Development of a next generation SNP genotyping array for wheat

High-throughput genotyping arrays have provided a cost-effective, reliable and interoperable system for genotyping hexaploid wheat and its relatives. Existing, highly cited arrays including our 35K Wheat Breeder's array and the Illumina 90K array were designed based on a limited amount of varietal sequence diversity and with imperfect knowledge of SNP positions. Recent progress in wheat sequencing has given us access to a vast pool of SNP diversity, whilst technological improvements have allowed us to fit significantly more probes onto a 384-well format Axiom array than previously possible. Here we describe a novel Axiom genotyping array, the 'Triticum aestivum Next Generation' array (TaNG), largely derived from whole genome skim sequencing of 204 elite wheat lines and 111 wheat landraces taken from the Watkins 'Core Collection'. We used a novel haplotype optimization approach to select SNPs with the highest combined varietal discrimination and a design iteration step to test and replace SNPs which failed to convert to reliable markers. The final design with 43 372 SNPs contains a combination of haplotype-optimized novel SNPs and legacy cross-platform markers. We show that this design has an improved distribution of SNPs compared to previous arrays and can be used to generate genetic maps with a significantly higher number of distinct bins than our previous array. We also demonstrate the improved performance of TaNGv1.1 for Genome-wide association studies (GWAS) and its utility for Copy Number Variation (CNV) analysis. The array is commercially available with supporting marker annotations and initial genotyping results freely available.

Revising a laparoscopic appendicectomy set to reduce reliance on disposable surgical instruments: supporting the transition to sustainable surgical practice

INTRODUCTION

After excluding anaesthetic gases, around one-third of carbon emissions from surgical procedures are from consumables. This sustainable quality improvement project revised the laparoscopic appendicectomy surgical set at a large teaching hospital, with the aim of reducing unnecessary usage of disposable laparoscopic ports and surgical instruments.

METHODS

A prospective audit of 25 consecutive laparoscopic appendicectomies (5% of annual appendicectomies performed at the Trust) was conducted to assess use of disposable instruments. The financial and environmental costs of the five most commonly used disposable instruments were calculated and annual cost of current practice determined. A revised surgical set was created to include additional reusable instruments and new reusable ports. A reaudit of disposable surgical instrument usage was conducted and the financial and environmental impact of the new set compared with the results from the initial audit.

RESULTS

A total of 109 disposable instruments were opened in 25 appendicectomies, costing an estimated £49,656 and 692kg CO2 equivalent (CO2e) annually. Following rollout of the revised appendicectomy set, there was a significant reduction in disposable instrument usage (median four versus one instruments per case, p<0.00001). The revised set is predicted to reduce annual disposable instrument usage from 2,180 to 705 instruments (68% reduction), saving £219,452 and 3.02 tonnes CO2e over the estimated seven-year lifecycle of the reusable instruments.

CONCLUSIONS

Updating a laparoscopic appendicectomy set to include additional/new reusable instruments can lead to a marked reduction in disposable surgical instrument usage. This results in significant projected financial and CO2e savings.

Identification, characterization, and rescue of CRISPR/Cas9 generated wheat SPO11-1 mutants

Increasing crop yields through plant breeding is time consuming and laborious, with the generation of novel combinations of alleles being limited by chromosomal linkage blocks and linkage-drag. Meiotic recombination is essential to create novel genetic variation via the reshuffling of parental alleles. The exchange of genetic information between homologous chromosomes occurs at crossover (CO) sites but CO frequency is often low and unevenly distributed. This bias creates the problem of linkage-drag in recombination 'cold' regions, where undesirable variation remains linked to useful traits. In plants, programmed meiosis-specific DNA double-strand breaks, catalysed by the SPO11 complex, initiate the recombination pathway, although only ~5% result in the formation of COs. To study the role of SPO11-1 in wheat meiosis, and as a prelude to manipulation, we used CRISPR/Cas9 to generate edits in all three SPO11-1 homoeologues of hexaploid wheat. Characterization of progeny lines shows plants deficient in all six SPO11-1 copies fail to undergo chromosome synapsis, lack COs and are sterile. In contrast, lines carrying a single copy of any one of the three wild-type homoeologues are phenotypically indistinguishable from unedited plants both in terms of vegetative growth and fertility. However, cytogenetic analysis of the edited plants suggests that homoeologues differ in their ability to generate COs and in the dynamics of synapsis. In addition, we show that the transformation of wheat mutants carrying six edited copies of SPO11-1 with the TaSPO11-1B gene, restores synapsis, CO formation, and fertility and hence opens a route to modifying recombination in this agronomically important crop.

