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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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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TaCol-B5 modifies spike architecture and enhances grain yield in wheat

Science, Journal Year: 2022, Volume and Issue: 376(6589), P. 180 - 183

Published: April 7, 2022

Spike architecture influences grain yield in wheat. We report the map-based cloning of a gene determining number spikelet nodes per spike common The cloned is named TaCOL-B5 and encodes CONSTANS-like protein that orthologous to COL5 plant species. Constitutive overexpression dominant TaCol-B5 allele but without region encoding B-boxes wheat cultivar increases produces more tillers spikes, thereby enhancing transgenic plants under field conditions. Allelic variation results amino acid substitutions leading differential phosphorylation by kinase TaK4. present emmer rare global collection modern cultivars.

Language: Английский

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Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69

Plant Communications, Journal Year: 2023, Volume and Issue: 5(1), P. 100646 - 100646

Published: July 6, 2023

Gene cloning in repeat-rich polyploid genomes remains challenging. Here we describe a strategy for overcoming major bottlenecks the of powdery mildew (Pm) resistance gene (R-gene) Pm69 derived from tetraploid wild emmer wheat (WEW). A conventional positional approach was not effective due to suppressed recombination. Chromosome sorting compromised by insufficient purity. physical map, constructed assembling Oxford Nanopore Technology (ONT) long-read genome sequences, revealed rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster with structural variations. single candidate NLR identified anchoring RNASeq reads susceptible mutants ONT contigs and validated virus-induced silencing. is likely newly evolved NLR, which discovered only one location across WEW distribution range Israel. successfully introgressed into cultivated wheat, diagnostic molecular marker used accelerate its deployment pyramiding other R-genes.

Language: Английский

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A CNL protein in wild emmer wheat confers powdery mildew resistance

New Phytologist, Journal Year: 2020, Volume and Issue: 228(3), P. 1027 - 1037

Published: June 25, 2020

Summary Powdery mildew, a fungal disease caused by Blumeria graminis f. sp. tritici ( Bgt ), has serious impact on wheat production. Loss of resistance in cultivars prompts continuing search for new sources resistance. Wild emmer Triticum turgidum ssp. dicoccoides , WEW), the progenitor both modern tetraploid and hexaploid wheats, harbors many powdery mildew genes. We report here positional cloning functional characterization Pm41 gene derived from WEW, which encodes coiled‐coil, nucleotide‐binding site leucine‐rich repeat protein (CNL). Mutagenesis stable genetic transformation confirmed function against infection wheat. demonstrated that was present at very low frequency (1.81%) only southern WEW populations. It absent other populations, domesticated emmer, durum, common wheat, suggesting ancestral restricted to its place origin not incorporated into Our findings emphasize importance conservation exploitation primary pool, as valuable resource discovery genes improvement cultivars.

Language: Английский

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Discovery of stripe rust resistance with incomplete dominance in wild emmer wheat using bulked segregant analysis sequencing

Communications Biology, Journal Year: 2022, Volume and Issue: 5(1)

Published: Aug. 17, 2022

Durable crop disease resistance is an essential component of global food security. Continuous pathogen evolution leads to a breakdown and there pressing need characterize new genes for use in plant breeding. Here we identified accession wild emmer wheat (Triticum turgidum ssp. dicoccoides), PI 487260, that highly resistant multiple stripe rust isolates. Genetic analysis revealed was conferred by single, incompletely dominant gene designated as Yr84. Through bulked segregant sequencing (BSA-Seq) 52.7 Mb resistance-associated interval on chromosome 1BS. Detected variants were used design genetic markers recombinant screening, further refining the Yr84 2.3-3.3 tetraploid genomes. This contains 34 candidate encoding protein domains involved responses. Furthermore, KASP closely-linked developed facilitate marker-assisted selection

Language: Английский

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Discovery of isoflavone phytoalexins in wheat reveals an alternative route to isoflavonoid biosynthesis

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Nov. 1, 2023

Abstract Isoflavones are a group of phenolic compounds mostly restricted to plants the legume family, where they mediate important interactions with plant-associated microbes, including in defense from pathogens and nodulation. Their well-studied health promoting attributes have made them prime target for metabolic engineering, both bioproduction isoflavones as high-value molecules, biofortification food crops. A key gene their biosynthesis, isoflavone synthase, was identified legumes over two decades ago, but little is known about formation outside this family. Here we identify specialized wheat-specific TaCYP71F53, which catalyzes different reaction leguminous synthases, thus revealing an alternative path isoflavonoid biosynthesis providing non-transgenic route engineering production wheat. TaCYP71F53 forms part biosynthetic cluster that produces naringenin-derived O -methylated isoflavone, 5-hydroxy-2′,4′,7-trimethoxyisoflavone, triticein. Pathogen-induced vitro antimicrobial activity triticein suggest defense-related role molecule Genomic analyses wheat ancestral grasses further show introduced into domesticated emmer through natural hybridization ~9000 years encodes pathogen-responsive pathway conserved modern bread varieties.

Language: Английский

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Global Patterns of Subgenome Evolution in Organelle-Targeted Genes of Six Allotetraploid Angiosperms

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(4)

Published: April 1, 2022

Abstract Whole-genome duplications (WGDs) are a prominent process of diversification in eukaryotes. The genetic and evolutionary forces that WGD imposes on cytoplasmic genomes not well understood, despite the central role cytonuclear interactions play eukaryotic function fitness. Cellular respiration photosynthesis depend successful interaction between 3,000+ nuclear-encoded proteins destined for mitochondria or plastids gene products multi-subunit complexes such as OXPHOS, organellar ribosomes, Photosystems I II, Rubisco. Allopolyploids thus faced with critical task coordinating nuclear genes were inherited from different species. Because share more recent history common descent maternal subgenome than paternal subgenome, “mismatches” allopolyploids might lead to accelerated rates evolution homoeologs allopolyploids, either through relaxed purifying selection strong directional rectify these mismatches. We report evidence six independently formed allotetraploids subgenomes exhibit unequal protein-sequence evolution, but we found no incompatibilities result altered trajectories organelle-targeted genes. analyses content revealed mixed whether lost rapidly non-organelle-targeted Together, global provide insights into complex dynamics showing allopolyploid have separate sharing same nucleus, generation time, ecological context.

Language: Английский

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Fine mapping of powdery mildew resistance gene MlWE74 derived from wild emmer wheat (Triticum turgidum ssp. dicoccoides) in an NBS-LRR gene cluster

Theoretical and Applied Genetics, Journal Year: 2022, Volume and Issue: 135(4), P. 1235 - 1245

Published: Jan. 10, 2022

Language: Английский

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