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

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-qu...

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Published inPloS one Vol. 14; no. 3; p. e0214519
Main Authors Sidhu, Jagdeep Singh, Ramakrishnan, Sai Mukund, Ali, Shaukat, Bernardo, Amy, Bai, Guihua, Abdullah, Sidrat, Ayana, Girma, Sehgal, Sunish K.
Format Journal Article
LanguageEnglish
Published United States Public Library of Science 28.03.2019
Public Library of Science (PLoS)
Subjects
Agronomy
Analysis
Ascomycota - physiology
Barley
Biodiversity
Biology and Life Sciences
Cereals
Chromosomes
Chromosomes, Plant - genetics
Clusters
Comparative analysis
Disease resistance (Plants)
Disease Resistance - genetics
Earth Sciences
Ecology and Environmental Sciences
Genes
Genetic aspects
Genetic diversity
Genetic improvement
Genetic polymorphisms
Genetic variation
Genome, Plant - genetics
Genome-wide association studies
Genome-Wide Association Study
Genomes
Genomics
Genotype
Genotyping
Germplasm
Harsh environments
Horticulture
Phenotypic variations
Plant Diseases - immunology
Plant Diseases - microbiology
Plant fungal diseases
Plant pathology
Plant sciences
Polymorphism
Polymorphism, Single Nucleotide
Quantitative trait loci
Quantitative Trait Loci - genetics
Race
Rye
Secale - genetics
Secale - growth & development
Secale - immunology
Secale - microbiology
Secale cereale
Semi arid areas
Semiarid environments
Semiarid zones
Single nucleotide polymorphisms
Single-nucleotide polymorphism
Structural analysis
Synteny
Tan spot
Triticale
Wheat
South Dakota
Australia
United States > US
Europe
China
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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.
AbstractList 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.
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.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.
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.
Audience Academic
Author Bernardo, Amy
Sidhu, Jagdeep Singh
Bai, Guihua
Ramakrishnan, Sai Mukund
Ali, Shaukat
Sehgal, Sunish K.
Abdullah, Sidrat
Ayana, Girma
AuthorAffiliation 2 Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
1 Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States of America
National Cheng Kung University, TAIWAN
3 USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States of America
AuthorAffiliation_xml – name: 3 USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States of America
– name: 1 Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States of America
– name: National Cheng Kung University, TAIWAN
– name: 2 Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
Author_xml – sequence: 1
  givenname: Jagdeep Singh
  surname: Sidhu
  fullname: Sidhu, Jagdeep Singh
– sequence: 2
  givenname: Sai Mukund
  surname: Ramakrishnan
  fullname: Ramakrishnan, Sai Mukund
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  givenname: Shaukat
  surname: Ali
  fullname: Ali, Shaukat
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  surname: Bernardo
  fullname: Bernardo, Amy
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  orcidid: 0000-0001-5644-7547
  surname: Sehgal
  fullname: Sehgal, Sunish K.
BackLink https://www.ncbi.nlm.nih.gov/pubmed/30921415$$D View this record in MEDLINE/PubMed
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Snippet 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...
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...
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StartPage e0214519
SubjectTerms Agronomy
Analysis
Ascomycota - physiology
Barley
Biodiversity
Biology and Life Sciences
Cereals
Chromosomes
Chromosomes, Plant - genetics
Clusters
Comparative analysis
Disease resistance (Plants)
Disease Resistance - genetics
Earth Sciences
Ecology and Environmental Sciences
Genes
Genetic aspects
Genetic diversity
Genetic improvement
Genetic polymorphisms
Genetic variation
Genome, Plant - genetics
Genome-wide association studies
Genome-Wide Association Study
Genomes
Genomics
Genotype
Genotyping
Germplasm
Harsh environments
Horticulture
Phenotypic variations
Plant Diseases - immunology
Plant Diseases - microbiology
Plant fungal diseases
Plant pathology
Plant sciences
Polymorphism
Polymorphism, Single Nucleotide
Quantitative trait loci
Quantitative Trait Loci - genetics
Race
Rye
Secale - genetics
Secale - growth & development
Secale - immunology
Secale - microbiology
Secale cereale
Semi arid areas
Semiarid environments
Semiarid zones
Single nucleotide polymorphisms
Single-nucleotide polymorphism
Structural analysis
Synteny
Tan spot
Triticale
Wheat
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Title Assessing the genetic diversity and characterizing genomic regions conferring Tan Spot resistance in cultivated rye
URI https://www.ncbi.nlm.nih.gov/pubmed/30921415
https://www.proquest.com/docview/2200224026
https://www.proquest.com/docview/2200775753
https://pubmed.ncbi.nlm.nih.gov/PMC6438500
https://doaj.org/article/92cfb3b999da42c884e26c58d8a20b76
http://dx.doi.org/10.1371/journal.pone.0214519
Volume 14
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