CerealsDB: A Whistle-Stop Tour of an Open Access SNP Resource

The CerealsDB website, created by members of the Functional Genomics Group at the University of Bristol, provides access to a database containing SNP and genotyping data for hexaploid wheat and, to a lesser extent, its progenitors and several of its relatives. The site is principally aimed at plant breeders and research scientists who wish to obtain information regarding SNP markers; for example, obtain primers used for their identification or the sequences upon which they are based. The database underpinning the website contains circa one million putative varietal SNPs of which several hundreds of thousands have been experimentally validated on a range of common genotyping platforms. For each SNP marker, the site also hosts the allelic scores for thousands of elite wheat varieties, landrace cultivars, and wheat relatives. Tools are available to help negotiate and visualize the datasets. The website has been designed to be simple and straightforward to use and is completely open access.

886 Healing Hands and Thrifty Plans! A Prospective, Cost-Effective Trial in Abscess Management

Aim

Cutaneous abscesses are ubiquitous presentations requiring surgical drainage in most cases. There is a wide variation across the UK in the surgical practice dealing with such common problem. The aim of this study was to reduce the costs incurred in surgical drainage of acute skin and soft tissue abscess.

Method

This was a prospective, cost-effective study of the expenses incurred in surgical drainage of acute cutaneous and subcutaneous abscesses treated under the general surgeons' care over one year.

Results

A consequential saving of £13,962 was achieved during the study period. Between October 2019 and October 2020, 322 patients with soft tissue abscesses were treated by incision and drainage in general surgery. We calculated a total cost of £55.26 per patient for this routine operation. These expenses were based on basic surgical drapes pack, standard surgical gowns, sterile gloves and obtaining and processing the microbiology specimens. We have designed and implemented a new theatre protocol specifically for this procedure, resulting in a substantial reduction of the costs to £11.90 per patient. The total savings of £13,962 do not include savings caused by abscess drainage under local anaesthesia and does not calculate the savings that occurred due to shorter inpatient stay. These extra savings will be calculated and added later.

Conclusions

Considering the increasing financial burden on the NHS, we could make significant savings of nearly 80% of the operative costs of surgical drainage of a cutaneous abscess. We could achieve that by implementing simple modifications in the current surgical pathways without compromising patients' safety.

Detecting SARS-CoV-2 variants with SNP genotyping

Tracking genetic variations from positive SARS-CoV-2 samples yields crucial information about the number of variants circulating in an outbreak and the possible lines of transmission but sequencing every positive SARS-CoV-2 sample would be prohibitively costly for population-scale test and trace operations. Genotyping is a rapid, high-throughput and low-cost alternative for screening positive SARS-CoV-2 samples in many settings. We have designed a SNP identification pipeline to identify genetic variation using sequenced SARS-CoV-2 samples. Our pipeline identifies a minimal marker panel that can define distinct genotypes. To evaluate the system, we developed a genotyping panel to detect variants-identified from SARS-CoV-2 sequences surveyed between March and May 2020 and tested this on 50 stored qRT-PCR positive SARS-CoV-2 clinical samples that had been collected across the South West of the UK in April 2020. The 50 samples split into 15 distinct genotypes and there was a 61.9% probability that any two randomly chosen samples from our set of 50 would have a distinct genotype. In a high throughput laboratory, qRT-PCR positive samples pooled into 384-well plates could be screened with a marker panel at a cost of < £1.50 per sample. Our results demonstrate the usefulness of a SNP genotyping panel to provide a rapid, cost-effective, and reliable way to monitor SARS-CoV-2 variants circulating in an outbreak. Our analysis pipeline is publicly available and will allow for marker panels to be updated periodically as viral genotypes arise or disappear from circulation.

