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Qureshi N, Singh RP, Gonzalez BM, Velazquez-Miranda H, Bhavani S. Genomic Regions Associated with Resistance to Three Rusts in CIMMYT Wheat Line "Mokue#1". Int J Mol Sci 2023; 24:12160. [PMID: 37569535 PMCID: PMC10418946 DOI: 10.3390/ijms241512160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Understanding the genetic basis of rust resistance in elite CIMMYT wheat germplasm enhances breeding and deployment of durable resistance globally. "Mokue#1", released in 2023 in Pakistan as TARNAB Gandum-1, has exhibited high levels of resistance to stripe rust, leaf rust, and stem rust pathotypes present at multiple environments in Mexico and Kenya at different times. To determine the genetic basis of resistance, a F5 recombinant inbred line (RIL) mapping population consisting of 261 lines was developed and phenotyped for multiple years at field sites in Mexico and Kenya under the conditions of artificially created rust epidemics. DArTSeq genotyping was performed, and a linkage map was constructed using 7892 informative polymorphic markers. Composite interval mapping identified three significant and consistent loci contributed by Mokue: QLrYr.cim-1BL and QLrYr.cim-2AS on chromosome 1BL and 2AS, respectively associated with stripe rust and leaf rust resistance, and QLrSr.cim-2DS on chromosome 2DS for leaf rust and stem rust resistance. The QTL on 1BL was confirmed to be the Lr46/Yr29 locus, whereas the QTL on 2AS represented the Yr17/Lr37 region on the 2NS/2AS translocation. The QTL on 2DS was a unique locus conferring leaf rust resistance in Mexico and stem rust resistance in Kenya. In addition to these pleiotropic loci, four minor QTLs were also identified on chromosomes 2DL and 6BS associated with stripe rust, and 3AL and 6AS for stem rust, respectively, using the Kenya disease severity data. Significant decreases in disease severities were also demonstrated due to additive effects of QTLs when present in combinations.
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Affiliation(s)
- Naeela Qureshi
- International Maize and Wheat Improvement Center (CIMMYT), Carretera Mexico-Veracruz Km. 45, El-Batan, Texcoco 56237, Mexico; (N.Q.); (R.P.S.); (B.M.G.); (H.V.-M.)
| | - Ravi Prakash Singh
- International Maize and Wheat Improvement Center (CIMMYT), Carretera Mexico-Veracruz Km. 45, El-Batan, Texcoco 56237, Mexico; (N.Q.); (R.P.S.); (B.M.G.); (H.V.-M.)
| | - Blanca Minerva Gonzalez
- International Maize and Wheat Improvement Center (CIMMYT), Carretera Mexico-Veracruz Km. 45, El-Batan, Texcoco 56237, Mexico; (N.Q.); (R.P.S.); (B.M.G.); (H.V.-M.)
| | - Hedilberto Velazquez-Miranda
- International Maize and Wheat Improvement Center (CIMMYT), Carretera Mexico-Veracruz Km. 45, El-Batan, Texcoco 56237, Mexico; (N.Q.); (R.P.S.); (B.M.G.); (H.V.-M.)
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), Carretera Mexico-Veracruz Km. 45, El-Batan, Texcoco 56237, Mexico; (N.Q.); (R.P.S.); (B.M.G.); (H.V.-M.)
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF Campus, United Nations Avenue, Gigiri, Nairobi P.O. Box 1041-00621, Kenya
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Negash T, Edae EA, Tilahun L, Anderson JA, Rouse MN, Bajgain P. Genome-wide association mapping for field and seedling resistance to the emerging Puccinia graminis f. sp. tritici race TTRTF in wheat. THE PLANT GENOME 2022; 15:e20274. [PMID: 36263894 DOI: 10.1002/tpg2.20274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Stem rust of wheat (Triticum spp.), caused by Puccinia graminis f. sp. tritici (Pgt), is one of the most impactful wheat diseases because of its threat to global wheat production. While disease mitigation has primarily been achieved through the deployment of resistant wheat varieties, emerging new virulent races continue to pose risks to the crop. For example, races such as Ug99 (TTKSK), TKTTF, and TTRTF have caused epidemics in different wheat growing regions of the world in recent years. A continual search for new and effective sources of resistance is therefore necessary to safeguard wheat production. This study assessed a breeding panel from the Ethiopian Institute of Agricultural Research (EIAR) wheat breeding program for seedling and field plant resistance to TTRTF and reports genomic regions conferring resistance to TTRTF. Trait correlations (r) were medium to strong (range = .38-.71) and heritabilities were moderate (.32-.56). Association analysis for resistance to TTRTF resulted in detection of 20 markers in 11 chromosomes; the marker S1B_175439851 was associated with resistance at both seedling and adult plant stages. Models with two to four QTL combinations reduced seedling and field disease severity by 12-48 and 9-17%, respectively. Genomic prediction for TTRTF resistance resulted in low to moderately-high predictions (mean correlations of .25-.47). Identification of resistant lines and QTL in the EIAR population is expected to assist in selection toward improved resistance to TTRTF. Specifically, the application of genomic selection (GS) in identifying resistant lines in future related breeding populations will further assist breeding efforts against this new stem rust pathogen race.
