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

Science, Journal Year: 2018, Volume and Issue: 361(6403)

Published: Aug. 17, 2018

Insights from the annotated wheat genome Wheat is one of major sources food for much world. However, because bread wheat's a large hybrid mix three separate subgenomes, it has been difficult to produce high-quality reference sequence. Using recent advances in sequencing, International Genome Sequencing Consortium presents an with detailed analysis gene content among subgenomes and structural organization all chromosomes. Examples quantitative trait mapping CRISPR-based modification show potential using this agricultural research breeding. Ramírez-González et al. exploited fruits endeavor identify tissue-specific biased expression coexpression networks during development exposure stress. These resources will accelerate our understanding genetic basis wheat. Science , issue p. eaar7191 ; see also eaar6089

Language: Английский

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Wild emmer genome architecture and diversity elucidate wheat evolution and domestication

Science, Journal Year: 2017, Volume and Issue: 357(6346), P. 93 - 97

Published: July 7, 2017

Wheat (Triticum spp.) is one of the founder crops that likely drove Neolithic transition to sedentary agrarian societies in Fertile Crescent more than 10,000 years ago. Identifying genetic modifications underlying wheat's domestication requires knowledge about genome its allo-tetraploid progenitor, wild emmer (T. turgidum ssp. dicoccoides). We report a 10.1-gigabase assembly 14 chromosomes tetraploid wheat, as well analyses gene content, architecture, and diversity. With this fully assembled polyploid wheat genome, we identified causal mutations Brittle Rachis 1 (TtBtr1) genes controlling shattering, key trait. A study genomic diversity among domesticated accessions revealed regions bearing signature selection under domestication. This reference will serve resource for accelerating genome-assisted improvement modern varieties.

Language: Английский

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Heat and Drought Stresses in Crops and Approaches for Their Mitigation

Frontiers in Chemistry, Journal Year: 2018, Volume and Issue: 6

Published: Feb. 19, 2018

Drought and heat are major abiotic stresses that reduce crop productivity weaken global food security, especially given the current growing impacts of climate change increases in occurrence severity both stress factors. Plants have developed dynamic responses at morphological, physiological biochemical levels allowing them to escape and/or adapt unfavourable environmental conditions. Nevertheless, even mildest drought negatively affects yield. Further, several independent studies shown increased temperature can yields by as much 50%. Response is complex involves factors including signaling, transcription factors, hormones, secondary metabolites. The reproductive phase development, leading grain production be more sensitive crops. Advances coming from biotechnology progress genomics information technology may mitigate detrimental effects through use agronomic management practices development varieties with under stress. This review presents recent key areas relevant plant tolerance. Furthermore, an overview implications physiological, genetic aspects context presented. Potential strategies improve discussed.

Language: Английский

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Genome sequence of the progenitor of the wheat D genome Aegilops tauschii

Nature, Journal Year: 2017, Volume and Issue: 551(7681), P. 498 - 502

Published: Nov. 1, 2017

A combination of advanced sequencing and mapping techniques is used to produce a reference genome Aegilops tauschii, progenitor the wheat D genome, providing valuable resource for comparative genetic studies. Sequencing genomes crops plants provides useful resources crop improvement breeding. Jan Dvořák, Katrien Devos, Steven Salzberg colleagues report diploid hexaploid wheat. They use ordered-clone sequencing, whole-genome shotgun BioNano optical assemble this large highly repetitive genome. This genomics studies tauschii wheat1 (Triticum aestivum, AABBDD) an important wheat2,3,4. The size nature Ae. has until now precluded development reference-quality sequence5. Here we array technologies, including mapping, generate sequence ssp. strangulata accession AL8/78, which closely related We show that compared other sequenced plant genomes, much larger conifer contains unprecedented amounts very similar repeated sequences. Our comparisons reveal greater number dispersed duplicated genes than its chromosomes have been structurally evolving order magnitude faster those grass genomes. decay colinearity with correlates recombination rates along chromosomes. propose vast sequences cause frequent errors in lead gene duplications structural chromosome changes drive fast evolution.

Language: Английский

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Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

Nucleic Acids Research, Journal Year: 2017, Volume and Issue: 46(D1), P. D802 - D808

Published: Oct. 24, 2017

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources vertebrate genomics developed in project (http://www.ensembl.org). Together, two provide a consistent set of programmatic and interactive interfaces to rich range including genome sequence, gene models, transcript genetic variation, comparative analysis. This paper provides update previous publications about resource, with focus on recent developments expansions. These include incorporation almost 20 000 additional sequences over 35 tracks RNA-Seq data, which have been aligned genomic sequence made available visualization. Other advances since 2015 release database Resource Description Framework (RDF) format, large increase community-derived curation, new high-performance protein search, cross-references, improved annotation non-protein-coding genes, launch pre-release archival sites. Collectively, these changes are part continuing response increasing quantity publicly-available consequent need archive, integrate, annotate disseminate using automated, scalable methods.

