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Rivera-Burgos L, VanGessel C, Guedira M, Smith J, Marshall D, Jin Y, Rouse M, Brown-Guedira G. Fine mapping of stem rust resistance derived from soft red winter wheat cultivar AGS2000 to an NLR gene cluster on chromosome 6D. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:206. [PMID: 39158718 PMCID: PMC11333525 DOI: 10.1007/s00122-024-04702-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 07/27/2024] [Indexed: 08/20/2024]
Abstract
The Puccinia graminis f. sp. tritici (Pgt) Ug99-emerging virulent races present a major challenge to global wheat production. To meet present and future needs, new sources of resistance must be found. Identification of markers that allow tracking of resistance genes is needed for deployment strategies to combat highly virulent pathogen races. Field evaluation of a DH population located a QTL for stem rust (Sr) resistance, QSr.nc-6D from the breeding line MD01W28-08-11 to the distal region of chromosome arm 6DS where Sr resistance genes Sr42, SrCad, and SrTmp have been identified. A locus for seedling resistance to Pgt race TTKSK was identified in a DH population and an RIL population derived from the cross AGS2000 × LA95135. The resistant cultivar AGS2000 is in the pedigree of MD01W28-08-11 and our results suggest that it is the source of Sr resistance in this breeding line. We exploited published markers and exome capture data to enrich marker density in a 10 Mb region flanking QSr.nc-6D. Our fine mapping in heterozygous inbred families identified three markers co-segregating with resistance and delimited QSr.nc-6D to a 1.3 Mb region. We further exploited information from other genome assemblies and identified collinear regions of 6DS harboring clusters of NLR genes. Evaluation of KASP assays corresponding to our co-segregating SNP suggests that they can be used to track this Sr resistance in breeding programs. However, our results also underscore the challenges posed in identifying genes underlying resistance in such complex regions in the absence of genome sequence from the resistant genotypes.
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Affiliation(s)
- L Rivera-Burgos
- Plant Science Research Unit, USDA-ARS, North Carolina State University, Raleigh, NC, 27695, USA
| | - C VanGessel
- Department of Crop and Soil Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - M Guedira
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - J Smith
- Plant Science Research Unit, USDA-ARS, North Carolina State University, Raleigh, NC, 27695, USA
| | - D Marshall
- Plant Science Research Unit, USDA-ARS, North Carolina State University, Raleigh, NC, 27695, USA
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Y Jin
- Cereal Disease Laboratory, USDA-ARS, University of Minnesota, St. Paul, MN, 55108, USA
| | - M Rouse
- Cereal Disease Laboratory, USDA-ARS, University of Minnesota, St. Paul, MN, 55108, USA
- Sugarcane Production Research Unit, USDA-ARS, Canal Point, FL, 33438, USA
| | - G Brown-Guedira
- Plant Science Research Unit, USDA-ARS, North Carolina State University, Raleigh, NC, 27695, USA.
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
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Mandal R, He X, Singh G, Kabir MR, Joshi AK, Singh PK. Screening of CIMMYT and South Asian Bread Wheat Germplasm Reveals Marker-Trait Associations for Seedling Resistance to Septoria Nodorum Blotch. Genes (Basel) 2024; 15:890. [PMID: 39062669 PMCID: PMC11276481 DOI: 10.3390/genes15070890] [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: 06/14/2024] [Revised: 07/02/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
Wheat (Triticum aestivum L.) production is adversely impacted by Septoria nodorum blotch (SNB), a fungal disease caused by Parastagonospora nodorum. Wheat breeders are constantly up against this biotic challenge as they try to create resistant cultivars. The genome-wide association study (GWAS) has become an efficient tool for identifying molecular markers linked with SNB resistance. This technique is used to acquire an understanding of the genetic basis of resistance and to facilitate marker-assisted selection. In the current study, a total of 174 bread wheat accessions from South Asia and CIMMYT were assessed for SNB reactions at the seedling stage in three greenhouse experiments at CIMMYT, Mexico. The results indicated that 129 genotypes were resistant to SNB, 39 were moderately resistant, and only 6 were moderately susceptible. The Genotyping Illumina Infinium 15K Bead Chip was used, and 11,184 SNP markers were utilized to identify marker-trait associations (MTAs) after filtering. Multiple tests confirmed the existence of significant MTAs on chromosomes 5B, 5A, and 3D, and the ones at Tsn1 on 5B were the most stable and conferred the highest phenotypic variation. The resistant genotypes identified in this study could be cultivated in South Asian countries as a preventative measure against the spread of SNB. This work also identified molecular markers of SNB resistance that could be used in future wheat breeding projects.
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Affiliation(s)
- Rupsanatan Mandal
- Visiting Scientist, International Maize and Wheat Improvement Center (CIMMYT), Texcoco 56237, Mexico;
- Department of Genetics and Plant Breeding, Uttar Banga Krishi Viswavidyalaya, Cooch Behar 736165, India
| | - Xinyao He
- International Maize and Wheat Improvement Centre, Texcoco 56237, Mexico;
| | - Gyanendra Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India;
| | | | - Arun Kumar Joshi
- International Maize and Wheat Improvement Center (CIMMYT)-India Office, New Delhi 110012, India;
- Borlaug Institute for South Asia, New Delhi 110012, India
| | - Pawan Kumar Singh
- International Maize and Wheat Improvement Centre, Texcoco 56237, Mexico;
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Binalf L, Shifa H, Tadesse W. Association mapping of septoria tritici blotch resistance in bread wheat in Bale and Arsi highlands, Ethiopia. Heliyon 2024; 10:e32265. [PMID: 38912495 PMCID: PMC11190591 DOI: 10.1016/j.heliyon.2024.e32265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/25/2024] Open
Abstract
Septoria tritici blotch (STB) caused by the fungal pathogen Zymoseptoria tritici, anamorph Septoria tritici Rob. ex Desm., is an important wheat pathogen worldwide, reported to be major wheat production threating factor, posing considerable yield loss every year. Developing resistant cultivars is an efficient, economical, environmentally friendly and simple approach for managing STB. This study was carried out to evaluate spring bread wheat lines for their reaction to STB disease under field conditions; to associate phenotypic and genotypic data for identification of STB disease resistance; and to identify genomic region(s) associated with resistance to STB in spring bread wheat lines. Two hundred forty (240) spring bread wheat lines were evaluated under field conditions in non-replicated trials, using an augmented design. The trials were conducted at three locations (Kulumsa Agricultural Research Center, Madda Walabu University Research Site and Sinana Agricultural Research Center) in 2017 main cropping season (July to December). Out of these 240 wheat lines, 123 of them were genotyped with 10263 single nucleotide polymorphism (SNPs) markers and population structure and association mapping analysis was done. The wheat lines showed significant variations in percentage disease severity and area under the disease progress curve at all the three locations they were evaluated. The wheat lines were classified as resistant, moderately resistant, moderately susceptible and susceptible based on the percentage disease severity scored. Five wheat lines were found to be resistant to STB in all the three locations and are recommended for direct release by the national program and parentage purposes in wheat breeding programs. The 123 wheat lines were clustered into 3 subpopulations in which the first cluster contained 99 wheat lines; the second 17 and the last one 7. Among the polymorphic 8127 SNPs markers, 26 markers on chromosomes 7B, 1D, 3A, 2B, 6B and 3D were found to be significantly (P < 0.001) associated with STB resistance so that they can be utilized for marker assisted selection and gene pyramiding in resistance breeding programs.