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Affiliation(s)
- Tamrat Negash
- Ethiopian Institute of Agricultural Research, Kulumsa, Ethiopia
| | - Erena Aka Edae
- Dep. of Plant Pathology, Univ. of Minnesota, St. Paul, MN, USA
| | - Lidiya Tilahun
- Ethiopian Institute of Agricultural Research, Kulumsa, Ethiopia
| | - James A Anderson
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, St. Paul, MN, USA
| | - Matthew N Rouse
- Dep. of Plant Pathology, Univ. of Minnesota, St. Paul, MN, USA
- USDA-ARS, Cereal Disease Laboratory, St. Paul, MN, 55108, USA
| | - Prabin Bajgain
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, St. Paul, MN, USA
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3
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Origin and genetic analysis of stem rust resistance in wheat line Tr129. Sci Rep 2022; 12:4585. [PMID: 35301415 PMCID: PMC8931155 DOI: 10.1038/s41598-022-08681-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/09/2022] [Indexed: 11/16/2022] Open
Abstract
Wheat line Tr129 is resistant to stem rust, caused by Puccinia graminis f. sp. tritici (Pgt). The resistance in Tr129 was reportedly derived from Aegilops triuncialis, but the origin and genetics of resistance have not been confirmed. Here, genomic in situ hybridization (GISH) showed that no Ae. triuncialis chromatin was present in Tr129. Genetic and phenotypic analysis was conducted on F2 and DH populations from the cross RL6071/Tr129. Seedlings were tested with six Pgt races and were genotyped using an Illumina iSelect 90 K SNP array and kompetitive allele specific PCR (KASP) markers. Mapping and phenotyping showed that Tr129 carried four stem rust resistance (Sr) genes on chromosome arms 2BL (Sr9b), 4AL (Sr7b), 6AS (Sr8a), and 6DS (SrTr129). SrTr129 co-segregated with markers for SrCad, however Tr129 has a unique haplotype suggesting the resistance could be new. Analysis of a RL6071/Peace population revealed that like SrTr129, SrCad is ineffective against three North American races. This new understanding of SrCad will guide its use in breeding. Tr129 and the DNA markers reported here are useful resources for improving stem rust resistance in cultivars.
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Luo J, Rouse MN, Hua L, Li H, Li B, Li T, Zhang W, Gao C, Wang Y, Dubcovsky J, Chen S. Identification and characterization of Sr22b, a new allele of the wheat stem rust resistance gene Sr22 effective against the Ug99 race group. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:554-563. [PMID: 34695276 PMCID: PMC8882774 DOI: 10.1111/pbi.13737] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/09/2021] [Accepted: 10/19/2021] [Indexed: 05/09/2023]
Abstract
Wheat stem (or black) rust, caused by Puccinia graminis f. sp. tritici (Pgt), has been historically among the most devastating global fungal diseases of wheat. The recent occurrence and spread of new virulent races such as Ug99 have prompted global efforts to identify and isolate more effective stem rust resistance (Sr) genes. Here, we report the map‐based cloning of the Ug99‐effective SrTm5 gene from diploid wheat Triticum monococcum accession PI 306540 that encodes a typical coiled‐coil nucleotide‐binding leucine‐rich repeat protein. This gene, designated as Sr22b, is a new allele of Sr22 with a rare insertion of a large (13.8‐kb) retrotransposon into its second intron. Biolistic transformation of an ~112‐kb circular bacterial artificial chromosome plasmid carrying Sr22b into the susceptible wheat variety Fielder was sufficient to confer resistance to stem rust. In a survey of 168 wheat genotypes, Sr22b was present only in cultivated T. monococcum subsp. monococcum accessions but absent in all tested tetraploid and hexaploid wheat lines. We developed a diagnostic molecular marker for Sr22b and successfully introgressed a T. monococcum chromosome segment containing this gene into hexaploid wheat to accelerate its deployment and pyramiding with other Sr genes in wheat breeding programmes. Sr22b can be a valuable component of gene pyramids or transgenic cassettes combining different resistance genes to control this devastating disease.
