Expanding the range of editable targets in the wheat genome using the variants of the Cas12a and Cas9 nucleases

Abstract Hexaploid bread wheat (Triticum aestivum L. em. Thell) is one of the world's most important crop plants and displays a very low level of intraspecific polymorphism. We report the development of highly polymorphic microsatellite markers using procedures optimized for the large wheat genome. The isolation of microsatellite-containing clones from hypomethylated regions of the wheat genome increased the proportion of useful markers almost twofold. The majority (80%) of primer sets developed are genome-specific and detect only a single locus in one of the three genomes of bread wheat (A, B, or D). Only 20% of the markers detect more than one locus. A total of 279 loci amplified by 230 primer sets were placed onto a genetic framework map composed of RFLPs previously mapped in the reference population of the International Triticeae Mapping Initiative (ITMI) Opata 85 × W7984. Sixty-five microsatellites were mapped at a LOD >2.5, and 214 microsatellites were assigned to the most likely intervals. Ninety-three loci were mapped to the A genome, 115 to the B genome, and 71 to the D genome. The markers are randomly distributed along the linkage map, with clustering in several centromeric regions.

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Evolution and identification of DREB transcription factors in the wheat genome: modeling, docking and simulation of DREB proteins associated with salt stress

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2021.1894980 ◽

2021 ◽

pp. 1-14

Author(s):

Sameer Hassan ◽

Katrin Berk ◽

Henrik Aronsson

Keyword(s):

Transcription Factors ◽

Salt Stress ◽

Wheat Genome ◽

Dreb Transcription Factors

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F-Box Genes in the Wheat Genome and Expression Profiling in Wheat at Different Developmental Stages

Genes ◽

10.3390/genes11101154 ◽

2020 ◽

Vol 11 (10) ◽

pp. 1154

Author(s):

Min Jeong Hong ◽

Jin-Baek Kim ◽

Yong Weon Seo ◽

Dae Yeon Kim

Keyword(s):

Developmental Stages ◽

Brachypodium Distachyon ◽

Triticum Aestivum L ◽

Wheat Genome ◽

Post Translational Modification ◽

Genome Wide ◽

A Genome ◽

High Sequence Homology ◽

Wide Scale

Genes of the F-box family play specific roles in protein degradation by post-translational modification in several biological processes, including flowering, the regulation of circadian rhythms, photomorphogenesis, seed development, leaf senescence, and hormone signaling. F-box genes have not been previously investigated on a genome-wide scale; however, the establishment of the wheat (Triticum aestivum L.) reference genome sequence enabled a genome-based examination of the F-box genes to be conducted in the present study. In total, 1796 F-box genes were detected in the wheat genome and classified into various subgroups based on their functional C-terminal domain. The F-box genes were distributed among 21 chromosomes and most showed high sequence homology with F-box genes located on the homoeologous chromosomes because of allohexaploidy in the wheat genome. Additionally, a synteny analysis of wheat F-box genes was conducted in rice and Brachypodium distachyon. Transcriptome analysis during various wheat developmental stages and expression analysis by quantitative real-time PCR revealed that some F-box genes were specifically expressed in the vegetative and/or seed developmental stages. A genome-based examination and classification of F-box genes provide an opportunity to elucidate the biological functions of F-box genes in wheat.

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Wheat genome structure and function: genome sequence data and the International Wheat Genome Sequencing Consortium

Australian Journal of Agricultural Research ◽

10.1071/ar06155 ◽

2007 ◽

Vol 58 (6) ◽

pp. 470 ◽

Cited By ~ 11

Author(s):

P. Moolhuijzen ◽

D. S. Dunn ◽

M. Bellgard ◽

M. Carter ◽

J. Jia ◽

...

Keyword(s):

Genome Sequencing ◽

Physical Map ◽

Genome Structure ◽

Genetic Research ◽

Structure And Function ◽

Wheat Genome ◽

D Genome ◽

Genome Sequencing Consortium ◽

And Function ◽

Bac Contigs

Genome sequencing and the associated bioinformatics is now a widely accepted research tool for accelerating genetic research and the analysis of genome structure and function of wheat because it leverages similar work from other crops and plants. The International Wheat Genome Sequencing Consortium addresses the challenge of wheat genome structure and function and builds on the research efforts of Professor Bob McIntosh in the genetics of wheat. Currently, expressed sequence tags (ESTs; ~500 000 to date) are the largest sequence resource for wheat genome analyses. It is estimated that the gene coverage of the wheat EST collection is ~60%, close to that of Arabidopsis, indicating that ~40% of wheat genes are not represented in EST collections. The physical map of the D-genome donor species Aegilops tauschii is under construction (http://wheat.pw.usda.gov/PhysicalMapping). The technologies developed in this analysis of the D genome provide a good model for the approach to the entire wheat genome, namely compiling BAC contigs, assigning these BAC contigs to addresses in a high resolution genetic map, filling in gaps to obtain the entire physical length of a chromosome, and then large-scale sequencing.

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Effective Isolation of Retrotransposons and Repetitive DNA Families from the Wheat Genome

Journal of Integrative Plant Biology ◽

10.1111/j.1744-7909.2010.00954.x ◽

2010 ◽

pp. no-no

Author(s):

Motonori Tomita ◽

Munenori Asao ◽

Aya Kuraki

Keyword(s):

Repetitive Dna ◽

Wheat Genome

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Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements

Genome Research ◽

10.1101/gr.275658.121 ◽

2021 ◽

pp. gr.275658.121

Author(s):

Yuyun Zhang ◽

Zijuan Li ◽

Yu'e Zhang ◽

Kande Lin ◽

Yuan Peng ◽

...