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Affiliation(s)
- Lakachew Binalf
- Department of Plant Science, College of Agriculture and Environmental Science, Debark University, Debark, Ethiopia
| | - Hassen Shifa
- Department of Plant Science, College of Agriculture and Natural Resources, Madda Walabu University, Bale Robe, Ethiopia
| | - Wuletaw Tadesse
- International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut, Lebanon
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Edae EA, Kosgey Z, Bajgain P, Ndung'u KC, Gemechu A, Bhavani S, Anderson JA, Rouse MN. The genetics of Ug99 stem rust resistance in spring wheat variety 'Linkert'. FRONTIERS IN PLANT SCIENCE 2024; 15:1343148. [PMID: 38516672 PMCID: PMC10954791 DOI: 10.3389/fpls.2024.1343148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/12/2024] [Indexed: 03/23/2024]
Abstract
Wheat stem rust caused by Puccinia graminis f. sp. tritici (Pgt) threatens wheat production worldwide. The objective of this study was to characterize wheat stem rust resistance in 'Linkert', a variety with adult plant resistance effective to emerging wheat stem rust pathogen strain Ug99. Two doubled haploid (DH) populations and one recombinant inbred line (RIL) population were developed with 'Linkert' as a stem rust resistant parent. Hard red spring wheat variety 'Forefront' and genetic stock 'LMPG' were used as stem rust susceptible parents of the DH populations. Breeding line 'MN07098-6' was used as a susceptible parent of the RIL population. Both DH and RIL populations with their parents were evaluated both at the seedling stage and in the field against Pgt races. Genotyping data of the DH populations were generated using the wheat iSelect 90k SNP assay. The RIL population was genotyped by genotyping-by-sequencing. We found QTL consistently associated with wheat stem rust resistance on chromosome 2BS for the Linkert/Forefront DH population and the Linkert/MN07098-6 RIL population both in Ethiopia and Kenya. Additional reliable QTL were detected on chromosomes 5BL (125.91 cM) and 4AL (Sr7a) for the Linkert/LMPG population in Ethiopia and Kenya. Different QTL identified in the populations reflect the importance of examining the genetics of resistance in populations derived from adapted germplasm (Forefront and MN07098-6) in addition to a genetic stock (LMPG). The associated markers in this study could be used to track and select for the identified QTL in wheat breeding programs.
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Affiliation(s)
- Erena A. Edae
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Zennah Kosgey
- Kenya Agricultural and Livestock Research Organization (KALRO), Food Crops Research Centre, Njoro, Kenya
| | - Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
| | - Kimani C. Ndung'u
- Kenya Agricultural and Livestock Research Organization (KALRO), Food Crops Research Centre, Njoro, Kenya
| | - Ashenafi Gemechu
- Ethiopian Institute of Agriculture, Debre Zeit Agricultural Research Center, Bishoftu, Ethiopia
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - James A. Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
| | - 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
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Yazdani M, Rouse MN, Steffenson BJ, Bajgain P, Patpour M, Johansson E, Rahmatov M. Developing adapted wheat lines with broad-spectrum resistance to stem rust: Introgression of Sr59 through backcrossing and selections based on genotyping-by-sequencing data. PLoS One 2023; 18:e0292724. [PMID: 37824577 PMCID: PMC10569509 DOI: 10.1371/journal.pone.0292724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023] Open
Abstract
Control of stem rust, caused by Puccinia graminis f.sp. tritici, a highly destructive fungal disease of wheat, faces continuous challenges from emergence of new virulent races across wheat-growing continents. Using combinations of broad-spectrum resistance genes could impart durable stem rust resistance. This study attempted transfer of Sr59 resistance gene from line TA5094 (developed through CSph1bM-induced T2DS·2RL Robertsonian translocation conferring broad-spectrum resistance). Poor agronomic performance of line TA5094 necessitates Sr59 transfer to adapted genetic backgrounds and utility evaluations for wheat improvement. Based on combined stem rust seedling and molecular analyses, 2070 BC1F1 and 1230 BC2F1 plants were derived from backcrossing BAJ#1, KACHU#1, and REEDLING#1 with TA5094. Genotyping-by-sequencing (GBS) results revealed the physical positions of 15,116 SNPs on chromosome 2R. The adapted genotypes used for backcrossing were found not to possess broad-spectrum resistance to selected stem rust races, whereas Sr59-containing line TA5094 showed resistance to all races tested. Stem rust seedling assays combined with kompetitive allele-specific PCR (KASP) marker analysis successfully selected and generated the BC2F2 population, which contained the Sr59 gene, as confirmed by GBS. Early-generation data from backcrossing suggested deviations from the 3:1 segregation, suggesting that multiple genes may contribute to Sr59 resistance reactions. Using GBS marker data (40,584 SNPs in wheat chromosomes) to transfer the recurrent parent background to later-generation populations resulted in average genome recovery of 71.2% in BAJ#1*2/TA5094, 69.8% in KACHU#1*2/TA5094, and 70.5% in REEDLING#1*2/TA5094 populations. GBS data verified stable Sr59 introgression in BC2F2 populations, as evidenced by presence of the Ph1 locus and absence of the 50,936,209 bp deletion in CSph1bM. Combining phenotypic selections, stem rust seedling assays, KASP markers, and GBS data substantially accelerated transfer of broad-spectrum resistance into adapted genotypes. Thus, this study demonstrated that the Sr59 resistance gene can be introduced into elite genetic backgrounds to mitigate stem rust-related yield losses.
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Affiliation(s)
- Mahboobeh Yazdani
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Matthew N. Rouse
- United States Department of Agriculture, Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN, United States of America
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States of America
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States of America
| | - Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States of America
| | - Mehran Patpour
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Mahbubjon Rahmatov
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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Guo F, Ye Y, Zhu K, Lin S, Wang Y, Dong Z, Yao R, Li H, Wang W, Liao Z, Guo B, Yan X. Genetic Diversity, Population Structure, and Environmental Adaptation Signatures of Chinese Coastal Hard-Shell Mussel Mytilus coruscus Revealed by Whole-Genome Sequencing. Int J Mol Sci 2023; 24:13641. [PMID: 37686445 PMCID: PMC10488143 DOI: 10.3390/ijms241713641] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
The hard-shell mussel (Mytilus coruscus) is widespread in the temperate coastal areas of the northwest Pacific and holds a significant position in the shellfish aquaculture market in China. However, the natural resources of this species have been declining, and population genetic studies of M. coruscus are also lacking. In this study, we conducted whole-genome resequencing (WGR) of M. coruscus from eight different latitudes along the Chinese coast and identified a total of 25,859,986 single nucleotide polymorphism (SNP) markers. Our findings indicated that the genetic diversity of M. coruscus from the Zhoushan region was lower compared with populations from other regions. Furthermore, we observed that the evolutionary tree clustered into two primary branches, and the Zhangzhou (ZZ) population was in a separate branch. The ZZ population was partly isolated from populations in other regions, but the distribution of branches was not geographically homogeneous, and a nested pattern emerged, consistent with the population differentiation index (FST) results. To investigate the selection characteristics, we utilized the northern M. coruscus populations (Dalian and Qingdao) and the central populations (Zhoushan and Xiangshan) as reference populations and the southern ZZ population as the target population. Our selection scan analysis identified several genes associated with thermal responses, including Hsp70 and CYP450. These genes may play important roles in the adaptation of M. coruscus to different living environments. Overall, our study provides a comprehensive understanding of the genomic diversity of coastal M. coruscus in China and is a valuable resource for future studies on genetic breeding and the evolutionary adaptation of this species.
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Affiliation(s)
- Feng Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
| | - Kecheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China;
| | - Shuangrui Lin
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
| | - Yuxia Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Zhenyu Dong
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Ronghui Yao
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Hongfei Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
| | - Weifeng Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Zhi Liao
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Baoying Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Xiaojun Yan
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
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Megerssa SH, Ammar K, Acevedo M, Bergstrom GC, Dreisigacker S, Randhawa M, Brown-Guedira G, Ward B, Sorrells ME. QTL mapping of seedling and field resistance to stem rust in DAKIYE/Reichenbachii durum wheat population. PLoS One 2022; 17:e0273993. [PMID: 36201474 PMCID: PMC9536579 DOI: 10.1371/journal.pone.0273993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 08/19/2022] [Indexed: 11/18/2022] Open
Abstract
Stem rust caused by the fungus Puccinia graminis f.sp. tritici Eriks. & E. Henn. (Pgt) threatens the global production of both durum wheat (Triticum turgidum L. ssp. durum (Desf.) Husnot) and common wheat (Triticum aestivum L.). The objective of this study was to evaluate a durum wheat recombinant inbred line (RIL) population from a cross between a susceptible parent 'DAKIYE' and a resistant parent 'Reichenbachii' developed by the International Center for the Improvement of Maize and Wheat (CIMMYT) 1) for seedling response to races JRCQC and TTRTF and 2) for field response to a bulk of the current Pgt races prevalent in Ethiopia and Kenya and 3) to map loci associated with seedling and field resistances in this population. A total of 224 RILs along with their parents were evaluated at the seedling stage in the Ethiopian Institute for Agricultural Research greenhouse at Debre Zeit, Ethiopia and in the EIAR and KALRO fields in Ethiopia and Kenya, for two seasons from 2019 to 2020. The lines were genotyped using the genotyping-by-sequencing approach. A total of 843 single nucleotide polymorphism markers for 175 lines were used for quantitative trait locus (QTL) analyses. Composite interval mapping (CIM) identified three QTL on chromosomes 3B, 4B and 7B contributed by the resistant parent. The QTL on chromosome 3B was identified at all growth stages and it explained 11.8%, 6.5%, 6.4% and 15.3% of the phenotypic variation for responses to races JRCQC, TTRTF and in the field trials ETMS19 and KNMS19, respectively. The power to identify additional QTL in this population was limited by the number of high-quality markers, since several markers with segregation distortion were eliminated. A cytological study is needed to understand the presence of chromosomal rearrangements. Future evaluations of additional durum lines and RIL families identification of durable adult plant resistance sources is crucial for breeding stem rust resistance in durum wheat in the future.