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Affiliation(s)
- Jing Luo
- Peking University Institute of Advanced Agricultural SciencesWeifangShandong261000China
| | - Matthew N. Rouse
- USDA‐ARS Cereal Disease Laboratory and Department of Plant PathologyUniversity of MinnesotaSt. PaulMN55108USA
| | - Lei Hua
- Peking University Institute of Advanced Agricultural SciencesWeifangShandong261000China
| | - Hongna Li
- Peking University Institute of Advanced Agricultural SciencesWeifangShandong261000China
| | - Boshu Li
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Tianya Li
- College of Plant ProtectionShenyang Agricultural UniversityShenyangLiaoning110000China
| | - Wenjun Zhang
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Yanpeng Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Jorge Dubcovsky
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
- Howard Hughes Medical InstituteChevy ChaseMD20815USA
| | - Shisheng Chen
- Peking University Institute of Advanced Agricultural SciencesWeifangShandong261000China
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Rauf Y, Bajgain P, Rouse MN, Khanzada KA, Bhavani S, Huerta-Espino J, Singh RP, Imtiaz M, Anderson JA. Molecular Characterization of Genomic Regions for Adult Plant Resistance to Stem Rust in a Spring Wheat Mapping Population. PLANT DISEASE 2022; 106:439-450. [PMID: 34353123 DOI: 10.1094/pdis-03-21-0672-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Adult plant resistance (APR) to wheat stem rust has been one of the approaches for resistance breeding since the evolution of the Ug99 race group and other races. This study was conducted to dissect and understand the genetic basis of APR to stem rust in spring wheat line 'Copio'. A total of 176 recombinant inbred lines (RILs) from the cross of susceptible parent 'Apav' with Copio were phenotyped for stem rust resistance in six environments. Composite interval mapping using 762 genotyping-by-sequencing markers identified 16 genomic regions conferring stem rust resistance. Assays with gene-linked molecular markers revealed that Copio carried known APR genes Sr2 and Lr46/Yr29/Sr58 in addition to the 2NS/2AS translocation that harbors race-specific genes Sr38, Lr37, and Yr17. Three quantitative trait loci (QTLs) were mapped on chromosomes 2B, two QTLs on chromosomes 3A, 3B, and 6A each, and one QTL on each of chromosomes 2A, 1B, 2D, 4B, 5D, 6D, and 7A. The QTL QSr.umn.5D is potentially a new resistance gene and contributed to quantitative resistance in Copio. The RILs with allelic combinations of Sr2, Sr38, and Sr58 had 27 to 39% less stem rust coefficient of infection in all field environments compared with RILs with none of these genes, and this gene combination was most effective in the U.S. environments. We conclude that Copio carries several genes that provide both race-specific and non-race-specific resistance to diverse races of stem rust fungus and can be used by breeding programs in pyramiding other effective genes to develop durable resistance in wheat.
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Affiliation(s)
- Yahya Rauf
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Matthew N Rouse
- Cereal Disease Lab, United States Department of Agriculture, St. Paul, MN 55108, U.S.A
| | - Khalil A Khanzada
- Cereal Disease Research Institute, Pakistan Agricultural Research Council, University of Karachi 75270, Pakistan
| | - Sridhar Bhavani
- Global Wheat Program, International Maize and Wheat Improvement Center, Mexico City, 06600, Mexico
| | - Julio Huerta-Espino
- Global Wheat Program, International Maize and Wheat Improvement Center, Mexico City, 06600, Mexico
| | - Ravi P Singh
- Global Wheat Program, International Maize and Wheat Improvement Center, Mexico City, 06600, Mexico
| | - Muhammad Imtiaz
- Global Wheat Program, International Maize and Wheat Improvement Center, National Agricultural Research Center, Islamabad 44000, Pakistan
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
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Li H, Hua L, Rouse MN, Li T, Pang S, Bai S, Shen T, Luo J, Li H, Zhang W, Wang X, Dubcovsky J, Chen S. Mapping and Characterization of a Wheat Stem Rust Resistance Gene in Durum Wheat "Kronos". FRONTIERS IN PLANT SCIENCE 2021; 12:751398. [PMID: 34721479 PMCID: PMC8555631 DOI: 10.3389/fpls.2021.751398] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/09/2021] [Indexed: 05/22/2023]
Abstract
Wheat stem (or black) rust is one of the most devastating fungal diseases, threatening global wheat production. Identification, mapping, and deployment of effective resistance genes are critical to addressing this challenge. In this study, we mapped and characterized one stem rust resistance (Sr) gene from the tetraploid durum wheat variety Kronos (temporary designation SrKN). This gene was mapped on the long arm of chromosome 2B and confers resistance to multiple virulent Pgt races, such as TRTTF and BCCBC. Using a large mapping population (3,366 gametes), we mapped SrKN within a 0.29 cM region flanked by the sequenced-based markers pku4856F2R2 and pku4917F3R3, which corresponds to 5.6- and 7.2-Mb regions in the Svevo and Chinese Spring reference genomes, respectively. Both regions include a cluster of nucleotide binding leucine-repeat (NLR) genes that likely includes the candidate gene. An allelism test failed to detect recombination between SrKN and the previously mapped Sr9e gene. This result, together with the similar seedling resistance responses and resistance profiles, suggested that SrKN and Sr9e may represent the same gene. We introgressed SrKN into common wheat and developed completely linked markers to accelerate its deployment in the wheat breeding programs. SrKN can be a valuable component of transgenic cassettes or gene pyramids that includes multiple resistance genes to control this devastating disease.
