Exploring the diversity of promoter and 5′UTR sequences in ancestral, historic and modern wheat

Hammond-Kosack, Michael C. U.; King, Robert C.; Kanyuka, K.; Hammond‐Kosack, K. E.

doi:10.1111/pbi.13672

Cited by 5 publications

(3 citation statements)

References 41 publications

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“…The same myBaits technology used for this new regulatory capture design was used successfully previously in a more limited analysis of a subset of wheat gene promoters (Hammond-Kosack, King, et al, 2021). That study explored the 1.7 Kbp upstream of the coding regions of 459 wheat genes associated with agriculturally important traits in 95 ancestral and commercial wheat accessions.…”

Section: Discussionmentioning

confidence: 99%

A second generation capture panel for cost-effective sequencing of genome regulatory regions in wheat and relatives

Zhang

Debernardi

Burguener

et al. 2022

Preprint

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As genome resources for wheat expand at a rapid pace, it is important to update targeted sequencing tools to incorporate improved sequence assemblies and regions of previously unknown significance. Here, we developed an updated regulatory region enrichment capture for wheat (Triticum L.) and other Triticeae species. The core target space includes sequences from two Kbp upstream of each gene predicted in the Chinese Spring wheat genome (IWGSC RefSeq Annotation v1.1) and regions of open chromatin identified with ATAC-seq from wheat leaf and root samples. To improve specificity, we aggressively filtered candidate repetitive sequences using a combination of BLASTN searches to the Triticeae Repetitive Sequence Database (TREP), identification of regions with read over-coverage from previous target enrichment experiments, and k-mer frequency analyses. The final design comprises 216 Mbp of predicted hybridization space in hexaploid wheat and showed increased specificity and coverage of targeted sequences relative to previous protocols. Test captures on hexaploid and tetraploid wheat and other diploid cereals show that the assay has broad potential utility for cost-effective promoter and open chromatin resequencing and general-purpose genotyping of various Triticeae species.

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Section: Discussionmentioning

confidence: 99%

A second generation capture panel for cost-effective sequencing of genome regulatory regions in wheat and relatives

Zhang

Debernardi

Burguener

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…The same myBaits technology used for this new regulatory capture design was used successfully previously in a more limited analysis of a subset of wheat gene promoters (Hammond‐Kosack et al., 2021). That study explored the 1.7‐Kbp upstream of the coding regions of 459 wheat genes associated with agriculturally important traits in 95 ancestral and commercial wheat accessions.…”

Section: Discussionmentioning

confidence: 99%

A second‐generation capture panel for cost‐effective sequencing of genome regulatory regions in wheat and relatives

et al. 2022

View full text Add to dashboard Cite

As genome resources for wheat (Triticum L.) expand at a rapid pace, it is important to update targeted sequencing tools to incorporate improved sequence assemblies and regions of previously unknown significance. Here, we developed an updated regulatory region enrichment capture for wheat and other Triticeae species. The core target space includes sequences from 2-Kbp upstream of each gene predicted in the Chinese Spring wheat genome (IWGSC RefSeq Annotation v1.0) and regions of open chromatin identified with an assay for transposase-accessible chromatin using sequencing from wheat leaf and root samples. To improve specificity, we aggressively filtered candidate repetitive sequences using a combination of nucleotide basic local alignment search tool (BLASTN) searches to the Triticeae Repetitive Sequence Database (TREP), identification of regions with read over-coverage from previous target enrichment experiments, and k-mer frequency analyses. The final design comprises 216.5 Mbp of predicted hybridization space in hexaploid wheat and showed increased specificity and coverage of targeted sequences relative to previous protocols. Test captures on hexaploid and tetraploid wheat and other diploid cereals show that the assay has broad potential utility for cost-effective promoter and open chromatin resequencing and general-purpose genotyping of various Triticeae species.

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“…As an important protein source, increasing wheat production is crucial for improving world food security [ 2 ]. Wheat faces expanding pressure to ensure food security with continued population growth and from deterioration of the natural environment [ 3 , 4 ]. Therefore, it is urgent to improve wheat yields by enhancing its ability to adapt to the complex natural environment.…”

Section: Introductionmentioning

confidence: 99%

Comparative Analysis of miRNA Expression Profiles under Salt Stress in Wheat

Qiao

Jiao

Wang

et al. 2023

Genes

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Salt stress is one of the important environmental factors that inhibit the normal growth and development of plants. Plants have evolved various mechanisms, including signal transduction regulation, physiological regulation, and gene transcription regulation, to adapt to environmental stress. MicroRNAs (miRNAs) play a role in regulating mRNA expression. Nevertheless, miRNAs related to salt stress are rarely reported in bread wheat (Triticum aestivum L.). In this study, using high−throughput sequencing, we analyzed the miRNA expression profile of wheat under salt stress. We identified 360 conserved and 859 novel miRNAs, of which 49 showed considerable changes in transcription levels after salt treatment. Among them, 25 were dramatically upregulated and 24 were downregulated. Using real−time quantitative PCR, we detected significant changes in the relative expression of miRNAs, and the results showed the same trend as the sequencing data. In the salt−treated group, miR109 had a higher expression level, while miR60 and miR202 had lower expression levels. Furthermore, 21 miRNAs with significant changes were selected from the differentially expressed miRNAs, and 1023 candidate target genes were obtained through the prediction of the website psRNATarget. Gene ontology (GO) analysis of the candidate target genes showed that the expressed miRNA may be involved in the response to biological processes, molecular functions, and cellular components. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis confirmed their important functions in RNA degradation, metabolic pathways, synthesis pathways, peroxisome, environmental adaptation, global and overview maps, and stress adaptation and the MAPK signal pathway. These findings provide a basis for further exploring the function of miRNA in wheat salt tolerance.

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Exploring the diversity of promoter and 5′UTR sequences in ancestral, historic and modern wheat

Cited by 5 publications

References 41 publications

A second generation capture panel for cost-effective sequencing of genome regulatory regions in wheat and relatives

A second generation capture panel for cost-effective sequencing of genome regulatory regions in wheat and relatives

A second‐generation capture panel for cost‐effective sequencing of genome regulatory regions in wheat and relatives

Comparative Analysis of miRNA Expression Profiles under Salt Stress in Wheat

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