Development of a minimal KASP marker panel for distinguishing genotypes in apple collections

Accurate identification of named accessions in germplasm collections is extremely important, especially for vegetatively propagated crops which are expensive to maintain. Thus, an inexpensive, reliable, and rapid genotyping method is essential because it avoids the need for laborious and time-consuming morphological comparisons. Single Nucleotide Polymorphism (SNP) marker panels containing large numbers of SNPs have been developed for many crop species, but such panels are much too large for basic cultivar identification. Here, we have identified a minimum set of SNP markers sufficient to distinguish apple cultivars held in the English and Welsh national collections providing a cheaper and automatable alternative to the markers currently used by the community. We show that SNP genotyping with a small set of well selected markers is equally efficient as microsatellites for the identification of apple cultivars and has the added advantage of automation and reduced cost when screening large numbers of samples.

A global analysis of SNX27-retromer assembly and cargo specificity reveals a function in glucose and metal ion transport

The PDZ-domain-containing sorting nexin 27 (SNX27) promotes recycling of internalized transmembrane proteins from endosomes to the plasma membrane by linking PDZ-dependent cargo recognition to retromer-mediated transport. Here, we employed quantitative proteomics of the SNX27 interactome and quantification of the surface proteome of SNX27- and retromer-suppressed cells to dissect the assembly of the SNX27 complex and provide an unbiased global view of SNX27-mediated sorting. Over 100 cell surface proteins, many of which interact with SNX27, including the glucose transporter GLUT1, the Menkes disease copper transporter ATP7A, various zinc and amino acid transporters, and numerous signalling receptors, require SNX27-retromer to prevent lysosomal degradation and maintain surface levels. Furthermore, we establish that direct interaction of the SNX27 PDZ domain with the retromer subunit VPS26 is necessary and sufficient to prevent lysosomal entry of SNX27 cargo. Our data identify the SNX27-retromer as a major endosomal recycling hub required to maintain cellular nutrient homeostasis.

Discovery and development of exome-based, co-dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivum L.)

Globally, wheat is the most widely grown crop and one of the three most important crops for human and livestock feed. However, the complex nature of the wheat genome has, until recently, resulted in a lack of single nucleotide polymorphism (SNP)-based molecular markers of practical use to wheat breeders. Recently, large numbers of SNP-based wheat markers have been made available via the use of next-generation sequencing combined with a variety of genotyping platforms. However, many of these markers and platforms have difficulty distinguishing between heterozygote and homozygote individuals and are therefore of limited use to wheat breeders carrying out commercial-scale breeding programmes. To identify exome-based co-dominant SNP-based assays, which are capable of distinguishing between heterozygotes and homozygotes, we have used targeted re-sequencing of the wheat exome to generate large amounts of genomic sequences from eight varieties. Using a bioinformatics approach, these sequences have been used to identify 95 266 putative single nucleotide polymorphisms, of which 10 251 were classified as being putatively co-dominant. Validation of a subset of these putative co-dominant markers confirmed that 96% were true polymorphisms and 65% were co-dominant SNP assays. The new co-dominant markers described here are capable of genotypic classification of a segregating locus in polyploid wheat and can be used on a variety of genotyping platforms; as such, they represent a powerful tool for wheat breeders. These markers and related information have been made publically available on an interactive web-based database to facilitate their use on genotyping programmes worldwide.

Gene induction following wounding of wild-type versus macrophage-deficient Drosophila embryos

By using a microarray screen to compare gene responses after sterile laser wounding of wild-type and 'macrophageless' serpent mutant Drosophila embryos, we show the wound-induced programmes that are independent of a pathogenic response and distinguish which of the genes are macrophage dependent. The evolutionarily conserved nature of this response is highlighted by our finding that one such new inflammation-associated gene, growth arrest and DNA damage-inducible gene 45 (GADD45), is upregulated in both Drosophila and murine repair models. Comparison of unwounded wild-type and serpent mutant embryos also shows a portfolio of 'macrophage-specific' genes, which suggest analogous functions with vertebrate inflammatory cells. Besides identifying the various classes of wound- and macrophage-related genes, our data indicate that sterile injury per se, in the absence of pathogens, triggers induction of a 'pathogen response', which might prime the organism for what is likely to be an increased risk of infection.

