Fig. 1: Assessment of reference bias in the alien introgression of wheat.
a The left panel shows the number of expressed genes in introgression lines (n = 50) and non-introgression lines (n = 278) along chromosome 1BS (0–300 Mb) on the basis of Chinese Spring RefSeq v1.1 as the reference genome, with a sliding window of 10 Mb and a step size of 2.5 Mb. The right panel presents boxplots comparing the number of expressed genes per window between introgression lines (n = 50) and non-introgression lines (n = 278) within the chromosome 1BS (0–240 Mb) (two-sided Wilcoxon rank-sum test, p < 2.2 × 10–16). b Average gene expression of genes shared between introgression and non-introgression lines in the chromosome 1BS (0–240 Mb) region, with Chinese Spring RefSeq v1.1 as the reference genome. c A heatmap displays missing genotype sites, and a boxplot illustrates the genotype loss rate with the Chinese Spring RefSeq v1.1 as the reference genome. In the heatmap, n represents the number of accessions, orange represents modern Chinese cultivars (MCCs), cornflower blue represents modern United States cultivars (USMCs), and green represents landraces (LRs). The upper red color bar indicates introgressed fragments, and four genotype categories are depicted: blue–green for homozygous reference alleles, gold for homozygous variant alleles, light gold for heterozygous variant alleles, and light gray for missing genotypes. The lower boxplot represents the missing genotype rates calculated with a 2 Mb sliding window and a 1 Mb step size, and the sample size for each boxplot matches the number ‘n’ shown in the heatmap above. Comparisons of all introgression regions vs. background regions for chromosomes 1 A, 1B, 2D, 3D, and 5B: two-sided Wilcoxon rank-sum test, p value < 2.2 × 10–16. In (a) and (c), the box shows the median and interquartile range (IQR). The end of the top line is the maximum or the third quartile (Q) + 1.5 × IQR. The end of the bottom line denotes either the minimum or the first Q − 1.5 × IQR. The dots are more or less than Q ± 1.5 × IQR. d The number of expressed genes was calculated using a merged reference genome of Chinese Spring (CS) and introgression donors. The method for quantifying expressed genes is consistent with that in Fig. 1a; non-introgression lines include only the 100 samples with the most consistent gene expression (gray lines). The sample sizes for the introgression lines are as follows: chromosomes 1 A (n = 8), 1B (n = 50), 2D (n = 49), 3D (n = 4) and 5B (n = 74) (red lines). The upper line chart shows the number of expressed genes from Chinese Spring in the merged genome, while the lower line chart displays the number of expressed genes from the introgressed reference genome in the merged assembly. ****p < 0.0001. Source data are provided as a Source Data file.
