Population size of Oystercatchers Haematopus ostralegus wintering in Iceland

The first ever survey of Oystercatchers wintering in Iceland found around 11 000 individuals. This is an estimated 30% of the Icelandic population, including juveniles, suggesting that approximately 26 000 Icelandic Oystercatchers migrate to western Europe in the autumn. More Oystercatchers winter in Iceland than at similar latitudes elsewhere in Europe, which may reflect the remoteness and milder winter temperatures on this oceanic island

The barley pan-genome reveals the hidden legacy of mutation breeding

Genetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (known as the ‘pan-genome’1). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley (Hordeum vulgare L.) is an important cereal crop with a long history of cultivation that is adapted to a wide range of agro-climatic conditions2. Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley—comprising landraces, cultivars and a wild barley—that were selected as representatives of global barley diversity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm; one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding

Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62

The wild relatives and progenitors of wheat have been widely used as sources of disease resistance (R) genes. Molecular identification and characterization of these R genes facilitates their manipulation and tracking in breeding programmes. Here, we develop a reference-quality genome assembly of the wild diploid wheat relative Aegilops sharonensis and use positional mapping, mutagenesis, RNA-Seq and transgenesis to identify the stem rust resistance gene Sr62, which has also been transferred to common wheat. This gene encodes a tandem kinase, homologues of which exist across multiple taxa in the plant kingdom. Stable Sr62 transgenic wheat lines show high levels of resistance against diverse isolates of the stem rust pathogen, highlighting the utility of Sr62 for deployment as part of a polygenic stack to maximize the durability of stem rust resistance

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Introduction: Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans. Consequently, wheat yields and production affect the global economy, and failed harvests can lead to social unrest. Breeders continuously strive to develop improved varieties by fine-tuning genetically complex yield and end-use quality parameters while maintaining stable yields and adapting the crop to regionally specific biotic and abiotic stresses. Rationale: Breeding efforts are limited by insufficient knowledge and understanding of wheat biology and the molecular basis of central agronomic traits. To meet the demands of human population growth, there is an urgent need for wheat research and breeding to accelerate genetic gain as well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genome sequence, including regulatory sequences and genome-diversity information, has promoted the development of systematic and more time-efficient approaches for the selection and understanding of important traits. Wheat has lagged behind, primarily owing to the challenges of assembling a genome that is more than five times as large as the human genome, polyploid, and complex, containing more than 85% repetitive DNA. To provide a foundation for improvement through molecular breeding, in 2005, the International Wheat Genome Sequencing Consortium set out to deliver a high-quality annotated reference genome sequence of bread wheat. Results: An annotated reference sequence representing the hexaploid bread wheat genome in the form of 21 chromosome-like sequence assemblies has now been delivered, giving access to 107,891 high-confidence genes, including their genomic context of regulatory sequences. This assembly enabled the discovery of tissue- and developmental stage–related gene coexpression networks using a transcriptome atlas representing all stages of wheat development. The dynamics of change in complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. Aspects of the future value of the annotated assembly for molecular breeding and research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editing of the flowering-time trait. Conclusion: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. Importantly, the bioinformatics capacity developed for model-organism genomes will facilitate a better understanding of the wheat genome as a result of the high-quality chromosome-based genome assembly. By necessity, breeders work with the genome at the whole chromosome level, as each new cross involves the modification of genome-wide gene networks that control the expression of complex traits such as yield. With the annotated and ordered reference genome sequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing

Strategies for Addressing Needle Debris: Scoping Review Protocol

Protocol for scoping reviewObjective: The objective of this scoping review is to explore the literature about needle debris associated with drug use in a community setting. Introduction: Needle debris in the community poses a public health concern. Needle debris and discarded drug paraphernalia could contribute to perceived social disorder associated with harm reduction services, like supervised consumption sites. Discarded needles represent a public safety risk for both people who use drugs and other community members. Currently, the existing research on this topic is scattered and has yet to be consolidated and reviewed. Addressing needle debris may decrease perceived community impact from harm reduction services, and increase support for these services among area residents, business owners, and others. This scoping review will be undertaken to inform a program of research around needle debris, to review available literature on the topic. Inclusion criteria: Studies that focus on strategies to address needle debris will be included, when referring to discarded needles and drug paraphernalia in the community. Exclusion criteria include strategies for people who use needles, who may generate needle waste inside homes and private property. Needle exchange programs and supervised consumption sites will be excluded when their primary purpose is to provide sterile supplies to prevent HIV/Hepatitis C transmission, and prevent and manage drug poisonings and overdoses, rather than prevent needles being discarded in the community. Methods: This scoping review protocol was established following the Joanna Briggs Institute (JBI) guidelines for developing a protocol (Peters et al., 2022). The databases that will be searched are MEDLINE(R) and Epub Ahead of Print, In-Process, In-Data-Review & Other Non-Indexed Citations and Daily (Ovid), CINAHL Plus with Full Text (EBSCO), APA PsycInfo (Ovid), EMBASE (Ovid), and Social Services Abstracts (ProQuest). The search will be conducted using subject headings and relevant keywords identified from analyzing seed articles. Studies will be limited to the English language. Data extraction will be completed using articles identified from the search that have substantial discussion on needle debris and the concept of disposal, retrieval, collection, prevention, and/or education. For a more comprehensive search, hand searching of reference lists and citation tracing will also be included. The proposed scoping review will be conducted in accordance with the JBI methodology for scoping reviews (Peters et al., 2020)