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Affiliation(s)
- Shitaye Homma Megerssa
- Ethiopian Institute of Agricultural (EIAR), Addis Ababa, Ethiopia
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States of America
- * E-mail:
| | - 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 of America
| | - Gary Carlton Bergstrom
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY, United States of America
| | | | - Mandeep Randhawa
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | | | - Brian Ward
- USDA-ARS Plant Science Unit, Raleigh, NC, United States of America
| | - Mark Earl Sorrells
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States of America
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Prather S, Schneider T, Gaham Godoy J, Odubiyi S, Bosque-Perez NA, Rashed A, Rynearson S, Pumphrey MO. Reliable DNA Markers for a Previously Unidentified, Yet Broadly Deployed Hessian Fly Resistance Gene on Chromosome 6B in Pacific Northwest Spring Wheat Varieties. FRONTIERS IN PLANT SCIENCE 2022; 13:779096. [PMID: 35769296 PMCID: PMC9234662 DOI: 10.3389/fpls.2022.779096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Hessian fly [Mayetiola destructor (Say)] is a major pest of wheat (Triticum aestivum L.) throughout the United States and in several other countries. A highly effective and economically feasible way to control Hessian fly is with resistant cultivars. To date, over 37 Hessian fly resistance genes have been discovered and their approximate locations mapped. Resistance breeding is still limited, though, by the genes' effectiveness against predominant Hessian fly biotypes in a given production area, genetic markers that are developed for low-throughput marker systems, poorly adapted donor germplasm, and/or the inadequacy of closely linked DNA markers to track effective resistance genes in diverse genetic backgrounds. The purposes of this study were to determine the location of the Hessian fly resistance gene in the cultivar "Kelse" (PI 653842) and to develop and validate Kompetitive Allele Specific PCR (KASP) markers for the resistance locus. A mapping population was genotyped and screened for Hessian fly resistance. The resulting linkage map created from 2,089 Single Nucleotide Polymorphism SNP markers placed the resistance locus on the chromosome 6B short arm, near where H34 has been reported. Three flanking SNPs near the resistance locus were converted to KASP assays which were then validated by fine-mapping and testing a large panel of breeding lines from hard and soft wheat germplasm adapted to the Pacific Northwest. The KASP markers presented here are tightly linked to the resistance locus and can be used for marker-assisted selection by breeders working on Hessian fly resistance and allow confirmation of this Hessian fly resistance gene in diverse germplasm.
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Affiliation(s)
- Samuel Prather
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Tavin Schneider
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Jayfred Gaham Godoy
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
- InterGrain Pty Ltd., Food Production, Bibra Lake, WA, Australia
| | - Steven Odubiyi
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID, United States
| | - Nilsa A. Bosque-Perez
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID, United States
| | - Arash Rashed
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID, United States
| | - Sheri Rynearson
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Michael O. Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
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Gaur A, Jindal Y, Singh V, Tiwari R, Kumar D, Kaushik D, Singh J, Narwal S, Jaiswal S, Iquebal MA, Angadi UB, Singh G, Rai A, Singh GP, Sheoran S. GWAS to Identify Novel QTNs for WSCs Accumulation in Wheat Peduncle Under Different Water Regimes. FRONTIERS IN PLANT SCIENCE 2022; 13:825687. [PMID: 35310635 PMCID: PMC8928439 DOI: 10.3389/fpls.2022.825687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/27/2022] [Indexed: 05/27/2023]
Abstract
Water-soluble carbohydrates (WSCs) play a vital role in water stress avoidance and buffering wheat grain yield. However, the genetic architecture of stem WSCs' accumulation is partially understood, and few candidate genes are known. This study utilizes the compressed mixed linear model-based genome wide association study (GWAS) and heuristic post GWAS analyses to identify causative quantitative trait nucleotides (QTNs) and candidate genes for stem WSCs' content at 15 days after anthesis under different water regimes (irrigated, rainfed, and drought). Glucose, fructose, sucrose, fructans, total non-structural carbohydrates (the sum of individual sugars), total WSCs (anthrone based) quantified in the peduncle of 301 bread wheat genotypes under multiple environments (E01-E08) pertaining different water regimes, and 14,571 SNPs from "35K Axiom Wheat Breeders" Array were used for analysis. As a result, 570 significant nucleotide trait associations were identified on all chromosomes except for 4D, of which 163 were considered stable. A total of 112 quantitative trait nucleotide regions (QNRs) were identified of which 47 were presumable novel. QNRs qWSC-3B.2 and qWSC-7A.2 were identified as the hotspots. Post GWAS integration of multiple data resources prioritized 208 putative candidate genes delimited into 64 QNRs, which can be critical in understanding the genetic architecture of stem WSCs accumulation in wheat under optimum and water-stressed environments. At least 19 stable QTNs were found associated with 24 prioritized candidate genes. Clusters of fructans metabolic genes reported in the QNRs qWSC-4A.2 and qWSC-7A.2. These genes can be utilized to bring an optimum combination of various fructans metabolic genes to improve the accumulation and remobilization of stem WSCs and water stress tolerance. These results will further strengthen wheat breeding programs targeting sustainable wheat production under limited water conditions.
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Affiliation(s)
- Arpit Gaur
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar, India
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Yogesh Jindal
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar, India
| | - Vikram Singh
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar, India
| | - Ratan Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Dinesh Kumar
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Deepak Kaushik
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar, India
| | - Jogendra Singh
- ICAR-Central Soil Salinity Research Institute, Karnal, India
| | - Sneh Narwal
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sarika Jaiswal
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ulavapp B. Angadi
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Gyanendra Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Sonia Sheoran
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
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10
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Saini DK, Chopra Y, Singh J, Sandhu KS, Kumar A, Bazzer S, Srivastava P. Comprehensive evaluation of mapping complex traits in wheat using genome-wide association studies. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:1. [PMID: 37309486 PMCID: PMC10248672 DOI: 10.1007/s11032-021-01272-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Genome-wide association studies (GWAS) are effectively applied to detect the marker trait associations (MTAs) using whole genome-wide variants for complex quantitative traits in different crop species. GWAS has been applied in wheat for different quality, biotic and abiotic stresses, and agronomic and yield-related traits. Predictions for marker-trait associations are controlled with the development of better statistical models taking population structure and familial relatedness into account. In this review, we have provided a detailed overview of the importance of association mapping, population design, high-throughput genotyping and phenotyping platforms, advancements in statistical models and multiple threshold comparisons, and recent GWA studies conducted in wheat. The information about MTAs utilized for gene characterization and adopted in breeding programs is also provided. In the literature that we surveyed, as many as 86,122 wheat lines have been studied under various GWA studies reporting 46,940 loci. However, further utilization of these is largely limited. The future breakthroughs in area of genomic selection, multi-omics-based approaches, machine, and deep learning models in wheat breeding after exploring the complex genetic structure with the GWAS are also discussed. This is a most comprehensive study of a large number of reports on wheat GWAS and gives a comparison and timeline of technological developments in this area. This will be useful to new researchers or groups who wish to invest in GWAS.
