Fig 1.
Geographic diversity of the panel of 178 accessions and the smaller diverse representative set of 32 accessions of Secale sp.
Color code: red, blue, green, and yellow map pins, correspond to Secale cereale subsp., S. strictum subsp., S. vavilovii, and S. sylvestre, respectively. Overlaid yellow triangles refer to accessions in smaller diverse representative set, which was selected from 160 cultivated rye (S. cereale subsp. cereale) accessions.
Table 1.
Number and chromosome location of SNPs discovered by genotyping-by-sequencing of 178 rye accessions.
Fig 2.
Pairwise dissimilarity-based neighbor-joining tree.
Smaller diverse representative set (red-dash clades) represents all the major clusters of Secale cereale subsp. cereale. S. strictum (green) and S. sylvestre (blue) and S. vavilovii (pink) are also shown.
Fig 3.
Structure analysis on (K = 3) 178 Secale sp. accessions.
Y-axis represents the estimated membership of individuals from populations and X-axis represents 178 Secale sp. accessions. Accessions are ordered according to the population ancestry.
Fig 4.
Principal component analysis (PCA) on 178 Secale sp. accessions to show the relationship of genetic clusters with population structure.
(A), Secale species investigated (B), spring or winter type habit (C), and the geographic origin (D).
Table 2.
Comparison of the diversity indices between smaller diverse representative set and geographically diverse set of 160 accessions of Secale cereale subsp. cereale.
Fig 5.
Genome-wide association scan for tan spot (PTR race 5) resistance in rye.
Three different model-based Manhattan plots represent–log10 (p-value) for SNPs distributed across all seven chromosomes of rye. Y-axis:–log10 (p-value) and x-axis: rye chromosomes. The dashed line stands as a threshold for significant markers with–log10 (p-value) of > 3 which correspond to a p-value <1 × 10−3. The arrows pointed two significant SNPs. On the right side of each model, Quantile-Quantile (QQ) plots represent expected null distribution of p-values vs observed p-values.
Fig 6.
Circular genome data visualization of synteny between wheat homoeologous groups (Group 2 – 2A, 2B, & 2D; Group 5 – 5A, 5B, & 5D; chromosome 4B) and rye chromosomes (2R and 5R) harboring tan spot (PTR race 5) resistance QTLs discovered in our study.
Each chromosome clockwise–short arm to long arm. QTs.sdsu-5R and QTs.sdsu-2R are shown on their corresponding rye chromosomes. QTs.sdsu-2R has a hit on wheat chromosome group 2 which harbors tan spot insensitivity gene—tsc 2 (2B) and tan spot resistance QTL (QTs.fcu-2A) (2A). QTs.sdsu-5R hits a small segment on wheat chromosome arm 4BL which harbors no tan spot related QTL, however, QTs.fcu-4B has been reported on the chromosome arm 4BS in wheat.