ArticleThe Plant journal : for cell and molecular biology2021
Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly.
Article in The Plant journal : for cell and molecular biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 340 papers.
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340 citing papers in PubMed.
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- Identification of septoria nodorum blotch susceptibility genes in hard winter wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Genetic architecture and evolution of stripe rust resistance uncovered using diverse panels of wheat lines and North American Puccinia striiformis f. sp. tritici isolates.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Unlocking the potential of spring wheat genetic resources: uncovering resistance sources against leaf rust and yellow rust.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Nonadditive gene expression and reduced homoeolog expression bias in an intraspecific hexaploid wheat hybrid.BMC plant biology · 2026Article
- Phylogenetic and Functional Analyses of WheatBiology · 2026Article
- Analysis of the TaNAS gene family in bread wheat identifies additional members and candidates for intragenic biofortification.Journal of experimental botany · 2026Article
- Chromosome-scale assembly of wheat cultivar Sumai 3, a major germplasm source for Fusarium head blight resistance.The plant genome · 2026Article
- Deletion of TaBSK3-2B attenuates BR signaling to regulate the Rht4 semi-dwarf phenotype and drought tolerance in wheat.The Plant journal : for cell and molecular biology · 2026Article
- Detailed re-analysis of satellitome mapping facilitated by the telomere-to-telomere (T2T) assembly of bread wheat genome.Plant molecular biology · 2026Article
- Identification of candidate gene for the wheat powdery mildew resistance gene Pm40 by bulked segregant analysis coupled with whole-genome sequencing (BSA-seq).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Characterization and Fine Mapping ofPlants (Basel, Switzerland) · 2026Article
- Genetic dissection of a key dynamic growth period QTL for source-sink-related traits and its breeding application potential in wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- A Water-Saving Drought Survival Phenotype in a Wheat TILLING Mutant Involves Survival-Biased Metabolic and Phosphorylation Reprogramming.Plant, cell & environment · 2026Article
- From QTL to candidate genes: a data-driven approach to unravel the genetic architecture of yellow rust resistance in central European wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
280 more citing papers are in PubMed but not listed here.
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Authors and funding
16 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Until recently, achieving a reference-quality genome sequence for bread wheat was long thought beyond the limits of genome sequencing and assembly technology, primarily due to the large genome size and > 80% repetitive sequence content. The release of the chromosome scale 14.5-Gb IWGSC RefSeq v1.0 genome sequence of bread wheat cv. Chinese Spring (CS) was, therefore, a milestone. Here, we used a direct label and stain (DLS) optical map of the CS genome together with a prior nick, label, repair and stain (NLRS) optical map, and sequence contigs assembled with Pacific Biosciences long reads, to refine the v1.0 assembly. Inconsistencies between the sequence and maps were reconciled and gaps were closed. Gap filling and anchoring of 279 unplaced scaffolds increased the total length of pseudomolecules by 168 Mb (excluding Ns). Positions and orientations were corrected for 233 and 354 scaffolds, respectively, representing 10% of the genome sequence. The accuracy of the remaining 90% of the assembly was validated. As a result of the increased contiguity, the numbers of transposable elements (TEs) and intact TEs have increased in IWGSC RefSeq v2.1 compared with v1.0. In total, 98% of the gene models identified in v1.0 were mapped onto this new assembly through development of a dedicated approach implemented in the MAGAAT pipeline. The numbers of high-confidence genes on pseudomolecules have increased from 105 319 to 105 534. The reconciled assembly enhances the utility of the sequence for genetic mapping, comparative genomics, gene annotation and isolation, and more general studies on the biology of wheat.
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