The importance of local tree resources around Gombe National Park, Western Tanzania: implications for humans and chimpanzees

Miombo woodlands and associated habitats provide a vital resource for both humans and chimpanzees in western Tanzania. A baseline survey was conducted to determine the perceived relative value of different woody species to local people in the six villages adjacent to Gombe National Park. This area also provides direct comparison of tree utilization by humans and chimpanzees since it has been the site of a long-term behavioral study on chimpanzees. Four hundred and fifty-two people, all over 30 years old, were interviewed and asked to select the 10 trees that they considered to be the most important in their everyday lives: 77% of the 4520 responses (represented by 260 species) were native and 23% (represented by 35 species) were exotic trees. In this study, particular focus was paid to the 25 tree species most frequently listed. Of these trees, 19 (representing 50% of all responses) were native, and 6 were exotic. There was a marked difference in the choices, especially with respect to native trees, by men and women. Many of the trees highly prized by humans are also of great importance in the diet of chimpanzees. It is recommended that a major effort be made to maintain the usage and availability of native trees outside the park boundary, which, in conjunction with the balanced planting of exotics for meeting local needs, should contribute to protecting the biodiversity of Gombe and the local ethnobotanical heritage.

Role of residue Y99 in tissue plasminogen activator

The crystal structure of the fibrinolytic enzyme tissue plasminogen activator (tPA) shows that the bulky side chain of Y99 hinders access to the active site by partially occluding the S2 site and may be responsible for the low catalytic activity of tPA toward plasminogen. We have tested the role of Y99 by replacing it with Leu, the residue found in more proficient proteases like trypsin and thrombin. The Y99L replacement results in an increase in the k(cat)/Km for chromogenic substrates due to enhanced diffusion into the active site. The increase is modest (threefold) for substrates specific for tPA that carry Pro or Gly at P2, but reaches 80-fold for less specific substrates carrying Arg at P2. On the other hand, the Y99L mutation has no effect on the activity of tPA toward the natural substrate plasminogen, that carries Gly at P2, and reduces more than 10-fold the inhibition of tPA by plasminogen activator inhibitor-1 (PAI-1), that carries Ala at P2. We conclude that the steric hindrance provided by Y99 in the crystal structure affects mostly nonphysiological substrates with bulky residues at P2. In addition, residue Y99 plays an active role in the recognition of PAI-1, but not plasminogen. Mutations of Y99 could therefore afford a resistance to inhibition by PAI-1 without compromising the fibrinolytic potency of tPA, a result of potential therapeutic relevance.

A comparative study of the mitochondrial genome organization in in vitro cultures of diploid, tetraploid, and hexaploid Triticum species

Southern-blot hybridizations of total DNA to mitochondrial DNA (mtDNA) probes were used to investigate the extent of mtDNA variability in cultures derived from immature embryos of diploid (Triticum monococcum, genomic formula: AA, T. tauschii, genomic formula: DD), allotetraploid (T. durum cv "Creso", genomic formula: AABB), and allohexaploid (T. aestivum, genomic formula: AABBDD) wheat species. Similar distinct changes in mtDNA organization were observed in in vitro cultures of the derived tetraploid and the hexaploid species with related genomes. The tetraploid and hexaploid species share the B genome and mtDNA variability in in vitro culture is known to be under nuclear control. These results suggest that a study of B genome diploids and other polyploid combinations would now shed light on whether or not mtDNA variability in tissue cultures is under B-genome control.

Atomic force microscopy of plant chromosomes

Atomic force microscopy has been used to image plant chromosomes from standard preparations without staining or coating. This has enabled the collection of high-resolution three-dimensional data on surface structure. The technique has been further applied to the imaging of C-banded chromosomes revealing structural changes resulting from the banding treatment. The bands were observed as localized areas of high relief.