Fig. 6: Genome-wide scan for the hulless grain trait.
From: Reference genome assemblies reveal the origin and evolution of allohexaploid oat
a, The spikelets and kernels of hulled and hulless oats. Scale bar, 1 cm. b, Population structure of 659 oat lines. Scatter plots of the first principle component (PC1) versus PC2 and PC1 versus PC3. c, Neighbor-joining tree constructed based on the Euclidean distance metrics between taxa. d, LD decay across the whole genome. The r2 values of LD were plotted against the physical distance (Mb). LD dropped to 0.2 at 2.29 Mb across the whole genome. e, Quantile–quantile plot of the MLM model for hulless grain. Linear regression was used to generate the P values. The dotted lines show the 95% confidence interval for the QQ-plot under the null hypothesis of no association between the SNP and the trait. f, Manhattan plot for candidate region association mapping of N1. The red horizontal line indicates the Bonferroni-adjusted significance threshold (−log10 P = 6.70). The zoomed-in region displays the physical positions of the markers GMI_ES22_c7478_431 and GMI_ES14_c19259_657 flanking the N1 locus42, and the mostly associated markers. g, Gene structure of the candidate gene A.satnudSFS4D01G000045. Green boxes are exons, and lines between the boxes are introns. The location of a SNP that resulted in an amino acid change is shown in the diamond shaped box. h, The association between A.satnudSFS4D01G000045 and the hulless trait was further confirmed by a KASP marker derived from the SNP. HEX, hexachloro fluorescein; FAM, fluorescein amidite. i, Expression level of A.satnudSFS4D01G000045 in RNA samples equally mixed from seven tissue/conditions of 10 hulled and 12 hulless oat lines. The central line for each box plot indicates the median. The top and bottom edges of the box indicate the first and third quartiles and the whiskers extend 1.5 times the interquartile range beyond the edges of the box. j, Comparison of expression levels of A.satnudSFS4D01G000045 in panicles at different developmental stages between Sanfensan (hulless) and Ogle (hulled). The data are presented as mean ± s.d. (n = 3 biological replicates). S1, S2, S3 and S4 represent panicles at the booting (Zadok’s 45), heading (Zadok’s 50 and 58) and grain dough (Zadok’s 83) stages, respectively. Two-tailed Student’s t test was used to generate the P values in panels i and j (*P < 0.05, **P < 0.01).
