Fig. 3: A chromosomal inversion linked to early heading.

a, Genome alignment of the ancestral chromosome 7D in the Australian cultivar Bilby and the inverted chromosome 7D in cultivar GS7 shows a large 450-Mb pericentric inversion and a small 50-Mb distal segment that are the same in both forms. The three small inversions at around 120 Mb, 200 Mb and 240 Mb are unique to the reference genome GS7. b, Haplotype plot of 307 CORE and hexaploid PanOat lines sorted by predicted inversion state (top, green, ancestral; bottom, yellow, inverted), on the basis of SNP calling against the GS7 genome. The red dashed line marks the inversion position. c, Significant kmerGWAS results for ten locations in 2010 and 2011. Two significant peaks are visible on chromosomes 7A and 7D. d, PCA plot of CORE³² lines (n = 292) using SNPs at the distal end of chromosome 7D (400–495 Mb) overlaid with PanOat assemblies (n = 24) (Supplementary Table 1). The box plot shows the difference in heading time in the Ithaca 2010 field trial between inverted (n = 240) and non-inverted (n = 52) lines. Box plots show the 25th (bottom edges) to 75th (top edges) percentiles, with median lines; whiskers extend to 1.5 × IQR; outlier points are observations beyond 1.5 × IQR (n = 292). TN1, A. sterilis TN1; TN4, A. sterilis TN4. e, Expression pattern (TPM, transcripts per million) across tissues of the FT1 gene on chromosome 7D (FT1-7D) and chromosome 7A (FT1-7A) in 21 annotated hexaploid PanOat accessions. Box plots show the 25th (bottom edges) to 75th (top edges) percentiles, with median lines; whiskers extend to 1.5 × IQR; outlier points are observations beyond 1.5 × IQR (n = 108 (FT1-7A) and n = 120 (FT1-7D)).