Applying Self-Directed Groupwork and Social Action Research Methodology with francophone parents of trans children and youth in Rural Quebec

Parental support is an important protective factor in preventing suicide among trans youth. However, parents often struggle to accept their child’s gender transition.  Having access to a group and to meeting other parents facilitates the acceptance process, but support groups are rare and even more so outside urban areas. The research project discussed in this article was developed to understand specifically the experience of parents of francophone trans youth living in rural and remote communities in Quebec. A Self-Directed Group approach (Mullender, Ward and Fleming 2013), combined with Social Action Research (Author et al. 2015) was initiated to offer a platform for parents to explore the specificities of parenting a trans child in rural francophone Quebec.  Parents were recruited through social and traditional media and a series of group meetings was planned to collect data and as well as to facilitate the parents' mobilization.  Despite applying the Self-Directed Groupwork principles and process, many challenges were encountered, stimulating a number of reflections on the use of self-directed group work and social action in remote geographical areas. This paper explores some of those challenges and discusses a possible way forward for research

The Green Wave: Reviewing the Environmental Impacts of the Invasive European Green Crab (Carcinus maenas) and Potential Management Approaches

The European green crab (Carcinus maenas), native to northwestern Europe and Africa, is among the top 100 most damaging invasive species globally. In some regions, including the Atlantic coast of North America, C. maenas has caused long-term degradation of eelgrass habitats and bivalve, crab, and finfish populations, while areas are near the beginning of the invasion cycle. Due to high persistence and reproductive potential of C. maenas populations, most local and regional mitigation efforts no longer strive for extirpation and instead focus on population control. Long-term monitoring and rapid response protocols can facilitate early detection of introductions that is critical to inform management decisions related to green crab control or extirpation. Once C. maenas are detected, local area managers will need to decide on management actions, including whether and what green crab control measures will be implemented, if local invasion might be prevented or extirpated, and if population reduction to achieve functional eradication is achievable. Due to the immense operational demands likely required to extirpate C. maenas populations, combined with limited resources for monitoring and removal, it is unlikely that any single government, conservation and/or academic organization would be positioned to adequately control or extirpate populations in local areas, highlighting the importance of collaborative efforts. Community-based monitoring, and emerging methods such as environmental DNA (eDNA), may help expand the spatial and temporal extent of monitoring, facilitating early detection and removal of C. maenas. While several C. maenas removal programs have succeeded in reducing their populations, to our knowledge, no program has yet successfully extirpated the invader; and the cost of any such program would likely be immense and unsustainable over the long-term. An alternative approach is functional eradication, whereby C. maenas populations are reduced below threshold levels such that ecosystem impacts are minimized. Less funding and effort would likely be required to achieve and maintain functional eradication compared to extirpation. In either case, continual control efforts will be required as C. maenas populations can quickly increase from low densities and larval re-introductions.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Long-read sequence assembly: a technical evaluation in barley

Sequence assembly of large and repeat-rich plant genomes has been challenging, requiring substantial computational resources and often several complementary sequence assembly and genome mapping approaches. The recent development of fast and accurate long-read sequencing by circular consensus sequencing (CCS) on the PacBio platform may greatly increase the scope of plant pan-genome projects. Here, we compare current long-read sequencing platforms regarding their ability to rapidly generate contiguous sequence assemblies in pan-genome studies of barley (Hordeum vulgare). Most long-read assemblies are clearly superior to the current barley reference sequence based on short-reads. Assemblies derived from accurate long reads excel in most metrics, but the CCS approach was the most cost-effective strategy for assembling tens of barley genomes. A downsampling analysis indicated that 20-fold CCS coverage can yield very good sequence assemblies, while even five-fold CCS data may capture the complete sequence of most genes. We present an updated reference genome assembly for barley with near-complete representation of the repeat-rich intergenic space. Long-read assembly can underpin the construction of accurate and complete sequences of multiple genomes of a species to build pan-genome infrastructures in Triticeae crops and their wild relatives