Assessing the genetic diversity and characterizing genomic regions conferring Tan Spot resistance in cultivated rye

Abstract

Rye (Secale cereale L.) is known for its wide adaptation due to its ability to tolerate harsh environments in semiarid areas. To assess the diversity in rye we genotyped a panel of 178 geographically diverse accessions of four Secale sp. from U.S. National Small Grains Collection using 4,037 high-quality SNPs (single nucleotide polymorphisms) developed by genotyping-by-sequencing (GBS). PCA and STRUCTURE analysis revealed three major clusters that separate S. cereale L. from S. strictum and S. sylvestre, however, genetic clusters did not correlate with geographic origins and growth habit (spring/winter). The panel was evaluated for response to Pyrenophora tritici-repentis race 5 (PTR race 5) and nearly 59% accessions showed resistance or moderate resistance. Genome-wide association study (GWAS) was performed on S. cereale subsp. cereale using the 4,037 high-quality SNPs. Two QTLs (QTs.sdsu-5R and QTs.sdsu-2R) on chromosomes 5R and 2R were identified conferring resistance to PTR race 5 (p < 0.001) that explained 13.1% and 11.6% of the phenotypic variation, respectively. Comparative analysis showed a high degree of synteny between rye and wheat with known rearrangements as expected. QTs.sdsu-2R was mapped in the genomic region corresponding to wheat chromosome group 2 and QTs.sdsu-5R was mapped to a small terminal region on chromosome 4BL. Based on the genetic diversity, a set of 32 accessions was identified to represents more than 99% of the allelic diversity with polymorphic information content (PIC) of 0.25. This set can be utilized for genetic characterization of useful traits and genetic improvement of rye, triticale, and wheat.

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.

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).

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.