Fig. 5

Structural variation of FtXIP controls the domestication of easily-dehulled type Tartary buckwheat. A Genome features of EDT. The outermost circle represents each chromosome of the genome. The second to fifth circles indicate gene density, SNPs density, deletion density, and insertion density, respectively, using a window size of 500-kb. B Gene dot map between easily-dehulled type buckwheat (EDT) and difficult-dehulled type (DDT) Tartary buckwheat. C Diagram representing the generation of the EDT x DDT recombinant inbred lines (RILs). D Genome wide Δ(SNP index) plot of the population derived from a cross between EDT and EDT. The black lines indicates tricube-smoothed Δ(SNP index), and the gray lines indicate corresponding two-sided 99% confidence intervals. E Insertions and deletions larger than 50 bp and within 5 kb of genes in the chr 2 QTL intervals. F Expression of genes with insertions and deletions in the QTL intervals in the seed coats of EDT and DDT at the 20-day after pollination (DAP) stage. Each small square represents the differentially expression level of a gene between EDT and DDT. Square with gene ID exhibited the differentially expressed genes. The red gene ID represents FtXIP. G Schematic diagram showing the deletion of 1,140 bp in the promoter region of MqXIP gene. H Transient expression assay was conducted to compare the transcription activity of MqXIP and an empty vector. I The expression level of XIP in DDT and EDT Tartary buckwheat. The error bars indicate the ± s. d, n = 6. The P value was calculated using two-tailed t-tests. P < 0.05