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ARS Home » Plains Area » Manhattan, Kansas » Center for Grain and Animal Health Research » Hard Winter Wheat Genetics Research » Research » Publications at this Location » Publication #366380
Research Project: Genetic Improvement of Biotic and Abiotic Stress Tolerance and Nutritional Quality in Hard Winter Wheat

Location: Hard Winter Wheat Genetics Research

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

Author
item SIDHU, JADDEEP SINPH - South Dakota State University
item RAMAKRISHNAN, SAI MUKUND - South Dakota State University
item ALI, SHAUKAT - South Dakota State University
item BERNANDO, AMY - Kansas State University
item Bai, Guihua
item ABDULLAH, SIDRAT - South Dakota State University
item AYANA, GIRMA - South Dakota State University
item SEHGAL, SUNISH - South Dakota State University

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/14/2019
Publication Date: 3/28/2019
Citation: Sidhu, J., Ramakrishnan, S., Ali, S., Bernando, A., Bai, G., Abdullah, S., Ayana, G., Sehgal, S.K. 2019. Assessing the genetic diversity and characterizing genomic regions conferring Tan Spot resistance in cultivated rye. PLoS One. https://doi.org/10.1371/journal.pone.0214519.
DOI: https://doi.org/10.1371/journal.pone.0214519

Interpretive Summary: Cultivated and wild species of rye are good sources of environmental stress tolerance and disease resistance. We assayed 178 geographically diverse accessions from cultivated and wild rye using DNA markers. We found that accessions were accurately clustered into the three known species Secale cereale, S. strictum, and S. sylvestre. Tests for resistance to tan spot disease identified 59% of accessions with resistance or moderate resistance. Genome-wide association study (GWAS) identified genes on chromosomes 5R and 2R conferring tan spot resistance. Based on the DNA marker data, a core set of 32 accessions was selected to represent 99% of the allelic diversity of the larger set. This set can be used for genetic improvement of rye, triticale, and wheat.

Technical 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 represent 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.