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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Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly

The Plant Journal, Journal Year: 2021, Volume and Issue: 107(1), P. 303 - 314

Published: April 24, 2021

Summary Until recently, achieving a reference‐quality genome sequence for bread wheat was long thought beyond the limits of sequencing and assembly technology, primarily due to large size > 80% repetitive content. The release chromosome scale 14.5‐Gb IWGSC RefSeq v1.0 cv. Chinese Spring (CS) was, therefore, milestone. Here, we used direct label stain (DLS) optical map CS together with prior nick, label, repair (NLRS) map, contigs assembled Pacific Biosciences reads, refine assembly. Inconsistencies between maps were reconciled gaps closed. Gap filling anchoring 279 unplaced scaffolds increased total length pseudomolecules by 168 Mb (excluding Ns). Positions orientations corrected 233 354 scaffolds, respectively, representing 10% sequence. accuracy remaining 90% validated. As result contiguity, numbers transposable elements (TEs) intact TEs have in v2.1 compared v1.0. In total, 98% gene models identified mapped onto this new through development dedicated approach implemented MAGAAT pipeline. high‐confidence genes on from 105 319 534. enhances utility genetic mapping, comparative genomics, annotation isolation, more general studies biology wheat.

Language: Английский

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Long-read sequence assembly: a technical evaluation in barley

The Plant Cell, Journal Year: 2021, Volume and Issue: 33(6), P. 1888 - 1906

Published: March 10, 2021

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

Language: Английский

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TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

Genome biology, Journal Year: 2019, Volume and Issue: 20(1)

Published: Dec. 1, 2019

Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent assembly efforts in the large-genome Triticeae crops wheat and barley have relied on commercial closed-source algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct scaffolds megabase-scale contiguity ordered into chromosomal pseudomolecules. evaluate performance of TRITEX publicly available tetraploid wild emmer hexaploid bread wheat, improved annotated reference cultivar Morex as a community resource.

Language: Английский

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Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential

Nature Genetics, Journal Year: 2021, Volume and Issue: 53(4), P. 564 - 573

Published: March 18, 2021

Abstract Rye ( Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary enable hybrid breeding. allogamous only recently domesticated, thus giving cultivated ryes access a diverse exploitable wild gene pool. To further enhance agronomic potential rye, we produced chromosome-scale annotated assembly 7.9-gigabase rye genome validated its quality by using suite molecular genetic resources. We demonstrate applications this resource with broad range investigations. present findings on rye’s incomplete isolation from relatives, mechanisms structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for breeding yield benefits rye–wheat introgressions.

Language: Английский

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Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement

Nature Biotechnology, Journal Year: 2021, Volume and Issue: 40(3), P. 422 - 431

Published: Nov. 1, 2021

Abstract Aegilops tauschii , the diploid wild progenitor of D subgenome bread wheat, is a reservoir genetic diversity for improving wheat performance and environmental resilience. Here we sequenced 242 Ae. accessions compared them to characterize genomic diversity. We found that rare lineage geographically restricted present-day Georgia contributed in independent hybridizations gave rise modern wheat. Through k -mer-based association mapping, identified discrete regions with candidate genes disease pest resistance demonstrated their functional transfer into by transgenesis wide crossing, including generation library hexaploids incorporating diverse genomes. Exploiting ancestral genome permits rapid trait discovery validation hexaploid background amenable breeding.

Language: Английский

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The mosaic oat genome gives insights into a uniquely healthy cereal crop

Nature, Journal Year: 2022, Volume and Issue: 606(7912), P. 113 - 119

Published: May 18, 2022

Cultivated oat (Avena sativa L.) is an allohexaploid (AACCDD, 2n = 6x 42) thought to have been domesticated more than 3,000 years ago while growing as a weed in wheat, emmer and barley fields Anatolia1,2. Oat has low carbon footprint, substantial health benefits the potential replace animal-based food products. However, lack of fully annotated reference genome hampered efforts deconvolute its complex evolutionary history functional gene dynamics. Here we present high-quality A. close relatives diploid longiglumis, AA, 14) tetraploid insularis, CCDD, 4x 28) progenitors. We reveal mosaic structure genome, trace large-scale genomic reorganizations polyploidization illustrate breeding barrier associated with architecture oat. showcase detailed analyses families implicated human nutrition, which adds evidence supporting safety gluten-free diets, perform mapping-by-sequencing agronomic trait related water-use efficiency. This resource for Avena genus will help leverage knowledge from other cereal genomes, improve understanding basic biology accelerate genomics-assisted reanalysis quantitative studies.

Language: Английский

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Chromosome-scale genome assembly of the transformation-amenable common wheat cultivar ‘Fielder’

DNA Research, Journal Year: 2021, Volume and Issue: 28(3)

Published: June 1, 2021

Abstract We have established a high-quality, chromosome-level genome assembly for the hexaploid common wheat cultivar ‘Fielder’, an American, soft, white, pastry-type released in 1974 and known its amenability to Agrobacterium tumefaciens-mediated transformation editing. Accurate, long-read sequences were obtained using PacBio circular consensus sequencing with HiFi approach. Sequence reads from 16 SMRT cells assembled hifiasm assembler produced assemblies N50 greater than 20 Mb. used Omni-C chromosome conformation capture technique order contigs into assemblies, resulting 21 pseudomolecules cumulative size of 14.7 0.3 Gb unanchored contigs. Mapping published short transgenic plant edited seed-dormancy gene, TaQsd1, identified four positions transgene insertion chromosomes. Detection guide RNA provided candidates off-target mutation induction. These results demonstrate efficiency chromosome-scale their application genome-editing studies.

Language: Английский

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The giant diploid faba genome unlocks variation in a global protein crop

Nature, Journal Year: 2023, Volume and Issue: 615(7953), P. 652 - 659

Published: March 8, 2023

Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss biodiversity1. However, production is hampered by lack a cool-season legume equivalent to soybean agronomic value2. Faba bean (Vicia faba L.) has high yield potential well suited for cultivation temperate regions, but genomic resources are scarce. Here, we report high-quality chromosome-scale assembly genome show that it expanded massive 13 Gb size through an imbalance between rates amplification elimination retrotransposons satellite repeats. Genes recombination events evenly dispersed across chromosomes gene space remarkably compact considering size, although with substantial copy number variation driven tandem duplication. Demonstrating practical application sequence, develop targeted genotyping assay use high-resolution genome-wide association analysis dissect genetic basis seed hilum colour. The presented constitute genomics-based breeding platform bean, enabling breeders geneticists accelerate improvement sustainable Mediterranean, subtropical northern agroecological zones.

Language: Английский

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

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: March 25, 2022

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

Language: Английский

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