Identification and validation of single nucleotide polymorphic markers linked to Ug99 stem rust resistance in spring wheat
Wheat stem rust (Puccinia graminis f. sp. tritici Eriks. and E. Henn.) is one of the most destructive diseases world-wide. Races belonging to Ug99 (or TTKSK) continue to cause crop losses in East Africa and threaten global wheat production. Developing and deploying wheat varieties with multiple race-specific genes or complex adult plant resistance is necessary to achieve durability. In the present study, we applied genome-wide association studies (GWAS) for identifying loci associated with the Ug99 stem rust resistance (SR) in a panel of wheat lines developed at the International Maize and Wheat Improvement Center (CIMMYT). Genotyping was carried out using the wheat 9K iSelect single nucleotide polymorphism (SNP) chip. Phenotyping was done in the field in Kenya by infection of Puccinia graminis f. sp. tritici race TTKST, the Sr24-virulent variant of Ug99. Marker-trait association identified 12 SNP markers significantly associated with resistance. Among them, 7 were mapped on five chromosomes. Markers located on chromosomes 4A and 4B overlapped with the location of the Ug99 resistance genes SrND643 and Sr37, respectively. Markers identified on 7DL were collocated with Sr25. Additional significant markers were located in the regions where no Sr gene has been reported. The chromosome location for five of the SNP markers was unknown. A BLASTN search of the NCBI database using the flanking sequences of the SNPs associated with Ug99 resistance revealed that several markers were linked to plant disease resistance analogues, while others were linked to regulatory factors or metabolic enzymes. A KASP (Kompetitive Allele Specific PCR) assay was used for validating six marker loci linked to genes with resistance to Ug99. Of those, four co-segregated with the Sr25-pathotypes while the rest identified unknown resistance genes. With further investigation, these markers can be used for marker-assisted selection in breeding for Ug99 stem rust resistance in wheat.
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2017
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Subjects: | AGRICULTURAL SCIENCES AND BIOTECHNOLOGY, WHEAT, RUSTS, GENETIC MARKERS, DISEASE RESISTANCE, |
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dig-cimmyt-10883-186082023-04-20T14:52:30Z Identification and validation of single nucleotide polymorphic markers linked to Ug99 stem rust resistance in spring wheat Long-Xi Yu Shiaoman Chao Singh, R.P. Sorrells, M.E. AGRICULTURAL SCIENCES AND BIOTECHNOLOGY WHEAT RUSTS GENETIC MARKERS DISEASE RESISTANCE Wheat stem rust (Puccinia graminis f. sp. tritici Eriks. and E. Henn.) is one of the most destructive diseases world-wide. Races belonging to Ug99 (or TTKSK) continue to cause crop losses in East Africa and threaten global wheat production. Developing and deploying wheat varieties with multiple race-specific genes or complex adult plant resistance is necessary to achieve durability. In the present study, we applied genome-wide association studies (GWAS) for identifying loci associated with the Ug99 stem rust resistance (SR) in a panel of wheat lines developed at the International Maize and Wheat Improvement Center (CIMMYT). Genotyping was carried out using the wheat 9K iSelect single nucleotide polymorphism (SNP) chip. Phenotyping was done in the field in Kenya by infection of Puccinia graminis f. sp. tritici race TTKST, the Sr24-virulent variant of Ug99. Marker-trait association identified 12 SNP markers significantly associated with resistance. Among them, 7 were mapped on five chromosomes. Markers located on chromosomes 4A and 4B overlapped with the location of the Ug99 resistance genes SrND643 and Sr37, respectively. Markers identified on 7DL were collocated with Sr25. Additional significant markers were located in the regions where no Sr gene has been reported. The chromosome location for five of the SNP markers was unknown. A BLASTN search of the NCBI database using the flanking sequences of the SNPs associated with Ug99 resistance revealed that several markers were linked to plant disease resistance analogues, while others were linked to regulatory factors or metabolic enzymes. A KASP (Kompetitive Allele Specific PCR) assay was used for validating six marker loci linked to genes with resistance to Ug99. Of those, four co-segregated with the Sr25-pathotypes while the rest identified unknown resistance genes. With further investigation, these markers can be used for marker-assisted selection in breeding for Ug99 stem rust resistance in wheat. 21 pages 2017-06-27T15:31:45Z 2017-06-27T15:31:45Z 2017 Article http://hdl.handle.net/10883/18608 10.1371/journal.pone.0171963 English https://ndownloader.figshare.com/articles/4698685/versions/1 CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose. Open Access Open Access PDF East Africa Kenya San Francisco (USA) Public Library of Science 2 12 PLoS ONE |