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Affiliation(s)
- Dinesh K. Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - Yuvraj Chopra
- College of Agriculture, Punjab Agricultural University, Ludhiana, 141004 India
| | - Jagmohan Singh
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Karansher S. Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163 USA
| | - Anand Kumar
- Department of Genetics and Plant Breeding, Chandra Shekhar Azad University of Agriculture and Technology, Kanpur, 202002 India
| | - Sumandeep Bazzer
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
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11
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Zatybekov A, Genievskaya Y, Rsaliyev A, Maulenbay A, Yskakova G, Savin T, Turuspekov Y, Abugalieva S. Identification of Quantitative Trait Loci for Leaf Rust and Stem Rust Seedling Resistance in Bread Wheat Using a Genome-Wide Association Study. PLANTS (BASEL, SWITZERLAND) 2021; 11:plants11010074. [PMID: 35009078 PMCID: PMC8747073 DOI: 10.3390/plants11010074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 05/22/2023]
Abstract
In recent years, leaf rust (LR) and stem rust (SR) have become a serious threat to bread wheat production in Kazakhstan. Most local cultivars are susceptible to these rusts, which has affected their yield and quality. The development of new cultivars with high productivity and LR and SR disease resistance, including using marker-assisted selection, is becoming an important priority in local breeding projects. Therefore, the search for key genetic factors controlling resistance in all plant stages, including the seedling stage, is of great significance. In this work, we applied a genome-wide association study (GWAS) approach using 212 local bread wheat accessions that were phenotyped for resistance to specific races of Puccinia triticina Eriks. (Pt) and Puccinia graminis f. sp. tritici (Pgt) at the seedling stages. The collection was genotyped using a 20 K Illumina iSelect SNP assay, and 11,150 polymorphic SNP markers were selected for the association mapping. Using a mixed linear model, we identified 11 quantitative trait loci (QTLs) for five out of six specific races of Pt and Pgt. The comparison of the results from this GWAS with those from previously published work showed that nine out of eleven QTLs for LR and SR resistance had been previously reported in a GWAS study at the adult plant stages of wheat growth. Therefore, it was assumed that these nine common identified QTLs were effective for all-stage resistance to LR and SR, and the two other QTLs appear to be novel QTLs. In addition, five out of these nine QTLs that had been identified earlier were found to be associated with yield components, suggesting that they may directly influence the field performance of bread wheat. The identified QTLs, including novel QTLs found in this study, may play an essential role in the breeding process for improving wheat resistance to LR and SR.
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Affiliation(s)
- Alibek Zatybekov
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.Z.); (Y.G.); (Y.T.)
| | - Yuliya Genievskaya
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.Z.); (Y.G.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050038, Kazakhstan
| | - Aralbek Rsaliyev
- Laboratory of Phytosanitary Safety, Research Institute of Biological Safety Problems, Gvardeisky 080409, Kazakhstan; (A.R.); (A.M.); (G.Y.)
| | - Akerke Maulenbay
- Laboratory of Phytosanitary Safety, Research Institute of Biological Safety Problems, Gvardeisky 080409, Kazakhstan; (A.R.); (A.M.); (G.Y.)
| | - Gulbahar Yskakova
- Laboratory of Phytosanitary Safety, Research Institute of Biological Safety Problems, Gvardeisky 080409, Kazakhstan; (A.R.); (A.M.); (G.Y.)
| | - Timur Savin
- Department of Science, S. Seifullin Kazakh Agro Technical University, Nur-Sultan 010011, Kazakhstan;
| | - Yerlan Turuspekov
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.Z.); (Y.G.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050038, Kazakhstan
| | - Saule Abugalieva
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.Z.); (Y.G.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050038, Kazakhstan
- Correspondence:
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12
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Francki MG, Stainer GS, Walker E, Rebetzke GJ, Stefanova KT, French RJ. Phenotypic Evaluation and Genetic Analysis of Seedling Emergence in a Global Collection of Wheat Genotypes ( Triticum aestivum L.) Under Limited Water Availability. FRONTIERS IN PLANT SCIENCE 2021; 12:796176. [PMID: 35003185 PMCID: PMC8739788 DOI: 10.3389/fpls.2021.796176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
The challenge in establishing an early-sown wheat crop in southern Australia is the need for consistently high seedling emergence when sowing deep in subsoil moisture (>10 cm) or into dry top-soil (4 cm). However, the latter is strongly reliant on a minimum soil water availability to ensure successful seedling emergence. This study aimed to: (1) evaluate 233 Australian and selected international wheat genotypes for consistently high seedling emergence under limited soil water availability when sown in 4 cm of top-soil in field and glasshouse (GH) studies; (2) ascertain genetic loci associated with phenotypic variation using a genome-wide association study (GWAS); and (3) compare across loci for traits controlling coleoptile characteristics, germination, dormancy, and pre-harvest sprouting. Despite significant (P < 0.001) environment and genotype-by-environment interactions within and between field and GH experiments, eight genotypes that included five cultivars, two landraces, and one inbred line had consistently high seedling emergence (mean value > 85%) across nine environments. Moreover, 21 environment-specific quantitative trait loci (QTL) were detected in GWAS analysis on chromosomes 1B, 1D, 2B, 3A, 3B, 4A, 4B, 5B, 5D, and 7D, indicating complex genetic inheritance controlling seedling emergence. We aligned QTL for known traits and individual genes onto the reference genome of wheat and identified 16 QTL for seedling emergence in linkage disequilibrium with coleoptile length, width, and cross-sectional area, pre-harvest sprouting and dormancy, germination, seed longevity, and anthocyanin development. Therefore, it appears that seedling emergence is controlled by multifaceted networks of interrelated genes and traits regulated by different environmental cues.
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Affiliation(s)
- Michael G. Francki
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Grantley S. Stainer
- Department of Primary Industries and Regional Development, Merredin, WA, Australia
| | - Esther Walker
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Gregory J. Rebetzke
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Katia T. Stefanova
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Robert J. French
- Department of Primary Industries and Regional Development, Merredin, WA, Australia
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13
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Gordon T, Jin Y, Gale S, Rouse M, Stoxen S, Wanyera R, Macharia G, Randhawa M, Bhavani S, Brown-Guedira G, Marshall D, Babiker E, Bockelman H, Bonman JM. Identification of Winter Habit Bread Wheat Landraces in the National Small Grains Collection with Resistance to Emerging Stem Rust Pathogen Variants. PLANT DISEASE 2021; 105:3998-4005. [PMID: 34232053 DOI: 10.1094/pdis-04-21-0743-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Wheat stem rust caused by Puccinia graminis f. sp. tritici is a widespread and recurring threat to wheat production. Emerging P. graminis f. sp. tritici variants are rapidly overcoming major gene resistance deployed in wheat cultivars and new sources of race-nonspecific resistance are urgently needed. The National Small Grains Collection (NSGC) contains thousands of wheat landrace accessions that may harbor unique and broadly effective sources of resistance to emerging P. graminis f. sp. tritici variants. All NSGC available facultative and winter-habit bread wheat landraces were tested in a field nursery in St. Paul, Minnesota, against a bulk collection of six common U.S. P. graminis f. sp. tritici races. Infection response and severity data were collected on 9,192 landrace accessions at the soft-dough stage and resistant accessions were derived from single spikes. Derived accessions were tested in St. Paul a second time to confirm resistance and in a field nursery in Njoro, Kenya against emerging races of P. graminis f. sp. tritici with virulence to many known resistance genes including Sr24, Sr31, Sr38, and SrTmp. Accessions resistant in the St. Paul field were also tested at the seedling stage with up to 13 P. graminis f. sp. tritici races, including TTKSK and TKTTF, and with 19 molecular markers linked with known stem rust resistance genes or genes associated with modern breeding practices. Forty-five accessions were resistant in both U.S. and Kenya field nurseries and lacked alleles linked with known stem rust resistance genes. Accessions with either moderate or strong resistance in the U.S. and Kenya field nurseries and with novel seedling resistance will be prioritized for further study.