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Affiliation(s)
- Hongna Li
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Lei Hua
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Matthew N. Rouse
- US Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory and Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Tianya Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Shuyong Pang
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Shengsheng Bai
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Tao Shen
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Jing Luo
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Hongyu Li
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Wenjun Zhang
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Xiaodong Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
- Howard Hughes Medical Institute, Chevy Chase, MD, United States
| | - Shisheng Chen
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
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Olivera PD, Bulbula WD, Badebo A, Bockelman HE, Edae EA, Jin Y. Field resistance to wheat stem rust in durum wheat accessions deposited at the USDA National Small Grains Collection. CROP SCIENCE 2021; 61:2565-2578. [PMID: 34413535 PMCID: PMC8361663 DOI: 10.1002/csc2.20466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 01/15/2021] [Indexed: 05/31/2023]
Abstract
Wheat stem rust, caused by Puccinia graminis f. sp. tritici, is a re-emerging disease, posing a significant threat to durum wheat production worldwide. The limited number of stem rust resistance genes in modern cultivars compels us to identify and incorporate new effective genes in durum wheat breeding programs. We evaluated 8,245 spring durum wheat accessions deposited at the USDA National Small Grains Collection (NSGC) for resistance in field stem rust nurseries in Debre Zeit, Ethiopia and St. Paul, MN (USA). A higher level of disease development was observed at the Debre Zeit nursery compared with St. Paul, and the effective alleles of Sr13 in this nursery did not display the level of resistance observed at the St. Paul nursery. Four hundred and ninety-one (∽6%) accessions exhibited resistant to moderately susceptible responses after three field evaluations at Debre Zeit and two at St. Paul. Nearly 70% of these accessions originated from Ethiopia, Mexico, Egypt, and USA. Eight additional countries, namely Portugal, Turkey, Italy, Canada, Chile, Australia, Syria, and Tunisia contributed to 19% of the resistant to moderately susceptible entries. Among the 491 resistant to moderately susceptible accessions, 53.8% (n = 265) were landraces, and 28.4% (n = 139) and 11.4% (n = 55) were breeding lines and cultivars, respectively. Breeding lines and cultivars displayed a higher level and frequency of resistance than the landraces. We concluded that a large number of durum wheat accessions from diverse origins deposited at the NSGC can be exploited for diversifying and improving stem rust resistance in wheat.
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Affiliation(s)
- Pablo D. Olivera
- Dep. of Plant PathologyUniv. of MinnesotaSt. PaulMinnesota55108USA
| | - Worku D. Bulbula
- Dep. of Plant PathologyUniv. of MinnesotaSt. PaulMinnesota55108USA
- Ethiopian Institute of Agricultural ResearchAddis AbabaEthiopia
| | | | - Harold E. Bockelman
- USDA‐Agricultural Research ServiceSmall Grains and Potato Germplasm Research UnitAberdeenIdaho83210USA
| | - Erena A. Edae
- Dep. of Plant PathologyUniv. of MinnesotaSt. PaulMinnesota55108USA
| | - Yue Jin
- USDA‐Agricultural Research ServiceCereal Disease LabSt. PaulMinnesota55108USA
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Megerssa SH, Sorrells ME, Ammar K, Acevedo M, Bergstrom GC, Olivera P, Brown-Guedira G, Ward B, Degete AG, Abeyo B. Genome-wide association mapping of seedling and adult plant response to stem rust in a durum wheat panel. THE PLANT GENOME 2021; 14:e20105. [PMID: 34145776 DOI: 10.1002/tpg2.20105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/19/2021] [Indexed: 05/26/2023]
Abstract
Many of the major stem rust resistance genes deployed in commercial wheat (Triticum spp.) cultivars and breeding lines become ineffective over time because of the continuous emergence of virulent races. A genome-wide association study (GWAS) was conducted using 26,439 single nucleotide polymorphism (SNP) markers and 280 durum wheat [Triticum turgidum L. subsp. Durum (Desf.) Husnot] lines from CIMMYT to identify genomic regions associated with seedling resistance to races TTKSK, TKTTF, JRCQC, and TTRTF and field resistance to TKTTF and JRCQC. The phenotypic data analysis across environments revealed 61-91 and 59-77% of phenotypic variation was explained by the genotypic component for seedling and adult plant response of lines, respectively. For seedling resistance, mixed linear model (MLM) identified eight novel and nine previously reported quantitative trait loci (QTL) while a fixed and random model circulating probability unification (FarmCPU) detected 12 novel and eight previously reported QTL. For field resistance, MLM identified 12 novel and seven previously reported loci while FarmCPU identified seven novel and nine previously reported loci. The regions of Sr7a, Sr8155B1, Sr11, alleles of Sr13, Sr17, Sr22/Sr25, and Sr49 were identified. Novel loci on chromosomes 3B, 4A, 6A, 6B, 7A, and 7B could be used as sources of resistance to the races virulent on durum wheat. Two large-effect markers on chromosome 6A could potentially be used to differentiate resistant haplotypes of Sr13 (R1 and R3). Allelism tests for Sr13, breaking the deleterious effect associated with Sr22/Sr25 and retaining the resistance allele at the Sr49 locus, are needed to protect future varieties from emerging races.