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AGRICULTURAL SCIENCES AND BIOTECHNOLOGY WHEAT RUSTS GENETIC MARKERS DISEASE RESISTANCE AGRICULTURAL SCIENCES AND BIOTECHNOLOGY WHEAT RUSTS GENETIC MARKERS DISEASE RESISTANCE |
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AGRICULTURAL SCIENCES AND BIOTECHNOLOGY WHEAT RUSTS GENETIC MARKERS DISEASE RESISTANCE AGRICULTURAL SCIENCES AND BIOTECHNOLOGY WHEAT RUSTS GENETIC MARKERS DISEASE RESISTANCE Long-Xi Yu Shiaoman Chao Singh, R.P. Sorrells, M.E. Identification and validation of single nucleotide polymorphic markers linked to Ug99 stem rust resistance in spring wheat |
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Wheat stem rust (Puccinia graminis f. sp. tritici Eriks. and E. Henn.) is one of the most destructive diseases world-wide. Races belonging to Ug99 (or TTKSK) continue to cause crop losses in East Africa and threaten global wheat production. Developing and deploying wheat varieties with multiple race-specific genes or complex adult plant resistance is necessary to achieve durability. In the present study, we applied genome-wide association studies (GWAS) for identifying loci associated with the Ug99 stem rust resistance (SR) in a panel of wheat lines developed at the International Maize and Wheat Improvement Center (CIMMYT). Genotyping was carried out using the wheat 9K iSelect single nucleotide polymorphism (SNP) chip. Phenotyping was done in the field in Kenya by infection of Puccinia graminis f. sp. tritici race TTKST, the Sr24-virulent variant of Ug99. Marker-trait association identified 12 SNP markers significantly associated with resistance. Among them, 7 were mapped on five chromosomes. Markers located on chromosomes 4A and 4B overlapped with the location of the Ug99 resistance genes SrND643 and Sr37, respectively. Markers identified on 7DL were collocated with Sr25. Additional significant markers were located in the regions where no Sr gene has been reported. The chromosome location for five of the SNP markers was unknown. A BLASTN search of the NCBI database using the flanking sequences of the SNPs associated with Ug99 resistance revealed that several markers were linked to plant disease resistance analogues, while others were linked to regulatory factors or metabolic enzymes. A KASP (Kompetitive Allele Specific PCR) assay was used for validating six marker loci linked to genes with resistance to Ug99. Of those, four co-segregated with the Sr25-pathotypes while the rest identified unknown resistance genes. With further investigation, these markers can be used for marker-assisted selection in breeding for Ug99 stem rust resistance in wheat. |
format |
Article |
topic_facet |
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY WHEAT RUSTS GENETIC MARKERS DISEASE RESISTANCE |
author |
Long-Xi Yu Shiaoman Chao Singh, R.P. Sorrells, M.E. |
author_facet |
Long-Xi Yu Shiaoman Chao Singh, R.P. Sorrells, M.E. |
author_sort |
Long-Xi Yu |
title |
Identification and validation of single nucleotide polymorphic markers linked to Ug99 stem rust resistance in spring wheat |
title_short |
Identification and validation of single nucleotide polymorphic markers linked to Ug99 stem rust resistance in spring wheat |
title_full |
Identification and validation of single nucleotide polymorphic markers linked to Ug99 stem rust resistance in spring wheat |
title_fullStr |
Identification and validation of single nucleotide polymorphic markers linked to Ug99 stem rust resistance in spring wheat |
title_full_unstemmed |
Identification and validation of single nucleotide polymorphic markers linked to Ug99 stem rust resistance in spring wheat |
title_sort |
identification and validation of single nucleotide polymorphic markers linked to ug99 stem rust resistance in spring wheat |
publisher |
Public Library of Science |
publishDate |
2017 |
url |
http://hdl.handle.net/10883/18608 |
work_keys_str_mv |
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_version_ |
1764985223671447552 |