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Affiliation(s)
- Tyler Gordon
- U.S. Department of Agriculture, Agricultural Research Service, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210, U.S.A
| | - Yue Jin
- U.S. Department of Agriculture, Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108, U.S.A
| | - Samuel Gale
- U.S. Department of Agriculture, Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108, U.S.A
| | - Matthew Rouse
- U.S. Department of Agriculture, Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108, U.S.A
| | - Samuel Stoxen
- U.S. Department of Agriculture, Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108, U.S.A
| | - Ruth Wanyera
- Kenya Agricultural and Livestock Research Organization, 20107 Njoro, Kenya
| | - Godwin Macharia
- Kenya Agricultural and Livestock Research Organization, 20107 Njoro, Kenya
| | - Mandeep Randhawa
- International Maize and Wheat Improvement Center-Kenya, 1041-00621 Nairobi, Kenya
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center, El Batán, Texcoco CP 56237, Edo. de México, Mexico
| | - Gina Brown-Guedira
- U.S. Department of Agriculture, Agricultural Research Service, Plant Science Research, Raleigh, NC 27695, U.S.A
| | - David Marshall
- U.S. Department of Agriculture, Agricultural Research Service, Plant Science Research, Raleigh, NC 27695, U.S.A
| | - Ebrahiem Babiker
- U.S. Department of Agriculture, Agricultural Research Service, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210, U.S.A
- U.S. Department of Agriculture, Agricultural Research Service, Southern Horticultural Research Laboratory, Poplarville, MS 39470, U.S.A
| | - Harold Bockelman
- U.S. Department of Agriculture, Agricultural Research Service, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210, U.S.A
| | - J Michael Bonman
- U.S. Department of Agriculture, Agricultural Research Service, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210, U.S.A
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14
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Eltaher S, Mourad AMI, Baenziger PS, Wegulo S, Belamkar V, Sallam A. Identification and Validation of High LD Hotspot Genomic Regions Harboring Stem Rust Resistant Genes on 1B, 2A ( Sr38), and 7B Chromosomes in Wheat. Front Genet 2021; 12:749675. [PMID: 34659366 PMCID: PMC8517078 DOI: 10.3389/fgene.2021.749675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/13/2021] [Indexed: 12/02/2022] Open
Abstract
Stem rust caused by Puccinia graminis f. sp. tritici Eriks. is an important disease of common wheat globally. The production and cultivation of genetically resistant cultivars are one of the most successful and environmentally friendly ways to protect wheat against fungal pathogens. Seedling screening and genome-wide association study (GWAS) were used to determine the genetic diversity of wheat genotypes obtained on stem rust resistance loci. At the seedling stage, the reaction of the common stem rust race QFCSC in Nebraska was measured in a set of 212 genotypes from F3:6 lines. The results indicated that 184 genotypes (86.8%) had different degrees of resistance to this common race. While 28 genotypes (13.2%) were susceptible to stem rust. A set of 11,911 single-nucleotide polymorphism (SNP) markers was used to perform GWAS which detected 84 significant marker-trait associations (MTAs) with SNPs located on chromosomes 1B, 2A, 2B, 7B and an unknown chromosome. Promising high linkage disequilibrium (LD) genomic regions were found in all chromosomes except 2B which suggested they include candidate genes controlling stem rust resistance. Highly significant LD was found among these 59 significant SNPs on chromosome 2A and 12 significant SNPs with an unknown chromosomal position. The LD analysis between SNPs located on 2A and Sr38 gene reveal high significant LD genomic regions which was previously reported. To select the most promising stem rust resistant genotypes, a new approach was suggested based on four criteria including, phenotypic selection, number of resistant allele(s), the genetic distance among the selected parents, and number of the different resistant allele(s) in the candidate crosses. As a result, 23 genotypes were considered as the most suitable parents for crossing to produce highly resistant stem rust genotypes against the QFCSC.
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Affiliation(s)
- Shamseldeen Eltaher
- Department of Plant Biotechnology, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City (USC), Sadat, Egypt
| | - Amira M I Mourad
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - P Stephen Baenziger
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Stephen Wegulo
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Vikas Belamkar
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Ahmed Sallam
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, Egypt
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15
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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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16
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Pradhan AK, Kumar S, Singh AK, Budhlakoti N, Mishra DC, Chauhan D, Mittal S, Grover M, Kumar S, Gangwar OP, Kumar S, Gupta A, Bhardwaj SC, Rai A, Singh K. Identification of QTLs/Defense Genes Effective at Seedling Stage Against Prevailing Races of Wheat Stripe Rust in India. Front Genet 2020; 11:572975. [PMID: 33329711 PMCID: PMC7728992 DOI: 10.3389/fgene.2020.572975] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/30/2020] [Indexed: 01/06/2023] Open
Abstract
Resistance in modern wheat cultivars for stripe rust is not long lasting due to the narrow genetic base and periodical evolution of new pathogenic races. Though nearly 83 Yr genes conferring resistance to stripe rust have been cataloged so far, few of them have been mapped and utilized in breeding programs. Characterization of wheat germplasm for novel sources of resistance and their incorporation into elite cultivars is required to achieve durable resistance and thus to minimize the yield losses. Here, a genome-wide association study (GWAS) was performed on a set of 391 germplasm lines with the aim to identify quantitative trait loci (QTL) using 35K Axiom® array. Phenotypic evaluation disease severity against four stripe rust pathotypes, i.e., 46S119, 110S119, 238S119, and 47S103 (T) at the seedling stage in a greenhouse providing optimal conditions was carried out consecutively for 2 years (2018 and 2019 winter season). We identified, a total of 17 promising QTl which passed FDR criteria. Moreover these 17 QTL identified in the current study were mapped at different genomic locations i.e. 1B, 2A, 2B, 2D, 3A, 3B, 3D, 4B, 5B and 6B. These 17 QTLs identified in the present study might play a key role in marker-assisted breeding for developing stripe rust resistant wheat cultivars.
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Affiliation(s)
- Anjan Kumar Pradhan
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sundeep Kumar
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Amit Kumar Singh
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Neeraj Budhlakoti
- Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dwijesh C Mishra
- Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Divya Chauhan
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Shikha Mittal
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Monendra Grover
- Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Suneel Kumar
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Om P Gangwar
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Subodh Kumar
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Arun Gupta
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Subhash C Bhardwaj
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Anil Rai
- Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Kuldeep Singh
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
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17
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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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Genievskaya Y, Turuspekov Y, Rsaliyev A, Abugalieva S. Genome-wide association mapping for resistance to leaf, stem, and yellow rusts of common wheat under field conditions of South Kazakhstan. PeerJ 2020; 8:e9820. [PMID: 32944423 PMCID: PMC7469934 DOI: 10.7717/peerj.9820] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/05/2020] [Indexed: 11/20/2022] Open
Abstract
Common or bread wheat (Triticum aestivum L.) is the most important cereal crop in the world, including Kazakhstan, where it is a major agricultural commodity. Fungal pathogens producing leaf, stem, and yellow (stripe) rusts of wheat may cause yield losses of up to 50-60%. One of the most effective methods for preventing these losses is to develop resistant cultivars with high yield potential. This goal can be achieved using complex breeding studies, including the identification of key genetic factors controlling rust disease resistance. In this study, a panel consisting of 215 common wheat cultivars and breeding lines from Kazakhstan, Russia, Europe, USA, Canada, Mexico, and Australia, with a wide range of resistance to leaf rust (LR), stem rust (SR), and yellow rust (YR) diseases, was analyzed under field conditions in Southern Kazakhstan. The collection was genotyped using the 20K Illumina iSelect DNA array, where 11,510 informative single-nucleotide polymorphism markers were selected for further genome-wide association study (GWAS). Evaluation of the phenotypic diversity over 2 years showed a mostly mixed reaction to LR, mixed reaction/moderate susceptibility to SR, and moderate resistance to YR among wheat accessions from Kazakhstan. GWAS revealed 45 marker-trait associations (MTAs), including 23 for LR, 14 for SR, and eight for YR resistances. Three MTAs for LR resistance and one for SR resistance appeared to be novel. The MTAs identified in this work can be used for marker-assisted selection of common wheat in Kazakhstan in breeding new cultivars resistant to LR, SR, and YR diseases. These findings can be helpful for pyramiding genes with favorable alleles in promising cultivars and lines.
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Affiliation(s)
- Yuliya Genievskaya
- Plant Molecular Genetics Laboratory, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Yerlan Turuspekov
- Plant Molecular Genetics Laboratory, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan.,Biodiversity and Bioresources, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Aralbek Rsaliyev
- Laboratory of Phytosanitary Safety, Research Institute of Biological Safety Problems, Gvardeisky, Zhambyl Region, Kazakhstan
| | - Saule Abugalieva
- Plant Molecular Genetics Laboratory, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan.,Kazakh National Agrarian University, Almaty, Kazakhstan
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Leonova IN, Skolotneva ES, Orlova EA, Orlovskaya OA, Salina EA. Detection of Genomic Regions Associated with Resistance to Stem Rust in Russian Spring Wheat Varieties and Breeding Germplasm. Int J Mol Sci 2020; 21:E4706. [PMID: 32630293 PMCID: PMC7369787 DOI: 10.3390/ijms21134706] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 06/28/2020] [Accepted: 06/28/2020] [Indexed: 11/20/2022] Open
Abstract
Stem rust caused by Puccinia graminis f. sp. tritici Eriks. is a dangerous disease of common wheat worldwide. Development and cultivation of the varieties with genetic resistance is one of the most effective and environmentally important ways for protection of wheat against fungal pathogens. Field phytopathological screening and genome-wide association study (GWAS) were used for assessment of the genetic diversity of a collection of spring wheat genotypes on stem rust resistance loci. The collection consisting of Russian varieties of spring wheat and introgression lines with alien genetic materials was evaluated over three seasons (2016, 2017 and 2018) for resistance to the native population of stem rust specific to the West Siberian region of Russia. The results indicate that most varieties displayed from moderate to high levels of susceptibility to P. graminis; 16% of genotypes had resistance or immune response. In total, 13,006 single-nucleotide polymorphism (SNP) markers obtained from the Infinium 15K array were used to perform genome-wide association analysis. GWAS detected 35 significant marker-trait associations (MTAs) with SNPs located on chromosomes 1A, 2A, 2B, 3B, 5A, 5B, 6A, 7A and 7B. The most significant associations were found on chromosomes 7A and 6A where known resistance genes Sr25 and Sr6Ai = 2 originated from Thinopyrum ssp. are located. Common wheat lines containing introgressed fragments from Triticum timopheevii and Triticum kiharae were found to carry Sr36 gene on 2B chromosome. It has been suggested that the quantitative trait loci (QTL) mapped to the chromosome 5BL may be new loci inherited from the T. timopheevii. It can be inferred that a number of Russian wheat varieties may contain the Sr17 gene, which does not currently provide effective protection against pathogen. This is the first report describing the results of analysis of the genetic factors conferring resistance of Russian spring wheat varieties to stem rust.
