Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies

Tulpová, Zuzana; Luo, Ming‐Cheng; Visendi, Paul; Hayashi, Satomi; Vojta, Petr; Paux, Etienne; Kilian, Andrzej; Abrouk, Michaël; Bartoš, Jan; Hajdúch, Marián; Batley, Jacqueline; Edwards, David; Doležel, Jaroslav; Šimková, Hana

doi:10.1016/j.nbt.2018.03.003

Cited by 9 publications

(8 citation statements)

References 46 publications

(89 reference statements)

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“…In order to span the entire TaeCsTr99 array, we employed short-read sequence assemblies of physical-map ordered 7DS BAC clones [30]. TaeCsTr99 was identified in four BAC clones belonging to 7DS physical-map contig 1059.…”

Section: Resultsmentioning

confidence: 99%

“…Organization of the TaeCsTr99 region. Positions of two TaeCsTr99 arrays (highlighted in orange and red) and an overall arrangement of the region were obtained by aligning ChrUn8536, IWGSC RefSeq v1.0 [3] and Triticum 3.1 [12] 7D pseudomolecules (blue bars) and BAC clones of 7DS physical-map contig 1059 [30] (violet bars) to 7DS optical map [26] (green bars). Numbers at the 7D pseudomolecules indicate assembly coordinates.…”

Section: Figurementioning

confidence: 99%

“…In this study, we identified three new tandem repeats specific for the short arm of wheat chromosome 7D (7DS) and interrogated their representation in recently published bread wheat assemblies, including (i) Triticum 3.1 [12], which combines short Illumina and long PacBio reads, (ii) IWGSC RefSeq v1.0 [3], which is based on short reads only, and (iii) Illumina assemblies of physical map-ordered 7DS-specific BAC clones [30]. While these assemblies comprised of arrays of all three repeats, they failed in unravelling organization of a repeat with unit size of 2726 bp, whose genome arrangement could only be resolved after adding information from nanopore sequencing of two BAC clones bearing arrays of this repeat and by using an optical map (OM) of the wheat 7DS arm [26] as a reference.…”

Section: Introductionmentioning

confidence: 99%

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The Dark Matter of Large Cereal Genomes: Long Tandem Repeats

Kapustová

Tulpová

Novák

et al. 2019

IJMS

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Reference genomes of important cereals, including barley, emmer wheat and bread wheat, were released recently. Their comparison with genome size estimates obtained by flow cytometry indicated that the assemblies represent not more than 88–98% of the complete genome. This work is aimed at identifying the missing parts in two cereal genomes and proposing techniques to make the assemblies more complete. We focused on tandemly organised repetitive sequences, known to be underrepresented in genome assemblies generated from short-read sequence data. Our study found arrays of three tandem repeats with unit sizes of 1242 to 2726 bp present in the bread wheat reference genome generated from short reads. However, this and another wheat genome assembly employing long PacBio reads failed in integrating correctly the 2726-bp repeat in the pseudomolecule context. This suggests that tandem repeats of this size, frequently incorporated in unassigned scaffolds, may contribute to shrinking of pseudomolecules without reducing size of the entire assembly. We demonstrate how this missing information may be added to the pseudomolecules with the aid of nanopore sequencing of individual BAC clones and optical mapping. Using the latter technique, we identified and localised a 470-kb long array of 45S ribosomal DNA absent from the reference genome of barley.

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Section: Resultsmentioning

confidence: 99%

Section: Figurementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

The Dark Matter of Large Cereal Genomes: Long Tandem Repeats

Kapustová

Tulpová

Novák

et al. 2019

IJMS

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“…The resulting 90 contigs, which were mostly doubled because of BAC overlaps, were manually merged in Geneious version 7.1.2 (http://www.geneious.com/, accessed 14 Feb. 2019)(Kearse et al, 2012), with support from BLAST and the 7DS BNG map of CS (Staňková et al, 2016). A larger gap in the clone TaaCsp7DS088E19 was closed with scaffolds assembled by SASSY from the 2 × 150 bp reads obtained from pooled 7DS BAC clones (Tulpová et al, 2019). The SASSY scaffolds did not close the 14.4‐kb gap identified in TaaCsp7DS086H04 .…”