Keyword(s):

Transposable Elements ◽

Genome Evolution ◽

Regulatory Networks ◽

Transcriptional Regulatory Network ◽

Sequence Similarity ◽

Purifying Selection ◽

Wheat Genome ◽

Specific Gene ◽

High Sequence Similarity ◽

Wheat Genome Evolution

More than 80% of the wheat genome consists of transposable elements (TEs), which act as one major driver of wheat genome evolution. However, their contributions to the regulatory evolution of wheat adaptations remain largely unclear. Here, we created genome-binding maps for 53 transcription factors (TFs) underlying environmental responses by leveraging DAP-seq in Triticum urartu, together with epigenomic profiles. Most TF-binding sites (TFBS) located distally from genes are embedded in TEs, whose functional relevance is supported by purifying selection and active epigenomic features. About 24% of the non-TE TFBS share significantly high sequence similarity with TE-embedded TFBS. These non-TE TFBS have almost no homologous sequences in non-Triticeae species and are potentially derived from Triticeae-specific TEs. The expansion of TE-derived TFBS linked to wheat-specific gene responses, suggesting TEs are an important driving force for regulatory innovations. Altogether, TEs have been significantly and continuously shaping regulatory networks related to wheat genome evolution and adaptation.

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Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome

Bioinformatics ◽

10.1093/bioinformatics/bty772 ◽

2018 ◽

Vol 35 (7) ◽

pp. 1159-1166

Author(s):

Ivana Piližota ◽

Clément-Marie Train ◽

Adrian Altenhoff ◽

Henning Redestig ◽

Christophe Dessimoz

Keyword(s):

Wheat Genome

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The Polymorphisms of Oligonucleotide Probes in Wheat Cultivars Determined by ND-FISH

Molecules ◽

10.3390/molecules24061126 ◽

2019 ◽

Vol 24 (6) ◽

pp. 1126 ◽

Cited By ~ 2

Author(s):

Tianheng Ren ◽

Maojie He ◽

Zixin Sun ◽

Feiquan Tan ◽

Peigao Luo ◽

...

Keyword(s):

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

Wheat Genome ◽

Oligonucleotide Probes ◽

Wheat Cultivars ◽

Fish Signal

Non-denaturing fluorescence in situ hybridization (ND-FISH) has been used to distinguish wheat chromosomes and to detect alien chromosomes in the wheat genome. In this study, five different oligonucleotide probes were used with ND-FISH to examine 21 wheat cultivars and lines. These oligonucleotide probes distinguished 42 wheat chromosomes and also detected rye chromatin in the wheat genome. Moreover, the signal patterns of the oligonucleotide probes Oligo-pTa535-1 and Oligo-pSc119.2-1 showed high polymorphism in the wheat chromosomes. A total of 17.6% of the A group chromosomes, 25.9% of the B group chromosomes and 8.9% of the D group chromosomes showed obvious mutations when they were compared to the standard ND-FISH signal patterns, and most of them were Oligo-pSc119.2-1 mutants. The results suggested that these polymorphisms could be induced by the crossing of wheat cultivars. The results provided more information for the further application of oligonucleotide probes and ND-FISH.

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A novel miniature transposon-like element discovered in the coding sequence of a gene that encodes for 5-formyltetrahydrofolate in wheat

BMC Plant Biology ◽

10.1186/s12870-019-2034-1 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 2

Author(s):

Katherine Domb ◽

Danielle Keidar-Friedman ◽

Khalil Kashkush

Keyword(s):

Stop Codon ◽

Structural Similarity ◽

Wheat Genome ◽

Wild Emmer ◽

Pcr Analysis ◽

Wheat Species ◽

Wheat Evolution ◽

Reading Frame ◽

Specific Pcr ◽

Pol Iii

Abstract Background Transposable elements (TEs) comprise over 80% of the wheat genome and usually possess unique features for specific super-families and families. However, the role of TEs in wheat evolution and reshaping the wheat genome remains largely unclear. Results In this study, we discovered a miniature (307 bp in length) TE-like sequence in exon 6 of a gene that encodes for 5-formyltetrahydrofolate, in two accessions of wild emmer wheat (T. turgidum ssp. dicoccoides) and has interfered with the gene translation by creating a shorter reading frame as a result of a stop codon. The sequence that was termed Mariam, does not show any structural similarity to known TEs. It does not possess terminal inverted repeats (TIRs) that would allow us to assign this element to one of the TIR DNA super-families, and it does not possess characteristic features of SINE, such as a Pol-III promotor or a poly-A tail. In-silico analysis of five publicly available genome drafts of Triticum and Aegilops species revealed that Mariam element appears in a very low copy number (1–3 insertions) in diploid wheat species and ~ 12 insertions in tetraploid and hexaploidy wheat species. In addition, Mariam element was found to be unique to wheat, as it was not found in other plant genomes. The dynamic nature of Mariam in the wheat genome was assessed by site-specific PCR analysis and revealed that it retained activity in wild emmer populations in a population-specific manner. Conclusions This study provides additional insight into the evolutionary impact of TEs in wheat.

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