corneas by microscopy following Victus-Tecnolas FSL treatment for straight-edge anterior lamellar keratoplasty (ALK). The corneas were dehydrated at room temperature under a laminar-flow hood. Results: To obtain the horizontal cut in rehydrated corneas, we increased the FSL pulse energy to 1.2 µJ from 0.80 µJ applied for the fresh corneas and obtained a clear-cut separation of the lamellar lenticule cap from the corneal bed. Light microscopy showed regular arrangement of stromal collagen lamellae, with spaces in between the fibers in the corneal stroma in the fresh and the rehydrated corneas, but the uppermost epithelial layers in the rehydrated corneas were lost. Transmission electron microscopy (TEM) revealed no signs of thermal or mechanical damage to the corneal structure. The epithelial basal membrane and Bowman's layer maintained their integrity. The epithelial basal layer and cells were separated by large spaces due to junction alteration in the rehydrated corneas. There were gaps between the lamellar layers in the stroma, especially in the rehydrated corneas. Keratocytes displayed normal structure in the fresh corneas but were devoid of microorganules in the rehydrated corneas. Minor irregularities were observed in the vertical incision and the horizontal stroma appeared smooth on scanning electron microscopy. Conclusion: The corneal stroma of rehydrated corneas maintained morphology and integrity, while corneal cellular components were generally altered. When corneas are intended for FSL-assisted ALK, effective stromal bed incision is best achieved at a laser power higher than that currently adopted for fresh corneas.

Outcomes of corneal transplantation in Europe: report by the European Cornea and Cell Transplantation Registry.

PURPOSE: To analyze real-world graft survival and visual acuity outcomes of corneal transplantation in Europe. SETTING: Corneal clinics in 10 European Union member states, the United Kingdom, and Switzerland. DESIGN: Multinational registry study. METHODS: All corneal transplant procedures registered in the European Cornea and Cell Transplantation Registry (ECCTR) were identified. Graft survival of primary corneal transplants were analyzed using Kaplan-Meier survival curves with log-rank test and Cox regression. Corrected distance visual acuities (CDVAs) are reported at baseline and 2 years postoperatively using the Lundström distribution matrix. RESULTS: A total of 12 913 corneal transplants were identified. Overall, 32-year graft survival of corneal transplants was high (89%) but differed between indications, ranging from 98% in keratoconus and 80% for trauma. Overall, CDVA improved postoperatively, but the risk for losing vision ranged from 7% (baseline vision ≤0.1 Snellen) to 58% (baseline vision ≥1.0 Snellen). CONCLUSIONS: This report provides a comprehensive overview of graft survival and visual outcomes of corneal transplantation in Europe. In addition, it provides real-world estimates of outcomes for a variety of indications and surgical techniques to support benchmarking and demonstrates the relationship between baseline and postoperative vision.

CerealsDB-new tools for the analysis of the wheat genome: update 2020.

CerealsDB (www.cerealsdb.uk.net) is an online repository of mainly hexaploid wheat (Triticum aestivum) single nucleotide polymorphisms (SNPs) and genotyping data. The CerealsDB website has been designed to enable wheat breeders and scientists to select the appropriate markers for research breeding tasks, such as marker-assisted selection. We report a large update of genotyping information for over 6000 wheat accessions and describe new webtools for exploring and visualizing the data. We also describe a new database of quantitative trait loci that links phenotypic traits to CerealsDB SNP markers and allelic scores for each of those markers. CerealsDB is an open-access website that hosts information on wheat SNPs considered useful for both plant breeders and research scientists. The latest CerealsDB database is available at https://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/indexNEW.php.

Segregation distortion: Utilizing simulated genotyping data to evaluate statistical methods.

Segregation distortion is the phenomenon in which genotypes deviate from expected Mendelian ratios in the progeny of a cross between two varieties or species. There is not currently a widely used consensus for the appropriate statistical test, or more specifically the multiple testing correction procedure, used to detect segregation distortion for high-density single-nucleotide polymorphism (SNP) data. Here we examine the efficacy of various multiple testing procedures, including chi-square test with no correction for multiple testing, false-discovery rate correction and Bonferroni correction using an in-silico simulation of a biparental mapping population. We find that the false discovery rate correction best approximates the traditional p-value threshold of 0.05 for high-density marker data. We also utilize this simulation to test the effect of segregation distortion on the genetic mapping process, specifically on the formation of linkage groups during marker clustering. Only extreme segregation distortion was found to effect genetic mapping. In addition, we utilize replicate empirical mapping populations of wheat varieties Avalon and Cadenza to assess how often segregation distortion conforms to the same pattern between closely related wheat varieties.