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Affiliation(s)
- Shitaye H Megerssa
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Mark E Sorrells
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Karim Ammar
- International Maize and Wheat Improvement Center (CIMMYT), Mexico, DF, Mexico
| | - Maricelis Acevedo
- Department of Global Development, Cornell University, Ithaca, NY, USA
| | - Gary C Bergstrom
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY, USA
| | - Pablo Olivera
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | | | - Brian Ward
- USDA-ARS Plant Science, Raleigh, NC, USA
| | - Ashenafi G Degete
- Debre Zeit Agricultural Research Center, Ethiopian Institute of Agricultural Research (EIAR), Debre Zeit, Ethiopia
| | - Bekele Abeyo
- International Maize and Wheat Improvement Center (CIMMYT), Addis Ababa, Ethiopia
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Gill BK, Klindworth DL, Rouse MN, Zhang J, Zhang Q, Sharma JS, Chu C, Long Y, Chao S, Olivera PD, Friesen TL, Zhong S, Jin Y, Faris JD, Fiedler JD, Elias EM, Liu S, Cai X, Xu SS. Function and evolution of allelic variations of Sr13 conferring resistance to stem rust in tetraploid wheat (Triticum turgidum L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1674-1691. [PMID: 33825238 PMCID: PMC8362117 DOI: 10.1111/tpj.15263] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/18/2021] [Indexed: 05/26/2023]
Abstract
The resistance gene Sr13 is one of the most important genes in durum wheat for controlling stem rust caused by Puccinia graminis f. sp. tritici (Pgt). The Sr13 functional gene CNL13 has haplotypes R1, R2 and R3. The R1/R3 and R2 haplotypes were originally designated as alleles Sr13a and Sr13b, respectively. To detect additional Sr13 alleles, we developed Kompetitive allele specific PCR (KASP™) marker KASPSr13 and four semi-thermal asymmetric reverse PCR markers, rwgsnp37-rwgsnp40, based on the CNL13 sequence. These markers were shown to detect R1, R2 and R3 haplotypes in a panel of diverse tetraploid wheat accessions. We also observed the presence of Sr13 in durum line CAT-A1, although it lacked any of the known haplotypes. Sequence analysis revealed that CNL13 of CAT-A1 differed from the susceptible haplotype S1 by a single nucleotide (C2200T) in the leucine-rich repeat region and differed from the other three R haplotypes by one or two additional nucleotides, confirming that CAT-A1 carries a new (R4) haplotype. Stem rust tests on the monogenic, transgenic and mutant lines showed that R1 differed from R3 in its susceptibility to races TCMJC and THTSC, whereas R4 differed from all other haplotypes for susceptibility to TTKSK, TPPKC and TCCJC. Based on these differences, we designate the R1, R3 and R4 haplotypes as alleles Sr13a, Sr13c and Sr13d, respectively. This study indicates that Sr13d may be the primitive functional allele originating from the S1 haplotype via a point mutation, with the other three R alleles probably being derived from Sr13d through one or two additional point mutations.
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Affiliation(s)
- Baljeet K. Gill
- Department of Plant SciencesNorth Dakota State UniversityFargoND58108USA
| | - Daryl L. Klindworth
- USDA‐ARSCereal Crops Research UnitEdward T. Schafer Agricultural Research CenterFargoND58102USA
| | | | - Jinglun Zhang
- Department of Plant SciencesNorth Dakota State UniversityFargoND58108USA
| | - Qijun Zhang
- Department of Plant SciencesNorth Dakota State UniversityFargoND58108USA
| | - Jyoti S. Sharma
- Department of Plant SciencesNorth Dakota State UniversityFargoND58108USA
| | | | - Yunming Long
- Department of Plant SciencesNorth Dakota State UniversityFargoND58108USA
| | - Shiaoman Chao
- USDA‐ARSCereal Crops Research UnitEdward T. Schafer Agricultural Research CenterFargoND58102USA
| | - Pablo D. Olivera
- Department of Plant PathologyUniversity of MinnesotaSt PaulMN55108USA
| | - Timothy L. Friesen
- USDA‐ARSCereal Crops Research UnitEdward T. Schafer Agricultural Research CenterFargoND58102USA
| | - Shaobin Zhong
- Department of Plant PathologyNorth Dakota State UniversityFargoND58108USA
| | - Yue Jin
- USDA‐ARSCereal Disease LaboratorySt PaulMN55108USA
| | - Justin D. Faris
- USDA‐ARSCereal Crops Research UnitEdward T. Schafer Agricultural Research CenterFargoND58102USA
| | - Jason D. Fiedler
- USDA‐ARSCereal Crops Research UnitEdward T. Schafer Agricultural Research CenterFargoND58102USA
| | - Elias M. Elias
- Department of Plant SciencesNorth Dakota State UniversityFargoND58108USA
| | - Shuyu Liu
- Texas A&M AgriLife ResearchAmarilloTX79106USA
| | - Xiwen Cai
- Department of Plant SciencesNorth Dakota State UniversityFargoND58108USA
| | - Steven S. Xu
- USDA‐ARSCereal Crops Research UnitEdward T. Schafer Agricultural Research CenterFargoND58102USA
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Aoun M, Rouse MN, Kolmer JA, Kumar A, Elias EM. Genome-Wide Association Studies Reveal All-Stage Rust Resistance Loci in Elite Durum Wheat Genotypes. FRONTIERS IN PLANT SCIENCE 2021; 12:640739. [PMID: 33912208 PMCID: PMC8072158 DOI: 10.3389/fpls.2021.640739] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/17/2021] [Indexed: 05/11/2023]
Abstract
Leaf rust, caused by Puccinia triticina (Pt), stripe rust caused by Puccinia striiformis f. sp. tritici (Pst), and stem rust caused by Puccinia graminis f. sp. tritici (Pgt) are major diseases to wheat production globally. Host resistance is the most suitable approach to manage these fungal pathogens. We investigated the phenotypic and genotypic structure of resistance to leaf rust, stem rust, and stripe rust pathogen races at the seedling stage in a collection of advanced durum wheat breeding lines and cultivars adapted to Upper Mid-West region of the United States. Phenotypic evaluation showed that the majority of the durum wheat genotypes were susceptible to Pt isolates adapted to durum wheat, whereas all the genotypes were resistant to common wheat type-Pt isolate. The majority of genotypes were resistant to stripe rust and stem rust pathogen races. The durum panel genotyped using Illumina iSelect 90 K wheat SNP assay was used for genome-wide association mapping (GWAS). The GWAS revealed 64 marker-trait associations (MTAs) representing six leaf rust resistance loci located on chromosome arms 2AS, 2AL, 5BS, 6AL, and 6BL. Two of these loci were identified at the positions of Lr52 and Lr64 genes, whereas the remaining loci are most likely novel. A total of 46 MTAs corresponding to four loci located on chromosome arms 1BS, 5BL, and 7BL were associated with stripe rust response. None of these loci correspond to designated stripe rust resistance genes. For stem rust, a total of 260 MTAs, representing 22 loci were identified on chromosome arms 1BL, 2BL, 3AL, 3BL, 4AL, 5AL, 5BL, 6AS, 6AL, 6BL, and 7BL. Four of these loci were located at the positions of known genes/alleles (Sr7b, Sr8155B1, Sr13a, and Sr13b). The discovery of known and novel rust resistance genes and their linked SNPs will help diversify rust resistance in durum wheat.
