7 research outputs found

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

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    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

    Interaural Time Difference Perception with a Cochlear Implant and a Normal Ear

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    Currently there is a growing population of cochlear-implant (CI) users with (near) normal hearing in the non-implanted ear. This configuration is often called SSD (single-sided deafness) CI. The goal of the CI is often to improve spatial perception, so the question raises to what extent SSD CI listeners are sensitive to interaural time differences (ITDs). In a controlled lab setup, sensitivity to ITDs was investigated in 11 SSD CI listeners. The stimuli were 100-pps pulse trains on the CI side and band-limited click trains on the acoustic side. After determining level balance and the delay needed to achieve synchronous stimulation of the two ears, the just noticeable difference in ITD was measured using an adaptive procedure. Seven out of 11 listeners were sensitive to ITDs, with a median just noticeable difference of 438 μs. Out of the four listeners who were not sensitive to ITD, one listener reported binaural fusion, and three listeners reported no binaural fusion. To enable ITD sensitivity, a frequency-dependent delay of the electrical stimulus was required to synchronize the electric and acoustic signals at the level of the auditory nerve. Using subjective fusion measures and refined by ITD sensitivity, it was possible to match a CI electrode to an acoustic frequency range. This shows the feasibility of these measures for the allocation of acoustic frequency ranges to electrodes when fitting a CI to a subject with (near) normal hearing in the contralateral ear.status: publishe

    Adding country resolution to EXIOBASE: impacts on land use embodied in trade

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    Multiregional input–output (MRIO) databases are used to analyze the impact of resource use and environmental impacts along global supply chains. To accurately account for pressures and impacts that are highly concentrated in specifc sectors or regions of the world, such as agricultural and land-use-related impacts, MRIO databases are being fueled by increasingly more detailed data. To date no MRIO database exists which couples a high level of harmonized sector detail with high country resolution. Currently available databases either aggregate minor countries into rest-of-the-world (WIOD and EXIOBASE 3), or the high country resolution is achieved at the cost of nonharmonized or lower sectoral detail (Eora, OECD-ICIO or the GTAP-MRIO). This aggrega‑ tion can cause potentially signifcant diferences in environmental and socioeconomic impact calculations. In this paper, we describe the development of an EXIOBASE 3 variant that expands regional coverage from 49 regions to 214 countries, while keeping the high and harmonized sectoral detail. We show the relevance of disaggregation for land-use accounting. Previous rest-of-the-world regions supply one-third of global land, which is used to produce a large range of diferent products under very diferent levels of productivity. We fnd that the aggregation of regions leads to a diference in the balance of land embodied in trade of up to 6% and a diference of land embodied in imports of up to 68% for individual countries and up to 600% for land-use-relevant sectors. Whilst the database can still be considered experimental, it is expected to increase the accuracy of estimates for environmental footprint studies of the original EXIOBASE countries, and provides the frst estimates for the countries in the previous rest-of-the world.publishedVersio

    Adding country resolution to EXIOBASE: impacts on land use embodied in trade

    No full text
    Multiregional input–output (MRIO) databases are used to analyze the impact of resource use and environmental impacts along global supply chains. To accurately account for pressures and impacts that are highly concentrated in specifc sectors or regions of the world, such as agricultural and land-use-related impacts, MRIO databases are being fueled by increasingly more detailed data. To date no MRIO database exists which couples a high level of harmonized sector detail with high country resolution. Currently available databases either aggregate minor countries into rest-of-the-world (WIOD and EXIOBASE 3), or the high country resolution is achieved at the cost of nonharmonized or lower sectoral detail (Eora, OECD-ICIO or the GTAP-MRIO). This aggrega‑ tion can cause potentially signifcant diferences in environmental and socioeconomic impact calculations. In this paper, we describe the development of an EXIOBASE 3 variant that expands regional coverage from 49 regions to 214 countries, while keeping the high and harmonized sectoral detail. We show the relevance of disaggregation for land-use accounting. Previous rest-of-the-world regions supply one-third of global land, which is used to produce a large range of diferent products under very diferent levels of productivity. We fnd that the aggregation of regions leads to a diference in the balance of land embodied in trade of up to 6% and a diference of land embodied in imports of up to 68% for individual countries and up to 600% for land-use-relevant sectors. Whilst the database can still be considered experimental, it is expected to increase the accuracy of estimates for environmental footprint studies of the original EXIOBASE countries, and provides the frst estimates for the countries in the previous rest-of-the world

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

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    Wheat is one of the major sources of food for much of the world. However, because bread wheat's genome is a large hybrid mix of three separate subgenomes, it has been difficult to produce a high-quality reference sequence. Using recent advances in sequencing, the International Wheat Genome Sequencing Consortium presents an annotated reference genome with a detailed analysis of gene content among subgenomes and the structural organization for all the chromosomes. Examples of quantitative trait mapping and CRISPR-based genome modification show the potential for using this genome in agricultural research and breeding. Ramírez-González et al. exploited the fruits of this endeavor to identify tissue-specific biased gene expression and coexpression networks during development and exposure to stress. These resources will accelerate our understanding of the genetic basis of bread wheat

    Multimessenger observations of a flaring blazar coincident with high-energy neutrino IceCube-170922A

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