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 4 publications

(2 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.

show abstract

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.

show abstract

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

Hammond-Kosack

King

Kanyuka

et al. 2021

Plant Biotechnology Journal

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A data set of promoter and 5′UTR sequences of homoeo‐alleles of 459 wheat genes that contribute to agriculturally important traits in 95 ancestral and commercial wheat cultivars is presented here. The high‐stringency myBaits technology used made individual capture of homoeo‐allele promoters possible, which is reported here for the first time. Promoters of most genes are remarkably conserved across the 83 hexaploid cultivars used with <7 haplotypes per promoter and 21% being identical to the reference Chinese Spring. InDels and many high‐confidence SNPs are located within predicted plant transcription factor binding sites, potentially changing gene expression. Most haplotypes found in the Watkins landraces and a few haplotypes found in Triticum monococcum, germplasms hitherto not thought to have been used in modern wheat breeding, are already found in many commercial hexaploid wheats. The full data set which is useful for genomic and gene function studies and wheat breeding is available at https://rrescloud.rothamsted.ac.uk/index.php/s/DMCFDu5iAGTl50u/authenticate.

show abstract

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

Cited by 4 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

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

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