Fig. 4

Differentially expressed transcripts between 5A NILs at T1 and T2. a Heatmap of normalised tpm (transcripts per million) of DE (differentially expressed) transcripts between NILs (\( \mathrm{T}{1}_{5\mathrm{A}+}^{5\mathrm{A}-} \) and \( \mathrm{T}{2}_{5\mathrm{A}+}^{5\mathrm{A}-} \) comparisons). Transcripts are first grouped based on whether they were differentially expressed at both time points (\( \mathrm{T}{1}_{5\mathrm{A}+}^{5\mathrm{A}-} \) and \( \mathrm{T}{2}_{5\mathrm{A}+}^{5\mathrm{A}-} \) common) or at only T1 or T2 (\( \mathrm{T}{1}_{5\mathrm{A}+}^{5\mathrm{A}-} \) unique and \( \mathrm{T}{2}_{5\mathrm{A}+}^{5\mathrm{A}-} \) unique, respectively), and then whether they are located on chromosome 5A or not. b Location of DE transcripts on chromosome 5A (black lines on grey rectangle). Line graph (blue) shows rolling mean of the number of transcripts located in 3 Mbp bins across chromosome 5A, alongside heatmap which shows the number of 90 k iSelect SNPs between the 5A- and 5A+ NILs in 3 similar sized bins. Orange lines on the SNP heatmap define the 491 Mbp introgression which differs between then NILs. Red lines on the chromosome indicate the positions of the flanking markers of the fine-mapped region of the 5A grain length QTL (BS00182017 and BA00228977). Bar charts show the mean tpm values at T1 and T2 of DE transcripts located in the fine mapped region (5A- NILs in grey, 5A+ NILs in purple). Only one transcript variant (.2) of the kinesin-like gene is shown. Error bars are standard error of the three biological replicates