Section: Methodsmentioning

confidence: 99%

Accessing a Russian Wheat Aphid Resistance Gene in Bread Wheat by Long‐Read Technologies

et al. 2019

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Core Ideas An accurate sequence of the Dn2401 region was generated from Illumina and nanopore reads. Structural variation in the region was analyzed by optical mapping and resequencing. New markers located Dn2401 within a 133.2‐kb interval with six high‐confidence genes. Epoxide hydrolase 2 was identified as the most likely resistance gene candidate. Russian wheat aphid (RWA) (Diuraphis noxia Kurdjumov) is a serious invasive pest of small‐grain cereals and many grass species. An efficient strategy to defy aphid attacks is to identify sources of natural resistance and transfer resistance genes into susceptible crop cultivars. Revealing the genes helps understand plant defense mechanisms and engineer plants with durable resistance to the pest. To date, more than 15 RWA resistance genes have been identified in wheat (Triticum aestivum L.) but none of them has been cloned. Previously, we genetically mapped the RWA resistance gene Dn2401 into an interval of 0.83 cM on the short arm of chromosome 7D and spanned it with five bacterial artificial chromosome (BAC) clones. Here, we used a targeted strategy combining traditional approaches toward gene cloning (genetic mapping and sequencing of BAC clones) with novel technologies, including optical mapping and long‐read nanopore sequencing. The latter, with reads spanning the entire length of a BAC insert, enabled us to assemble the whole region, a task that was not achievable with short reads. Long‐read optical mapping validated the DNA sequence in the interval and revealed a difference in the locus organization between resistant and susceptible genotypes. The complete and accurate sequence of the Dn2401 region facilitated the identification of new markers and precise annotation of the interval, revealing six high‐confidence genes. Identification of Epoxide hydrolase 2 as the most likely Dn2401 candidate opens an avenue for its validation through functional genomics approaches.

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“…The assembly was conducted with the Newbler and SSPACE algorithms [ 50 , 51 ], leading to 13,227 scaffolds with an N50 of 351 kb and a cumulative length of 920 Mb [ 22 ]. In parallel, BREEDWHEAT also contributed to the construction of other physical maps such as that of chromosome 7DS by providing genetic mapping data of the Chinese Spring × Renan population for physical contig anchoring and ordering [ 52 ].…”

Section: A Genomics Toolbox For Wheat Research and Breedingmentioning

confidence: 99%

Breeding for Economically and Environmentally Sustainable Wheat Varieties: An Integrated Approach from Genomics to Selection

Paux

Lafarge

Balfourier

et al. 2022

Biology

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There is currently a strong societal demand for sustainability, quality, and safety in bread wheat production. To address these challenges, new and innovative knowledge, resources, tools, and methods to facilitate breeding are needed. This starts with the development of high throughput genomic tools including single nucleotide polymorphism (SNP) arrays, high density molecular marker maps, and full genome sequences. Such powerful tools are essential to perform genome-wide association studies (GWAS), to implement genomic and phenomic selection, and to characterize the worldwide diversity. This is also useful to breeders to broaden the genetic basis of elite varieties through the introduction of novel sources of genetic diversity. Improvement in varieties particularly relies on the detection of genomic regions involved in agronomical traits including tolerance to biotic (diseases and pests) and abiotic (drought, nutrient deficiency, high temperature) stresses. When enough resolution is achieved, this can result in the identification of candidate genes that could further be characterized to identify relevant alleles. Breeding must also now be approached through in silico modeling to simulate plant development, investigate genotype × environment interactions, and introduce marker–trait linkage information in the models to better implement genomic selection. Breeders must be aware of new developments and the information must be made available to the world wheat community to develop new high-yielding varieties that can meet the challenge of higher wheat production in a sustainable and fluctuating agricultural context. In this review, we compiled all knowledge and tools produced during the BREEDWHEAT project to show how they may contribute to face this challenge in the coming years.

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Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies

Cited by 9 publications

References 46 publications

The Dark Matter of Large Cereal Genomes: Long Tandem Repeats

The Dark Matter of Large Cereal Genomes: Long Tandem Repeats

Accessing a Russian Wheat Aphid Resistance Gene in Bread Wheat by Long‐Read Technologies

Breeding for Economically and Environmentally Sustainable Wheat Varieties: An Integrated Approach from Genomics to Selection

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