Abstract

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.

Highlights

  • Wheat provides about one fifth of the calories consumed by humans globally and contributes the greatest source of proteins to the human diet (FAOSTAT, 2017a,b)

  • Ten commercial traits for wheat improvement were selected and known or candidate genes underlying these traits were collated by dedicated trait coordinators. 459 wheat genes of interest with a total of 1273 unique homoeo-allele sequences were chosen for sequence capture and detailed analyses (Table 1 and Data S1)

  • The high-quality data set presented here allows for the first time detailed analysis of individual homoeologue promoters of wheat genes across the three sub-genomes

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Summary

Introduction

Wheat provides about one fifth of the calories consumed by humans globally and contributes the greatest source of proteins to the human diet (FAOSTAT, 2017a,b). A fully annotated, high-quality sequence assembly of the large and complex hexaploid wheat genome (2n = 6x = 42; AABBDD), IWGSCrefseq_v1.0 was used (The IWGSC et al, 2018). The 14.5Gbp genome of the wheat landrace Chinese Spring (CS) contains nearly 270 000 genes, of which 107 891 were predicted with high-confidence. Development of a gene expression atlas representing all stages of wheat development together with the accurate genome assembly has enabled the discovery of tissueand developmental stage-related gene co-expression networks (The IWGSC et al, 2018) and an exploration of the relative expression levels of the homoeo-alleles of each predicted gene on the A, B and D sub-genomes (Allen et al, 2017; Arora et al, 2019; Ramırez-Gonzalez et al, 2018; Winfield et al, 2018)

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