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Affiliation(s)
- Meriem Aoun
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
- *Correspondence: Meriem Aoun,
| | - Matthew N. Rouse
- Cereal Disease Laboratory, United States Department of Agriculture–Agricultural Research Service, St. Paul, MN, United States
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - James A. Kolmer
- Cereal Disease Laboratory, United States Department of Agriculture–Agricultural Research Service, St. Paul, MN, United States
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Elias M. Elias
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
- Elias M. Elias,
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11
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Edae EA, Rouse MN. Association mapping of resistance to emerging stem rust pathogen races in spring wheat using genotyping-by-sequencing. THE PLANT GENOME 2020; 13:e20050. [PMID: 33217214 DOI: 10.1002/tpg2.20050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 06/11/2023]
Abstract
The identification and characterization of resistance genes should outpace the rapid emergence of new P. graminis f. sp. tritici races, such as TTRTF and TTKTT, to mitigate stem rust damage to wheat. The objective of the current study was to identify and characterize P. graminis f. sp. tritici race resistance association signals. A total of 250 North American spring wheat lines were evaluated at the seedling stage with a total of seven isolates including TKKTP, TKTTF, TKTTF, TRTTF, TTRTF, TTKSK, and TTKTT. The lines were genotyped by a GBS platform and 9,042 SNPs were used for identification of chromosome regions associated with resistance against the seven isolates. Strong association signals were detected on chromosomes 6BL (Sr11 gene region) and 4AL, likely Sr7a, for resistance against both TKKTP and TKTTF. Similarly, association signals were also detected on chromosomes 4AL (race TTRTF resistance) and 4BS (race TTKSK and TTKTT resistance). Association analysis based on mean phenotypic differences between closely related isolates identified QTL that were not elucidated by direct association mapping of the responses, individually. Overall, with the exception of race TRTTF, each race shared at least one association signal with another race. However, the number of race-specific association signals are larger than that of association signals common among races suggesting the need for identifying and characterizing QTL/genes for newly emerging stem rust pathogen races. There was also high concordance between PCA-based GWAS association signals and association signals from that of both single and multi-locus mixed models.
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Affiliation(s)
- Erena A Edae
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55018, USA
| | - Matthew N Rouse
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55018, USA
- USDA-ARS, Cereal Disease Laboratory, 1551 Lindig Street, St. Paul, MN, 55018, USA
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Megerssa SH, Ammar K, Acevedo M, Brown-Guedira G, Ward B, Degete AG, Randhawa MS, Sorrells ME. Multiple-Race Stem Rust Resistance Loci Identified in Durum Wheat Using Genome-Wide Association Mapping. FRONTIERS IN PLANT SCIENCE 2020; 11:598509. [PMID: 33391309 PMCID: PMC7773921 DOI: 10.3389/fpls.2020.598509] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 11/13/2020] [Indexed: 05/22/2023]
Abstract
Stem rust of wheat caused by Puccinia graminis Pers. f.sp. trtici Eriks and E. Henn., is the most damaging fungal disease of both common (Triticum aestivum L.) and durum (Triticum turgidum L., ssp. Durum) wheat. Continuously emerging races virulent to many of the commercially deployed qualitative resistance genes have caused remarkable loss worldwide and threaten global wheat production. The objectives of this study were to evaluate the response of a panel of 283 durum wheat lines assembled by the International Maize and Wheat Improvement Center (CIMMYT) to multiple races of stem rust in East Africa at the adult plant stage and map loci associated with field resistance. The lines were evaluated in Debre Zeit, Ethiopia and Njoro, Kenya from 2018 to 2019 in five environments (year × season). The panel was genotyped using genotyping-by-sequencing. After filtering, 26,439 Single Nucleotide Polymorphism (SNP) markers and 280 lines and three checks were retained for analysis. Population structure was assessed using principal component analysis. Genome-wide association analysis (GWAS) was conducted using Genomic Association and Prediction Integrated Tool (GAPIT). The broad-sense heritability of the phenotype data revealed that 64-83% of the variation in stem rust response explained by the genotypes and lines with multiple race resistance were identified. GWAS analysis detected a total of 160 significant marker trait associations representing 42 quantitative trait loci. Of those, 21 were potentially novel and 21 were mapped to the same regions as previously reported loci. Known stem rust resistance genes/alleles were postulated including Sr8a, Sr8155B1, SrWeb/Sr9h, Sr11, Sr12, Sr13/Sr13 alleles, Sr17, Sr28/Sr16, Sr22, and Sr49. Lines resistant to multiple races in East Africa can be utilized as parents in durum wheat breeding programs. Further studies are needed to determine if there are new alleles at the Sr13 locus and potential markers for the known Sr13 alleles.