Genome Sequence of Lecanicillium fungicola 150-1, the Causal Agent of Dry Bubble Disease.

The fungus Lecanicillium fungicola causes dry bubble disease in the white button mushroom Agaricus bisporus Control strategies are limited, as both the host and pathogen are fungi, and there is limited understanding of the interactions in this pathosystem. Here, we present the genome sequence of Lecanicillium fungicola strain 150-1.

Comparative study of biofilm formation on biocidal antifouling and fouling-release coatings using next-generation DNA sequencing.

The bacterial and eukaryotic communities forming biofilms on six different antifouling coatings, three biocidal and three fouling-release, on boards statically submerged in a marine environment were studied using next-generation sequencing. Sequenced amplicons of bacterial 16S ribosomal DNA and eukaryotic ribosomal DNA internal transcribed spacer were assigned taxonomy by comparison to reference databases and relative abundances were calculated. Differences in species composition, bacterial and eukaryotic, and relative abundance were observed between the biofilms on the various coatings; the main difference was between coating type, biocidal compared to fouling-release. Species composition and relative abundance also changed through time. Thus, it was possible to group replicate samples by coating and time point, indicating that there are fundamental and reproducible differences in biofilms assemblages. The routine use of next-generation sequencing to assess biofilm formation will allow evaluation of the efficacy of various commercial coatings and the identification of targets for novel formulations.

Conversion of array-based single nucleotide polymorphic markers for use in targeted genotyping by sequencing in hexaploid wheat (Triticum aestivum).

Wheat breeders and academics alike use single nucleotide polymorphisms (SNPs) as molecular markers to characterize regions of interest within the hexaploid wheat genome. A number of SNP-based genotyping platforms are available, and their utility depends upon factors such as the available technologies, number of data points required, budgets and the technical expertise required. Unfortunately, markers can rarely be exchanged between existing and newly developed platforms, meaning that previously generated data cannot be compared, or combined, with more recently generated data sets. We predict that genotyping by sequencing will become the predominant genotyping technology within the next 5-10 years. With this in mind, to ensure that data generated from current genotyping platforms continues to be of use, we have designed and utilized SNP-based capture probes from several thousand existing and publicly available probes from Axiom® and KASP™ genotyping platforms. We have validated our capture probes in a targeted genotyping by sequencing protocol using 31 previously genotyped UK elite hexaploid wheat accessions. Data comparisons between targeted genotyping by sequencing, Axiom® array genotyping and KASP™ genotyping assays, identified a set of 3256 probes which reliably bring together targeted genotyping by sequencing data with the previously available marker data set. As such, these probes are likely to be of considerable value to the wheat community. The probe details, full probe sequences and a custom built analysis pipeline may be freely downloaded from the CerealsDB website (http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/sequence_capture.php).

High-density genotyping of the A.E. Watkins Collection of hexaploid landraces identifies a large molecular diversity compared to elite bread wheat.

The importance of wheat as a food crop makes it a major target for agricultural improvements. As one of the most widely grown cereal grains, together with maize and rice, wheat is the leading provider of calories in the global diet, constituting 29% of global cereal production in 2015. In the last few decades, however, yields have plateaued, suggesting that the green revolution, at least for wheat, might have run its course and that new sources of genetic variation are urgently required. The overall aim of our work was to identify novel variation that may then be used to enable the breeding process. As landraces are a potential source of such diversity, here we have characterized the A.E. Watkins Collection alongside a collection of elite accessions using two complementary high-density and high-throughput genotyping platforms. While our results show the importance of using the appropriate SNP collection to compare diverse accessions, they also show that the Watkins Collection contains a substantial amount of novel genetic diversity which has either not been captured in current breeding programmes or which has been lost through previous selection pressures. As a consequence of our analysis, we have identified a number of accessions which carry an array of novel alleles along with a number of interesting chromosome rearrangements which confirm the variable nature of the wheat genome.