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Affiliation(s)
- Irina N. Leonova
- The Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (E.S.S.); (E.A.O.); (E.A.S.)
| | - Ekaterina S. Skolotneva
- The Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (E.S.S.); (E.A.O.); (E.A.S.)
| | - Elena A. Orlova
- The Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (E.S.S.); (E.A.O.); (E.A.S.)
| | - Olga A. Orlovskaya
- Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, 220072 Minsk, Belarus;
| | - Elena A. Salina
- The Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (E.S.S.); (E.A.O.); (E.A.S.)
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20
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Francki MG, Walker E, McMullan CJ, Morris WG. Multi-Location Evaluation of Global Wheat Lines Reveal Multiple QTL for Adult Plant Resistance to Septoria Nodorum Blotch (SNB) Detected in Specific Environments and in Response to Different Isolates. FRONTIERS IN PLANT SCIENCE 2020; 11:771. [PMID: 32655592 PMCID: PMC7325896 DOI: 10.3389/fpls.2020.00771] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 05/15/2020] [Indexed: 05/26/2023]
Abstract
The slow rate of genetic gain for improving resistance to Septoria nodorum blotch (SNB) is due to the inherent complex interactions between host, isolates, and environments. Breeding for improved SNB resistance requires evaluation and selection of wheat genotypes consistently expressing low SNB response in different target production environments. The study focused on evaluating 232 genotypes from global origins for resistance to SNB in the flag leaf expressed in different Western Australian environments. The aim was to identify resistant donor germplasm against historical and contemporary pathogen isolates and enhance our knowledge of the genetic basis of genotype-by-environment interactions for SNB response. Australian wheat varieties, inbred lines from Centro Internacional de Mejoramiento de Maiz y Trigo (CIMMYT), and International Center for Agricultural Research in the Dry Areas (ICARDA), and landraces from discrete regions of the world showed low to moderate phenotypic correlation for disease response amongst genotypes when evaluated with historical and contemporary isolates at two locations across 3 years in Western Australia (WA). Significant (P < 0.001) genotype-by-environment interactions were detected regardless of same or different isolates used as an inoculum source. Joint regression analysis identified 19 genotypes that consistently expressed low disease severity under infection with different isolates in multi-locations. The CIMMYT inbred lines, 30ZJN09 and ZJN12 Qno25, were particularly pertinent as they had low SNB response and highest trait stability at two locations across 3 years. Genome wide association studies detected 20 QTL associated with SNB resistance on chromosomes 1A, 1B, 4B, 5A, 5B, 6A, 7A, 7B, and 7D. QTL on chromosomes 1B and 5B were previously reported in similar genomic regions. Multiple QTL were identified on 1B, 5B, 6A, and 5A and detected in response to SNB infection against different isolates and specific environments. Known SnTox-Snn interactions were either not evident or variable across WA environments and SNB response may involve other multiple complex biological mechanisms.
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Affiliation(s)
- Michael G. Francki
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Esther Walker
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | | | - W. George Morris
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
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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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23
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Genievskaya Y, Fedorenko Y, Sarbayev A, Amalova A, Abugalieva S, Griffiths S, Turuspekov Y. Identification of QTLs for resistance to leaf and stem rusts in bread wheat (Triticum aestivum L.) using a mapping population of ‘Pamyati Azieva × Paragon’. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Leaf rust (LR) and stem rust (SR) are harmful fungal diseases of bread wheat (Triticum aestivum L.). The purpose of this study was to identify QTLs for resistance to LR and SR that are effective in two wheat-growing regions of Kazakhstan. To accomplish this task, a population of recombinant inbred lines (RILs) of ‘Pamyati Azieva × Paragon’ was grown in the northern and southeastern parts of Kazakhstan, phenotyped for LR/SR severities, and analyzed for key yield components. The study revealed a negative correlation between disease severity and plant productivity in both areas. The mapping population was genotyped using a 20,000 Illumina SNP array. A total of 4595 polymorphic SNP markers were further selected for linkage analysis after filtering based on missing data percentage and segregation distortion. Windows QTL Cartographer was applied to identify QTLs associated with LR and SR resistances in the RIL mapping population studied. Two QTLs for LR resistance and eight for SR resistance were found in the north, and the genetic positions of eight of them have matched the positions of the known Lr and Sr genes, while two QTLs for SR were novel. In the southeast, eight QTLs for LR and one for SR were identified in total. The study is an initial step of the genetic mapping of LR and SR resistance loci of bread wheat in Kazakhstan. Field trials in two areas of the country and the genotyping of the selected mapping population have allowed identification of key QTLs that will be effective in regional breeding projects for better bread wheat productivity.
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Affiliation(s)
| | | | - A. Sarbayev
- Kazakh Research Institute of Agriculture and Plant Industry
| | - A. Amalova
- Institute of Plant Biology and Biotechnology
| | - S. Abugalieva
- Institute of Plant Biology and Biotechnology; al-Farabi Kazakh National University, Faculty of Biology and Biotechnology, Department of Biodiversity and Bioresources
| | | | - Y. Turuspekov
- Institute of Plant Biology and Biotechnology; al-Farabi Kazakh National University, Faculty of Biology and Biotechnology, Department of Biodiversity and Bioresources
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24
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Hundie B, Girma B, Tadesse Z, Edae E, Olivera P, Abera EH, Bulbula WD, Abeyo B, Badebo A, Cisar G, Brown-Guedira G, Gale S, Jin Y, Rouse MN. Characterization of Ethiopian Wheat Germplasm for Resistance to Four Puccinia graminis f. sp. tritici Races Facilitated by Single-Race Nurseries. PLANT DISEASE 2019; 103:2359-2366. [PMID: 31355733 PMCID: PMC7779970 DOI: 10.1094/pdis-07-18-1243-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In Ethiopia, breeding rust resistant wheat cultivars is a priority for wheat production. A stem rust epidemic during 2013 to 2014 on previously resistant cultivar Digalu highlighted the need to determine the effectiveness of wheat lines to multiple races of Puccinia graminis f. sp. tritici in Ethiopia. During 2014 and 2015, we evaluated a total of 97 bread wheat and 14 durum wheat genotypes against four P. graminis f. sp. tritici races at the seedling stage and in single-race field nurseries. Resistance genes were postulated using molecular marker assays. Bread wheat lines were resistant to race JRCQC, the race most virulent to durum wheat. Lines with stem rust resistance gene Sr24 possessed the most effective resistance to the four races. Only three lines with adult plant resistance possessed resistance effective to the four races comparable with cultivars with Sr24. Although responses of the wheat lines across races were positively correlated, wheat lines were identified that possessed adult plant resistance to race TTKSK but were relatively susceptible to race TKTTF. This study demonstrated the importance of testing wheat lines for response to multiple races of the stem rust pathogen to determine if lines possessed non-race-specific resistance. Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Bekele Hundie
- Kulumsa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Kulumsa, Ethiopia
| | - Bedada Girma
- Kulumsa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Kulumsa, Ethiopia
| | - Zerihun Tadesse
- Kulumsa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Kulumsa, Ethiopia
| | - Erena Edae
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Pablo Olivera
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Endale Hailu Abera
- Ambo Plant Protection Research Center, Ethiopian Institute of Agricultural Research, Ambo, Ethiopia
| | - Worku Denbel Bulbula
- Debre Zeit Agricultural Research Center, Ethiopian Institute of Agricultural Research, Debre Zeit, Ethiopia
| | - Bekele Abeyo
- International Maize and Wheat Improvement Center, Addis Ababa, Ethiopia
| | - Ayele Badebo
- International Maize and Wheat Improvement Center, Addis Ababa, Ethiopia
| | - Gordon Cisar
- International Programs of the College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14853, U.S.A
| | - Gina Brown-Guedira
- Plant Science Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Raleigh, NC 27695, U.S.A
| | - Sam Gale
- Cereal Disease Laboratory, U.S. Department of Agriculture-Agricultural Research Service, St. Paul, MN 55108, U.S.A
| | - Yue Jin
- Cereal Disease Laboratory, U.S. Department of Agriculture-Agricultural Research Service, St. Paul, MN 55108, U.S.A
| | - Matthew N Rouse
- Cereal Disease Laboratory, U.S. Department of Agriculture-Agricultural Research Service, St. Paul, MN 55108, U.S.A
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25
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Mourad AMI, Sallam A, Belamkar V, Wegulo S, Bai G, Mahdy E, Bakheit B, Abo El-Wafa A, Jin Y, Baenziger PS. Molecular marker dissection of stem rust resistance in Nebraska bread wheat germplasm. Sci Rep 2019; 9:11694. [PMID: 31406132 PMCID: PMC6691005 DOI: 10.1038/s41598-019-47986-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 07/23/2019] [Indexed: 12/20/2022] Open
Abstract
Stem rust (caused by Puccinia graminis f. sp. tritici) is a major disease of wheat. To understand the genetic basis of stem rust resistance in Nebraska winter wheat, a set of 330 genotypes representing two nurseries (DUP2015 and TRP2015) were evaluated for resistance to a Nebraska stem rust race (QFCSC) in two replications. The TRP2015 nursery was also evaluated for its resistance to an additional 13 stem rust races. The analysis of variance revealed significant variation among genotypes in both populations for stem rust resistance. Nine stem rust genes, Sr6, Sr31, Sr1RSAmigo, Sr24, Sr36, SrTmp, Sr7b, Sr9b, and Sr38, were expected and genotyped using gene-specific markers. The results of genetic analysis confirmed the presence of seven stem rust resistance genes. One genotype (NE15680) contained target alleles for five stem rust resistance genes and had a high level of stem rust resistance against different races. Single marker analysis indicated that Sr24 and Sr38 were highly significantly associated with stem rust resistance in the DUP2015 and TRP2015 nurseries, respectively. Linkage disequilibrium analysis identified the presence of 17 SNPs in high linkage with the Sr38-specific marker. These SNPs potentially tagging the Sr38 gene could be used in marker-assisted selection after validating them in additional genetic backgrounds.