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Affiliation(s)
- Shitaye H. Megerssa
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- *Correspondence: Shitaye H. Megerssa,
| | - Karim Ammar
- International Maize and Wheat Improvement Center (CIMMYT), Mexico D.F., Mexico
| | - Maricelis Acevedo
- Department of Global Development, Cornell University, Ithaca, NY, United States
| | | | - Brian Ward
- USDA-ARS Plant Science Unit, Raleigh, NC, United States
| | - Ashenafi G. Degete
- Debre Zeit Agricultural Research Center, Ethiopian Institute of Agricultural Research (EIAR), Debre Zeit, Ethiopia
| | | | - Mark E. Sorrells
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- Mark E. Sorrells,
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Kosgey ZC, Edae EA, Dill-Macky R, Jin Y, Bulbula WD, Gemechu A, Macharia G, Bhavani S, Randhawa MS, Rouse MN. Mapping and Validation of Stem Rust Resistance Loci in Spring Wheat Line CI 14275. FRONTIERS IN PLANT SCIENCE 2020; 11:609659. [PMID: 33510752 PMCID: PMC7835402 DOI: 10.3389/fpls.2020.609659] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/08/2020] [Indexed: 05/22/2023]
Abstract
Stem rust caused by Puccinia graminis f. sp. tritici (Pgt) remains a constraint to wheat production in East Africa. In this study, we characterized the genetics of stem rust resistance, identified QTLs, and described markers associated with stem rust resistance in the spring wheat line CI 14275. The 113 recombinant inbred lines, together with their parents, were evaluated at the seedling stage against Pgt races TTKSK, TRTTF, TPMKC, TTTTF, and RTQQC. Screening for resistance to Pgt races in the field was undertaken in Kenya, Ethiopia, and the United States in 2016, 2017, and 2018. One gene conferred seedling resistance to race TTTTF, likely Sr7a. Three QTL were identified that conferred field resistance. QTL QSr.cdl-2BS.2, that conferred resistance in Kenya and Ethiopia, was validated, and the marker Excalibur_c7963_1722 was shown to have potential to select for this QTL in marker-assisted selection. The QTL QSr.cdl-3B.2 is likely Sr12, and QSr.cdl-6A appears to be a new QTL. This is the first study to both detect and validate an adult plant stem rust resistance QTL on chromosome arm 2BS. The combination of field QTL QSr.cdl-2BS.2, QSr.cdl-3B.2, and QSr.cdl-6A has the potential to be used in wheat breeding to improve stem rust resistance of wheat varieties.
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Affiliation(s)
- Zennah C. Kosgey
- Kenya Agricultural and Livestock Research Organization, Njoro, Kenya
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
- *Correspondence: Zennah C. Kosgey,
| | - Erena A. Edae
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Yue Jin
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, Saint Paul, MN, United States
| | - Worku Denbel Bulbula
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
- Debre Zeit Agricultural Research Center, Ethiopian Institute of Agricultural Research, Bishoftu, Ethiopia
| | - Ashenafi Gemechu
- Debre Zeit Agricultural Research Center, Ethiopian Institute of Agricultural Research, Bishoftu, Ethiopia
| | - Godwin Macharia
- Kenya Agricultural and Livestock Research Organization, Njoro, Kenya
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | - Matthew N. Rouse
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, Saint Paul, MN, United States
- Matthew N. Rouse,
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Mapping of Novel Leaf Rust and Stem Rust Resistance Genes in the Portuguese Durum Wheat Landrace PI 192051. G3-GENES GENOMES GENETICS 2019; 9:2535-2547. [PMID: 31278174 PMCID: PMC6686931 DOI: 10.1534/g3.119.400292] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Leaf rust caused by Puccinia triticina Erikss. (Pt) and stem rust caused by Puccinia graminis f. sp. tritici Erikss. & E. Henn (Pgt) are serious constraints to production of durum wheat (Triticum turgidum L). The objective of this study was to identify leaf rust resistance (Lr) and stem rust resistance (Sr) genes/QTL in Portuguese durum landrace PI 192051. Four Pt-isolates, representing three virulence phenotypes (BBBQJ, BBBSJ & EEEEE) and six Pgt-races TTKSK, JRCQC, TKTTF, QFCFC, TPMKC and TMLKC were used to evaluate 180 recombinant inbred lines (RILs) derived from the cross Rusty (rust susceptible) × PI 192051-1 (rust resistant) at the seedling stage. The RILs were also phenotyped at the adult-plant stage in a stem rust nursery in Ethiopia in 2017. The RILs were genotyped using the Illumina iSelect 9K wheat SNP array. PI 192051-1 carries a previously unidentified major Sr gene designated as QSr.ace-7A on chromosome arm 7AS and Lr gene Lr.ace-4A in the pericentromeric region of chromosome 4A. In addition, three minor Sr QTL QSr.ace-1A, QSr.ace-2B and QSr.ace-4A were mapped in PI 192051-1 on chromosomes 1AL, 2BL, and 4A, respectively Lr.ace-4A could be co-located or tightly linked to QSr.ace-4A. Markers linked to the identified QTL/genes can be used for marker assisted selection. These findings enrich the genetic basis of rust resistance in both durum and common wheat.