Developing a High-Throughput SNP-Based Marker System to Facilitate the Introgression of Traits From Aegilops Species Into Bread Wheat (Triticum aestivum).

The genus Aegilops contains a diverse collection of wild species exhibiting variation in geographical distribution, ecological adaptation, ploidy and genome organization. Aegilops is the most closely related genus to Triticum which includes cultivated wheat, a globally important crop that has a limited gene pool for modern breeding. Aegilops species are a potential future resource for wheat breeding for traits, such as adaptation to different ecological conditions and pest and disease resistance. This study describes the development and application of the first high-throughput genotyping platform specifically designed for screening wheat relative species. The platform was used to screen multiple accessions representing all species in the genus Aegilops. Firstly, the data was demonstrated to be useful for screening diversity and examining relationships within and between Aegilops species. Secondly, markers able to characterize and track introgressions from Aegilops species in hexaploid wheat were identified and validated using two different approaches.

High-Density SNP Genotyping Array for Hexaploid Wheat and Its Relatives.

A lack of genetic diversity between wheat breeding lines has been recognized as a significant block to future yield increases. Wheat breeding and prebreeding strategies are increasingly using material from wheat ancestors or wild relatives to reintroduce diversity. Where molecular markers are polymorphic between the host and introgressed material, they may be used to track the size and location of the introgressed material through generations of backcrossing. To generate markers for this purpose, sequence capture targeted resequencing was carried out for a range of wheat varieties, wheat relatives, and wheat progenitors. From these sequences, putative SNPs were identified and used to generate the Axiom® Wheat HD array. A selection of varieties representing a selection of elite wheat breeding material, progenitor species, and wild relatives were used to validate the array. The procedures used are described here in detail.

Draft Genome Sequence of the Coprinoid Mushroom Coprinopsis strossmayeri.

Coprinopsis strossmayeri is a coprinoid mushroom favoring the habitat of herbivore dung. As a result of this highly competitive environment, C. strossmayeri is anticipated to produce a wide array of antimicrobial secondary metabolites (SMs) of potential pharmaceutical importance. Here, we present the draft genome sequence of C. strossmayeri.

Amniotic membrane in ophthalmology: properties, preparation, storage and indications for grafting-a review.

The use of amniotic membrane in ophthalmic surgery and other surgical procedures in the fields of dermatology, plastic surgery, genitourinary medicine and otolaryngology is on the increase. Furthermore, amniotic membrane and its epithelial and mesenchymal cells have broad use in regenerative medicine and hold great promise in anticancer treatment. Amniotic membrane is a rich source of biologically active factors and as such, promotes healing and acts as an effective material for wound dressing. Amniotic membrane supports epithelialization and exhibits anti-fibrotic, anti-inflammatory, anti-angiogenic and anti-microbial features. Placentas utilised in the preparation of amniotic membrane are retrieved from donors undergoing elective caesarean section. Maternal blood must undergo serological screening at the time of donation and, in the absence of advanced diagnostic testing techniques, 6 months postpartum in order to cover the time window for the potential transmission of communicable diseases. Amniotic membrane is prepared by blunt dissection under strict aseptic conditions, then is typically transferred onto a nitrocellulose paper carrier, usually with the epithelial side up, and cut into multiple pieces of different dimensions. Amniotic membrane can be stored under various conditions, most often cryopreserved in glycerol or dimethyl sulfoxide or their mixture with culture medium or buffers. Other preservation methods include lyophilisation and air-drying. In ophthalmology, amniotic membrane is increasingly used for ocular surface reconstruction, including the treatment of persistent epithelial defects and non-healing corneal ulcers, corneal perforations and descemetoceles, bullous keratopathy, as well as corneal disorders with associated limbal stem cell deficiency, pterygium, conjunctival reconstruction, corneoscleral melts and perforations, and glaucoma surgeries.

Ethical Issues in Transnational Eye Banking.