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Affiliation(s)
- Amira M I Mourad
- Department of Agronomy and Horticulture, Plant Science Hall, UNL, Lincoln, NE, USA. .,Agronomy Department, Faculty of Agriculture, Assiut University, Assiut, Egypt.
| | - Ahmed Sallam
- Department of Agronomy and Horticulture, Plant Science Hall, UNL, Lincoln, NE, USA.,Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Vikas Belamkar
- Department of Agronomy and Horticulture, Plant Science Hall, UNL, Lincoln, NE, USA
| | - Stephen Wegulo
- Department of Plant Pathology, Plant Science Hall, UNL, Lincoln, NE, USA
| | - Guihua Bai
- USDA-ARS Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Manhattan, KS, USA
| | - Ezzat Mahdy
- Agronomy Department, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Bahy Bakheit
- Agronomy Department, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Atif Abo El-Wafa
- Agronomy Department, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Yue Jin
- USDA-ARS Cereal Disease Lab, St. Paul, MN, USA
| | - P Stephen Baenziger
- Department of Agronomy and Horticulture, Plant Science Hall, UNL, Lincoln, NE, USA
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26
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Scheben A, Verpaalen B, Lawley CT, Chan CKK, Bayer PE, Batley J, Edwards D. CropSNPdb: a database of SNP array data for Brassica crops and hexaploid bread wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:142-152. [PMID: 30548723 DOI: 10.1111/tpj.14194] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 05/23/2023]
Abstract
Advances in sequencing technology have led to a rapid rise in the genomic data available for plants, driving new insights into the evolution, domestication and improvement of crops. Single nucleotide polymorphisms (SNPs) are a major component of crop genomic diversity, and are invaluable as genetic markers in research and breeding programs. High-throughput SNP arrays, or 'SNP chips', can generate reproducible sets of informative SNP markers and have been broadly adopted. Although there are many public repositories for sequencing data, which are routinely uploaded, there are no formal repositories for crop SNP array data. To make SNP array data more easily accessible, we have developed CropSNPdb (http://snpdb.appliedbioinformatics.com.au), a database for SNP array data produced by the Illumina Infinium™ hexaploid bread wheat (Triticum aestivum) 90K and Brassica 60K arrays. We currently host SNPs from datasets covering 526 Brassica lines and 309 bread wheat lines, and provide search, download and upload utilities for users. CropSNPdb provides a useful repository for these data, which can be applied for a range of genomics and molecular crop-breeding activities.
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Affiliation(s)
- Armin Scheben
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Brent Verpaalen
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | | | - Chon-Kit K Chan
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
- Australian Genome Research Facility, Melbourne, Vic., 3000, Australia
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
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Lewien MJ, Murray TD, Jernigan KL, Garland-Campbell KA, Carter AH. Genome-wide association mapping for eyespot disease in US Pacific Northwest winter wheat. PLoS One 2018; 13:e0194698. [PMID: 29608579 PMCID: PMC5880388 DOI: 10.1371/journal.pone.0194698] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 03/07/2018] [Indexed: 12/20/2022] Open
Abstract
Eyespot, caused by the soil-borne necrotrophic fungi Oculimacula yallundae and O. acuformis, is a disease of major economic significance for wheat, barley and rye. Pacific Northwest (PNW) winter wheat (Triticum aestivum L.) grown in areas of high rainfall and moderate winters is most vulnerable to infection. The objective of this research was to identify novel genomic regions associated with eyespot resistance in winter wheat adapted to the PNW. Two winter wheat panels of 469 and 399 lines were compiled for one of the first genome-wide association studies (GWAS) of eyespot resistance in US winter wheat germplasm. These panels were genotyped with the Infinium 9K and 90K iSelect SNP arrays. Both panels were phenotyped for disease resistance in a two-year field study and in replicated growth chamber trials. Growth chamber trials were used to evaluate the genetic resistance of O. acuformis and O. yallundae species separately. Best linear unbiased predictors (BLUPs) were calculated across all field and growth chamber environments. A total of 73 marker-trait associations (MTAs) were detected on nine different chromosomes (1A, 2A, 2B, 4A, 5A, 5B, 7A, 7B and 7D) that were significantly associated (p-value <0.001) with eyespot resistance in Panel A, and 19 MTAs on nine different chromosomes (1A, 1B, 2A, 2D, 3B, 5A, 5B, 7A, and 7B) in Panel B. The most significant SNPs were associated with Pch1 and Pch2 resistance genes on the long arms of chromosome 7D and 7A. Most of the novel MTAs appeared to have a minor effect on reducing eyespot disease. Nevertheless, eyespot disease scores decreased as the number of resistance alleles increased. Seven SNP markers, significantly associated with reducing eyespot disease across environments and in the absence and presence of Pch1 were identified. These markers were located on chromosomes 2A (IWB8331), 5A (IWB73709), 5B (IWB47298), 7AS (IWB47160), 7B (IWB45005) and two SNPs (Ex_c44379_2509 and IAAV4340) had unknown map positions. The additive effect of the MTAs explained most of the remaining phenotypic variation not accounted for by Pch1 or Pch2. This study provides breeders with adapted germplasm and novel sources of eyespot resistance to be used in the development of superior cultivars with increased eyespot resistance.