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Saccomanno A, Matny O, Marone D, Laidò G, Petruzzino G, Mazzucotelli E, Desiderio F, Blanco A, Gadaleta A, Pecchioni N, De Vita P, Steffenson B, Mastrangelo AM. Genetic Mapping of Loci for Resistance to Stem Rust in a Tetraploid Wheat Collection. Int J Mol Sci 2018; 19:E3907. [PMID: 30563213 PMCID: PMC6321032 DOI: 10.3390/ijms19123907] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/04/2018] [Accepted: 12/04/2018] [Indexed: 01/31/2023] Open
Abstract
Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a major biotic constraint to wheat production worldwide. Disease resistant cultivars are a sustainable means for the efficient control of this disease. To identify quantitative trait loci (QTLs) conferring resistance to stem rust at the seedling stage, an association mapping panel consisting of 230 tetraploid wheat accessions were evaluated for reaction to five Pgt races under greenhouse conditions. A high level of phenotypic variation was observed in the panel in response to all of the races, allowing for genome-wide association mapping of resistance QTLs in wild, landrace, and cultivated tetraploid wheats. Twenty-two resistance QTLs were identified, which were characterized by at least two marker-trait associations. Most of the identified resistance loci were coincident with previously identified rust resistance genes/QTLs; however, six regions detected on chromosomes 1B, 5A, 5B, 6B, and 7B may be novel. Availability of the reference genome sequence of wild emmer wheat accession Zavitan facilitated the search for candidate resistance genes in the regions where QTLs were identified, and many of them were annotated as NOD (nucleotide binding oligomerization domain)-like receptor (NLR) genes or genes related to broad spectrum resistance.
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Affiliation(s)
- Antonietta Saccomanno
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA.
| | - Daniela Marone
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Giovanni Laidò
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Giuseppe Petruzzino
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinfomatics, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Francesca Desiderio
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinfomatics, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Antonio Blanco
- Department of Agricultural & Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, 70126 Bari, Italy.
| | - Agata Gadaleta
- Department of Agricultural & Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, 70126 Bari, Italy.
| | - Nicola Pecchioni
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Pasquale De Vita
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Brian Steffenson
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA.
| | - Anna Maria Mastrangelo
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 24126 Bergamo (BG), Italy.
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Randhawa MS, Singh RP, Dreisigacker S, Bhavani S, Huerta-Espino J, Rouse MN, Nirmala J, Sandoval-Sanchez M. Identification and Validation of a Common Stem Rust Resistance Locus in Two Bi-parental Populations. FRONTIERS IN PLANT SCIENCE 2018; 9:1788. [PMID: 30555507 PMCID: PMC6283910 DOI: 10.3389/fpls.2018.01788] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/16/2018] [Indexed: 05/28/2023]
Abstract
Races belonging to Ug99 lineage of stem rust fungus Puccinia graminis f. sp. tritici (Pgt) continue to pose a threat to wheat (Triticum aestivum L.) production in various African countries. Growing resistant varieties is the most economical and environmentally friendly control measure. Recombinant inbred line (RIL) populations from the crosses of susceptible parent 'Cacuke' with the resistant parents 'Huhwa' and 'Yaye' were phenotyped for resistance at the seedling stage to Pgt race TTKSK (Ug99) and in adult plants in field trials at Njoro, Kenya for two seasons in 2016. Using the Affymetrix Axiom breeders SNP array, two stem rust resistance genes, temporarily designated as SrH and SrY, were identified and mapped on chromosome arm 2BL through selective genotyping and bulked segregant analysis (BSA), respectively. Kompetitive allele specific polymorphism (KASP) markers and simple sequence repeat (SSR) markers were used to saturate chromosome arm 2BL in both RIL populations. SrH mapped between markers cim109 and cim114 at a distance of 0.9 cM proximal, and cim117 at 2.9 cM distal. SrY was flanked by markers cim109 and cim116 at 0.8 cM proximal, and IWB45932 at 1.9 cM distal. Two Ug99-effective stem rust resistance genes derived from bread wheat, Sr9h and Sr28, have been reported on chromosome arm 2BL. Infection types and map position in Huhwa and Yaye indicated that Sr28 was absent in both the parents. However, susceptible reactions produced by resistant lines from both populations against Sr9h-virulent race TTKSF+ confirmed the presence of a common resistance locus Sr9h in both lines. Test of allelism is required to establish genetic relationships between genes identified in present study and Sr9h. Marker cim117 linked to SrH was genotyped on set of wheat lines with Huhwa in the pedigree and is advised to be used for marker assisted selection for this gene, however, a combination of phenotypic and genotypic assays is desirable for both genes especially for selection of Sr9h in breeding programs.
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Affiliation(s)
| | - Ravi P. Singh
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | | | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | | | - Matthew N. Rouse
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, United States
| | - Jayaveeramuthu Nirmala
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, United States
| | - Maricarmen Sandoval-Sanchez
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
- Colegio de Postgraduados, Texcoco, Mexico
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