Fig. 7: Co-association of grain colour, width, and EPOD concentration with multiple regions.

Plots of k-mers associated with a grain colour, b grain width, and c grain EPOD concentration. k-mers are grouped according to their association level and genomic coordinates (10 kb bins) and coloured according to the direction of association. In (a), brown denotes association with brown grain colour and white with white grain colour. In (b and c), red denotes association with lower trait values, and blue with higher trait values. Point size is proportional to the number of k-mers rounded upwards to the nearest 10. Nine regions are labelled with black and green numbers, denoting whether the region is significant or not significant for the plotted trait, respectively. Diagrams of LTR Copia insertions into TT2 homoeologs on d chromosome 4A, e chromosome 4B. Top: structure of TT2 in Dabbi (brown-grained). Centre: structure of TT2 in Tsedey (white-grained). Bottom: detail of LTR Copia insertions. Narrower exons indicate presumed protein truncations. Black DNA bases denote 5 bp target-site duplications. Green DNA bases denote the start of the retrotransposon insertions. Single-letter amino acid codes show the introduction of premature stop codons (*). The first 22 bp of the TT2 open reading frame on 4B is not assembled in the Tsedey genome (greyed out, black arrowhead). Gene annotations derive from ref. ¹¹. and do not include 5’ and 3’ untranslated regions.