Language: Английский

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

Nature, Journal Year: 2020, Volume and Issue: 588(7837), P. 284 - 289

Published: Nov. 25, 2020

Abstract Genetic diversity is key to crop improvement. Owing pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence species (known as ‘pan-genome’ 1 ). Multiple high-quality assemblies are an indispensable component pan-genome infrastructure. Barley ( Hordeum vulgare L.) important cereal with long history cultivation that adapted wide range agro-climatic conditions 2 . Here we report construction chromosome-scale for genotypes 20 varieties barley—comprising landraces, cultivars and wild barley—that were selected representatives global barley diversity. We catalogued presence/absence variants explored use quantitative genetic analysis through whole-genome shotgun sequencing 300 gene bank accessions. discovered abundant large inversion polymorphisms analysed in detail two inversions frequently found current elite germplasm; one probably product mutation breeding other tightly linked locus involved expansion geographical range. This first-generation makes previously hidden variation accessible studies breeding.

Language: Английский

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Genome sequence of the progenitor of wheat A subgenome Triticum urartu

Nature, Journal Year: 2018, Volume and Issue: 557(7705), P. 424 - 428

Published: May 1, 2018

Triticum urartu (diploid, AA) is the progenitor of A subgenome tetraploid (Triticum turgidum, AABB) and hexaploid aestivum, AABBDD) wheat1,2. Genomic studies T. have been useful for investigating structure, function evolution polyploid wheat genomes. Here we report generation a high-quality genome sequence by combining bacterial artificial chromosome (BAC)-by-BAC sequencing, single molecule real-time whole-genome shotgun sequencing3, linked reads optical mapping4,5. We assembled seven chromosome-scale pseudomolecules identified protein-coding genes, suggest model chromosomes. Comparative analyses with genomes other grasses showed gene loss amplification in numbers transposable elements genome. Population genomics analysis 147 accessions from across Fertile Crescent clustering three groups, differences altitude biostress, such as powdery mildew disease. The assembly provides valuable resource studying genetic variation related grasses, promises to facilitate discovery genes that could be improvement. urartu, wheat, insight into duplication during grass evolution.

Language: Английский

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Heat stress effects and management in wheat. A review

Agronomy for Sustainable Development, Journal Year: 2017, Volume and Issue: 37(5)

Published: Aug. 23, 2017

Language: Английский

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The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum

GigaScience, Journal Year: 2017, Volume and Issue: 6(11)

Published: Oct. 23, 2017

Abstract Common bread wheat, Triticum aestivum, has one of the most complex genomes known to science, with 6 copies each chromosome, enormous numbers near-identical sequences scattered throughout, and an overall haploid size more than 15 billion bases. Multiple past attempts assemble genome have produced assemblies that were well short estimated size. Here we report first near-complete assembly T. using deep sequencing coverage from a combination Illumina reads very long Pacific Biosciences reads. The final contains 344 693 583 bases weighted average (N50) contig 232 659 This represents by far complete contiguous wheat date, providing strong foundation for future genetic studies this important food crop. We also how used recently published Aegilops tauschii, diploid ancestor D genome, identify 4 179 762 575 bp aestivum correspond its components.

Language: Английский

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Impact of transposable elements on genome structure and evolution in bread wheat

Genome biology, Journal Year: 2018, Volume and Issue: 19(1)

Published: Aug. 3, 2018

Transposable elements (TEs) are major components of large plant genomes and main drivers genome evolution. The most recent assembly hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context enabled a detailed view into dynamics TEs A, B, D subgenomes. overall content is very similar between subgenomes, although we find no evidence for bursts amplification after polyploidization events. Despite near-complete turnover since subgenome lineages diverged from common ancestor, 76% families still present proportions each subgenome. Moreover, spacing syntenic genes also conserved, even though have been replaced by new insertions over time, suggesting that distances genes, but not sequences, under evolutionary constraints. composition immediate gene vicinity differs core intergenic regions. We same to be enriched or depleted near all three Evaluations at subfamily level timed long terminal repeat-retrotransposon highlight independent evolution diploid before cases concerted proliferation AB tetraploid. Even changed turnover, unexpected preservation observed subgenomes features like family proportions, spacing, enrichment genes.

Language: Английский

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