PURPOSE: To review ethical issues that may arise in the setting of transnational eye banking activities, such as when exporting or importing corneal tissue for transplantation. METHODS: A principle-based normative analysis of potential common dilemmas in transnational eye banking activities was performed. RESULTS: Transnational activities in eye banking, like those in other fields involving procurement and use of medical products of human origin, may present a number of ethical issues for policy makers and professionals. Key ethical concerns include the potential impact of export or import activities on self-sufficiency of corneal tissue supply within exporting and importing countries; potential disclosure requirements when obtaining consent or authorization for ocular tissue donation when donations may be exported; and difficulties inherent in assuring equity in the allocation of tissues available for export and in establishing and respecting standards of safety and quality across different jurisdictions. CONCLUSIONS: Further analysis of specific ethical issues in eye banking is necessary to inform development of guidelines and other governance tools that will assist policy makers and professionals to support ethical practice.

Characterization of a Wheat Breeders' Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum).

Targeted selection and inbreeding have resulted in a lack of genetic diversity in elite hexaploid bread wheat accessions. Reduced diversity can be a limiting factor in the breeding of high yielding varieties and crucially can mean reduced resilience in the face of changing climate and resource pressures. Recent technological advances have enabled the development of molecular markers for use in the assessment and utilization of genetic diversity in hexaploid wheat. Starting with a large collection of 819 571 previously characterized wheat markers, here we describe the identification of 35 143 single nucleotide polymorphism-based markers, which are highly suited to the genotyping of elite hexaploid wheat accessions. To assess their suitability, the markers have been validated using a commercial high-density Affymetrix Axiom® genotyping array (the Wheat Breeders' Array), in a high-throughput 384 microplate configuration, to characterize a diverse global collection of wheat accessions including landraces and elite lines derived from commercial breeding communities. We demonstrate that the Wheat Breeders' Array is also suitable for generating high-density genetic maps of previously uncharacterized populations and for characterizing novel genetic diversity produced by mutagenesis. To facilitate the use of the array by the wheat community, the markers, the associated sequence and the genotype information have been made available through the interactive web site 'CerealsDB'.

CerealsDB 3.0: expansion of resources and data integration.

BACKGROUND: The increase in human populations around the world has put pressure on resources, and as a consequence food security has become an important challenge for the 21st century. Wheat (Triticum aestivum) is one of the most important crops in human and livestock diets, and the development of wheat varieties that produce higher yields, combined with increased resistance to pests and resilience to changes in climate, has meant that wheat breeding has become an important focus of scientific research. In an attempt to facilitate these improvements in wheat, plant breeders have employed molecular tools to help them identify genes for important agronomic traits that can be bred into new varieties. Modern molecular techniques have ensured that the rapid and inexpensive characterisation of SNP markers and their validation with modern genotyping methods has produced a valuable resource that can be used in marker assisted selection. CerealsDB was created as a means of quickly disseminating this information to breeders and researchers around the globe. DESCRIPTION: CerealsDB version 3.0 is an online resource that contains a wide range of genomic datasets for wheat that will assist plant breeders and scientists to select the most appropriate markers for use in marker assisted selection. CerealsDB includes a database which currently contains in excess of a million putative varietal SNPs, of which several hundreds of thousands have been experimentally validated. In addition, CerealsDB also contains new data on functional SNPs predicted to have a major effect on protein function and we have constructed a web service to encourage data integration and high-throughput programmatic access. CONCLUSION: CerealsDB is an open access website that hosts information on SNPs that are considered useful for both plant breeders and research scientists. The recent inclusion of web services designed to federate genomic data resources allows the information on CerealsDB to be more fully integrated with the WheatIS network and other biological databases.

High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool.

In wheat, a lack of genetic diversity between breeding lines has been recognized as a significant block to future yield increases. Species belonging to bread wheat's secondary and tertiary gene pools harbour a much greater level of genetic variability, and are an important source of genes to broaden its genetic base. Introgression of novel genes from progenitors and related species has been widely employed to improve the agronomic characteristics of hexaploid wheat, but this approach has been hampered by a lack of markers that can be used to track introduced chromosome segments. Here, we describe the identification of a large number of single nucleotide polymorphisms that can be used to genotype hexaploid wheat and to identify and track introgressions from a variety of sources. We have validated these markers using an ultra-high-density Axiom(®) genotyping array to characterize a range of diploid, tetraploid and hexaploid wheat accessions and wheat relatives. To facilitate the use of these, both the markers and the associated sequence and genotype information have been made available through an interactive web site.