Wheat research and breeding in the new era of a high-quality reference genome

Appels, R.

doi:10.15302/j-fase-2019265

Cited by 9 publications

(10 citation statements)

References 28 publications

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“…Wicker used the aforementioned 80/80/80 rule to cluster sequences into subfamilies: sequences are clustered such that all members of the subfamily share at least 80% sequence identity and at least 80% sequence coverage with length greater than 80 bp. A strategy to define subfamilies was used in the analysis of bread wheat subgenomes by applying a 90/90 or 95/95 rule in which 90 or 95% sequence identity and 90 or 95% sequence coverage was used to cluster sequences into subfamilies [ 47 , 48 ]. However, further testing should be completed to determine if this type of threshold accurately splits sequences into subfamilies of all TE types across a wide array of species.…”

Section: Future Challenges/directionsmentioning

confidence: 99%

The Dfam community resource of transposable element families, sequence models, and genome annotations

et al. 2021

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Dfam is an open access database of repetitive DNA families, sequence models, and genome annotations. The 3.0–3.3 releases of Dfam (https://dfam.org) represent an evolution from a proof-of-principle collection of transposable element families in model organisms into a community resource for a broad range of species, and for both curated and uncurated datasets. In addition, releases since Dfam 3.0 provide auxiliary consensus sequence models, transposable element protein alignments, and a formalized classification system to support the growing diversity of organisms represented in the resource. The latest release includes 266,740 new de novo generated transposable element families from 336 species contributed by the EBI. This expansion demonstrates the utility of many of Dfam’s new features and provides insight into the long term challenges ahead for improving de novo generated transposable element datasets.

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Section: Future Challenges/directionsmentioning

confidence: 99%

The Dfam community resource of transposable element families, sequence models, and genome annotations

et al. 2021

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“…In addition, a genetic map could also improve the quality of genome assembly including accuracy, continuity, and completeness. Among 122,620 mapped markers in the genetic map, 1,028 SNP markers were located on the unknown chromosome based on the reference of CS (IWGSC RefSeq v1.0; Supplementary Table S5; Appels et al 2018). These SNPs were dispersed in all 22 linkage groups in the genetic map (Supplementary Table S6).…”

Section: The Genetic and Physical Map Showed Good Collinearitymentioning

confidence: 99%

A Wheat 660 K SNP array-based high-density genetic map facilitates QTL mapping of flag leaf-related traits in wheat

Niu

Tian

et al. 2023

Theor Appl Genet

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Flag leaf plays an important role in photosynthetic capacity and yield potential in wheat. In this study, we used a recombinant inbred line (RIL) population containing 188 lines derived from a cross between Lankao86 (LK86) and Ermangmai (EMM) to construct a genetic map using the Wheat 660K single nucleotide polymorphism (SNP) array. The high-density genetic map contains 122,620 SNP markers spanning 5,185.06 cM. It shows good collinearity with the physical map of Chinese Spring, and anchors multiple sequences of previously unplaced scaffolds (ChrUn) onto chromosomes. Based on the highdensity genetic map, we identi ed seven and twelve quantitative trait loci (QTL) for ag leaf length (FLL) and width (FLW) across eight environments, respectively. Among them, three QTL for FLL and one for FLW are major and stably express in more than ve environments. The physical distance between the anking markers for QFll.igdb-3B is only 444 kb containing eight high con dence genes. These results suggested that we could directly map the candidate genes in a relatively small region by the high-density genetic map constructed with the Wheat 660K array. Furthermore, the identi cation of environmentally stable QTL for ag leaf morphology laid a foundation for the following gene cloning and ag leaf morphology improvement. Key MessagesA high-density genetic map containing122,620 SNP markers was constructed, which facilitated the identi cation of four major ag leaf related QTL in relatively narrow intervals.

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“…In the recent past, the availability of annotated genomes of a few wild wheats along with genome sequences of more than 14 hexaploid or tetraploid wheat accessions has greatly facilitated the map-based cloning of disease resistance genes in wheat 35,36,48,[62][63][64][65][66] . However, due to large sequence differences among different accessions within the same species, the availability of one reference genome sequence sometimes hinders the ability to identify novel functional genes in different accessions of the same species or related species 11,13 .…”

Section: Recently Resistance Genes Encoding Kinase Fusion Proteins Ha...mentioning

confidence: 99%

Wheat powdery mildew resistance gene Pm13 from Aegilops longissima encodes a unique mixed lineage kinase domain-like protein

Liu

Men

et al. 2023

Preprint

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Wheat powdery mildew is one of the most destructive diseases threatening global wheat production. The wild relatives of wheat comprise rich sources of diversity for powdery mildew resistance. Here, we report map-based cloning of broad-spectrum powdery mildew resistance gene Pm13 from wild wheat species Aegilops longissima. Pm13 encodes a novel mixed lineage kinase domain-like (MLKL) protein which contains an N-terminal HeLo domain and a C-terminal authentic serine/threonine kinase (STK) domain, a unique domain architecture that has not been reported in plant disease-resistance genes. The resistance function of Pm13 was validated by loss-of-function mutants, gene silencing, transgenic assay, and allelic association analyses. Thus, Pm13 represents a special class of plant resistance genes revealing a novel aspect of host-pathogen interactions. Though introgressed into wheat ~30 years ago it was hardly exploited due to linkage drag. The new lines with small Ae. longissima Pm13 segment will lead to wide-scale deployment in wheat cultivars.

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Wheat research and breeding in the new era of a high-quality reference genome

Abstract: The publications of the International Wheat Genome Sequencing Consortium (IWGSC) released in August 2018 are reviewed and placed into the context of developments arising from the availability of the highquality wheat genome assembly.

Cited by 9 publications

References 28 publications

The Dfam community resource of transposable element families, sequence models, and genome annotations

The Dfam community resource of transposable element families, sequence models, and genome annotations

A Wheat 660 K SNP array-based high-density genetic map facilitates QTL mapping of flag leaf-related traits in wheat

Wheat powdery mildew resistance gene Pm13 from Aegilops longissima encodes a unique mixed lineage kinase domain-like protein

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