Michael C.U. Hammond-Kosack,Robert King,Kostya Kanyuka,Kim E. Hammond-Kosack.

Plant Biotechnology Journal; First published: 21 July 2021; https://doi.org/10.1111/pbi.13672

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.

See https://onlinelibrary.wiley.com/doi/10.1111/pbi.13672

Figure 5

Loss or gain of Transcription Factor Binding Sites (TFBS) caused by individual SNPs and small deletions in all biotic stress gene promoters. (a) Shown are seven examples of TFBS in three Trait 4 (Biotic Stress) gene promoters (T4-5A (TraesCS2A02G343100), T4-1A (TraesCS7A02G264400) and T4-4D (TraesCS3D02G049300)) across single SNPs in two commercial cultivars (AL = Alcedo, KR = Kronos) and 1 landrace from the Watkins collection (W624). Sequences were selected ±5 bp around the SNP position, and each 11 bp fragment was analysed for TFBSs without (WT) (green bars) and with the SNP (yellow bars). The numbers next to the yellow bars indicate the potential gain or loss of TFBS compared to WT. The number of TFBS found was filtered to include only TFBS with 100% match and without species duplications. (b) For the gene T4-5A, the positions of the seven cv. Alcedo SNPs are shown. This exact SNP pattern also occurs in one landrace, W246, and 18 commercial cultivars (BR, BU, CL, CG, CR, EI, HF, IS, IQ, JB, KSA, MH, OA, RE, RV, RO, SC and ST (Data S4)). (c) Details of TFBS found across two of the T4-5A cv. Alcedo SNPs (SNP1 (blue) & SNP4 (green)). For T4-5A-AL-SNP1, the mutation results in the loss of the DRE binding site (Binding Factor TaDREB2, T. durum) but a gain of an I-box motif, whereas for SNP4 there are no recognized plant TFBS in the WT sequence but the mutation results in three potential TFBS, including one from T. aestivum (TiMYB2R-1). (d) Summary of all small deletions observed in any of the promoter sequences of the 171 Trait 4 genes. All deletions are labelled as follows: [trait category (T4)]-[gene number and homoeologue (e.g. 45D)]-[cultivar (e.g. MK = Marksman)]_deletion#. Deletions are ordered by size from 116 bp (T4-29B-CE_del) to 4 bp (T4-52A-M043_del1). Blue bars = deletion length (bp), orange bars = number of potential TFBS (100% match, no species duplications) found within the corresponding sequence in CS (IWGSCrefseq_v1.0). Of the 53 observed deletions, 17 (32%) contain no recognized TFBS. Exact details for each small deletion (for all traits) including sequence and position relative to the ATG start codon for all analysed promoters are given in Data S6. (e and f) details of the positions of TFBSs found for two deletions occurring in MK for del1 (e) and del2 (f). Please note that the MK haplotype including these 2 deletions also includes 14 SNPs and that this haplotype (del1, del2 and 14 SNPs) is shared by three other commercial cultivars (Piko, Revelation and Skyfall) (Data S4).