Fig. 3: Expression patterns of introgressed genes in wheat and their donor species.

a Percentage of expressed genes within the chromosome 1RS (0–280 Mb) region of the rye translocation lines 1RS.1AL, 1RS.1BL and rye lines. b Percentage of expressed specific and conserved genes within the chromosome 1RS (0–280 Mb) region in the rye translocation lines 1RS.1AL, 1RS.1BL, and rye lines. In (a) and (b), each dot represents one sample, and n indicates the number of samples. Two-tailed Student’s t test. c Relationships between the conservation of rye and wheat genes and the number of expressed genes in the 1RS.1BL introgression lines; n indicates the number of samples. d Functional enrichment analysis of differentially expressed introgressed genes between the 1RS.1BL translocation lines and rye lines. Two-sided Fisher’s exact test, Benjamini–Hochberg for multiple comparisons, p-adjust < 0.05. Bubble size corresponds to the number of genes annotated to a given term, and the color scale represents fold enrichment. e RT‒qPCR-based validation of differentially expressed genes between the three 1RS.1BL translocation lines and three rye lines using RT‒qPCR, with Tatublin as the internal control, and the results were calculated using the comparative CT method. RT‒qPCR was performed three times for each sample, and each time as a technical replicate. The error bars represent the mean ± SDs (n  =  3 biological replicates). Two-tailed Student’s t test. f–i Analytical images of Th. ponticum introgression lines using Th. elongatum as the reference, corresponding to the analyses in panels (a–d). In (f–h), each dot represents one sample, and n indicates the number of samples. In (f–g) Two-tailed Student’s t test. The box depicts the median and interquartile range (IQR). The whiskers extend to the most extreme data points within 1.5 × IQR from the quartiles. In (i), the top terms, fold enrichment, and bubble size were determined as in (d). Source data are provided as a Source Data file.