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Affiliation(s)
- Megan J Lewien
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United State of America
| | - Timothy D Murray
- Department of Plant Pathology, Washington State University, Pullman, WA, United State of America
| | - Kendra L Jernigan
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United State of America
| | - Kimberly A Garland-Campbell
- USDA-ARS Wheat Health, Genetics, and Quality Unit, Washington State University, Pullman, WA, United State of America
| | - Arron H Carter
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United State of America
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Ando K, Rynearson S, Muleta KT, Gedamu J, Girma B, Bosque-Pérez NA, Chen MS, Pumphrey MO. Genome-wide associations for multiple pest resistances in a Northwestern United States elite spring wheat panel. PLoS One 2018; 13:e0191305. [PMID: 29415008 PMCID: PMC5802848 DOI: 10.1371/journal.pone.0191305] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/01/2018] [Indexed: 12/01/2022] Open
Abstract
Northern areas of the western United States are one of the most productive wheat growing regions in the United States. Increasing productivity through breeding is hindered by several biotic stresses which slow and constrain targeted yield improvement. In order to understand genetic variation for stripe rust (Puccinia striiformis f. sp. tritici), Septoria tritici blotch (Mycosphaerella graminicola), and Hessian fly (Mayetiola destructor) in regional germplasm, a panel of 408 elite spring wheat lines was characterized and genotyped with an Illumina 9K wheat single nucleotide polymorphism (SNP) chip to enable genome-wide association study (GWAS) analyses. Significant marker-trait associations were identified for stripe rust (38 loci), Septoria tritici blotch (8) and Hessian fly (9) resistance. Many of the QTL corresponded with previously reported gene locations or QTL, but we also discovered new resistance loci for each trait. We validated one of the stripe rust resistance loci detected by GWAS in a bi-parental mapping population, which confirmed the detection of Yr15 in the panel. This study elucidated well-defined chromosome regions for multiple pest resistances in elite Northwest germplasm. Newly identified resistance loci, along with SNPs more tightly linked to previously reported genes or QTL will help future breeding and marker assisted selection efforts.
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Affiliation(s)
- Kaori Ando
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Sheri Rynearson
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Kebede T. Muleta
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Jhonatan Gedamu
- Ethiopian Institute of Agricultural Research, Holeta Agricultural Research Center, Holeta, Ethiopia
| | - Bedada Girma
- Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Assela, Ethiopia
| | - Nilsa A. Bosque-Pérez
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, Idaho, United States of America
| | - Ming-Shun Chen
- United States Department of Agriculture–Agricultural Research Service and Department of Entomology, Kansas State University, Manhattan, Kansas, United States of America
| | - Mike O. Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
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Godoy JG, Rynearson S, Chen X, Pumphrey M. Genome-Wide Association Mapping of Loci for Resistance to Stripe Rust in North American Elite Spring Wheat Germplasm. PHYTOPATHOLOGY 2018; 108:234-245. [PMID: 28952421 DOI: 10.1094/phyto-06-17-0195-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a major yield-limiting foliar disease of wheat (Triticum aestivum) worldwide. In this study, the genetic variability of elite spring wheat germplasm from North America was investigated to characterize the genetic basis of effective all-stage and adult plant resistance (APR) to stripe rust. A genome-wide association study was conducted using 237 elite spring wheat lines genotyped with an Illumina Infinium 90K single-nucleotide polymorphism array. All-stage resistance was evaluated at seedling stage in controlled conditions and field evaluations were conducted under natural disease pressure in eight environments across Washington State. High heritability estimates and correlations between infection type and severity were observed. Ten loci for race-specific all-stage resistance were confirmed from previous mapping studies. Three potentially new loci associated with race-specific all-stage resistance were identified on chromosomes 1D, 2A, and 5A. For APR, 11 highly significant quantitative trait loci (QTL) (false discovery rate < 0.01) were identified, of which 3 QTL on chromosomes 3A, 5D, and 7A are reported for the first time. The QTL identified in this study can be used to enrich the current gene pool and improve the diversity of resistance to stripe rust disease.
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Affiliation(s)
- Jayfred Gaham Godoy
- First, second, and fourth authors: Department of Crop and Soil Sciences, Washington State University, Pullman 99164-6420; and third author: United States Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, Washington State University, Pullman 99164-6430
| | - Sheri Rynearson
- First, second, and fourth authors: Department of Crop and Soil Sciences, Washington State University, Pullman 99164-6420; and third author: United States Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, Washington State University, Pullman 99164-6430
| | - Xianming Chen
- First, second, and fourth authors: Department of Crop and Soil Sciences, Washington State University, Pullman 99164-6420; and third author: United States Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, Washington State University, Pullman 99164-6430
| | - Michael Pumphrey
- First, second, and fourth authors: Department of Crop and Soil Sciences, Washington State University, Pullman 99164-6420; and third author: United States Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, Washington State University, Pullman 99164-6430
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Edae EA, Pumphrey MO, Rouse MN. A Genome-Wide Association Study of Field and Seedling Response to Individual Stem Rust Pathogen Races Reveals Combinations of Race-Specific Genes in North American Spring Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:52. [PMID: 29441083 PMCID: PMC5797647 DOI: 10.3389/fpls.2018.00052] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/10/2018] [Indexed: 05/22/2023]
Abstract
Stem rust of wheat caused by the fungal pathogen Puccinia graminis f. sp. tritici historically caused major yield losses of wheat worldwide. To understand the genetic basis of stem rust resistance in contemporary North American spring wheat, genome-wide association analysis (GWAS) was conducted on an association mapping panel comprised of 250 elite lines. The lines were evaluated in separate nurseries each inoculated with a different P. graminis f. sp. tritici race for 3 years (2013, 2015, and 2016) at Rosemount, Minnesota allowing the evaluation of race-specificity separate from the effect of environment. The lines were also challenged with the same four races at the seedling stage in a greenhouse facility at the USDA-ARS Cereal Disease Laboratory. A total of 22,310 high-quality SNPs obtained from the Infinium 90,000 SNPs chip were used to perform association analysis. We observed often negative and sometimes weak correlations between responses to different races that highlighted the abundance of race-specific resistance and the inability to predict the response of the lines across races. Markers strongly associated with resistance to the four races at seedling and field environments were identified. At the seedling stage, the most significant marker-trait associations were detected in the regions of known major genes (Sr6, Sr7a, and Sr9b) except for race QFCSC where a strong association was detected on chromosome arm 1AL. We postulated the presence of Sr2, Sr6, Sr7a, Sr8a, Sr9b, Sr11, Sr12, Sr24, Sr25, Sr31, and Sr57 (Lr34) in this germplasm based on phenotypic and marker data. We found over half of the panel possessed three or more Sr genes, and most commonly included various combinations of Sr6, Sr7a, Sr8a, Sr9b, Sr11, Sr12, and Sr57. Most of these genes confer resistance to specific P. graminis f. sp. tritici races accounting for the prevalent stem rust resistance in North American spring wheat.
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Affiliation(s)
- Erena A. Edae
- Cereal Disease Laboratory, United States Department of Agriculture - Agricultural Research Service (USDA ARS), St. Paul, MN, United States
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Michael O. Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Matthew N. Rouse
- Cereal Disease Laboratory, United States Department of Agriculture - Agricultural Research Service (USDA ARS), St. Paul, MN, United States
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
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Wang R, Chen J, Anderson JA, Zhang J, Zhao W, Wheeler J, Klassen N, See DR, Dong Y. Genome-Wide Association Mapping of Fusarium Head Blight Resistance in Spring Wheat Lines Developed in the Pacific Northwest and CIMMYT. PHYTOPATHOLOGY 2017; 107:1486-1495. [PMID: 28703042 DOI: 10.1094/phyto-02-17-0073-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Fusarium head blight (FHB) is a destructive disease of wheat in humid and semihumid areas of the world. It has emerged in the Pacific Northwest (PNW) in recent years because of changing climate and crop rotation practices. Our objectives in the present study were to identify and characterize quantitative trait loci (QTL) associated with FHB resistance in spring wheat lines developed in the PNW and the International Maize and Wheat Improvement Center. In total, 170 spring wheat lines were evaluated in field and greenhouse trials in 2015 and 2016. Fourteen lines showing consistent resistance in multiple environments were identified. These lines are valuable resources in wheat variety improvement of FHB resistance because they have no Sumai 3 or Sumai 3-related background. The 170 lines were genotyped using a high-density Illumina 90K single-nucleotide polymorphisms (SNP) assay and 10 other non-SNP markers. A genome-wide association analysis was conducted with a mixed model (Q+K). Consistent, significant SNP associations with multiple traits were found on chromosomes 1B, 2B, 4B, 5A, 5B, and 6A. The locus on chromosome 5B for reduced deoxynivalenol content may be novel. The identified QTL are being validated in additional mapping studies and the identified resistant lines are being used in variety development for FHB resistance and facilitated by marker-assisted selection.
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Affiliation(s)
- Rui Wang
- First, second, fifth, sixth, and seventh authors: Department of Plant, Soil, and Entomological Sciences, University of Idaho, Aberdeen; third author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul; fourth author: Department of Plant Sciences, University of California-Davis, Davis; eighth author: United States Department of Agriculture-Agricultural Research Service, Wheat Genetics, Quality, Physiology and Disease Research Unit, Pullman, WA 99164; and ninth author: Department of Plant Pathology, University of Minnesota, St. Paul
| | - Jianli Chen
- First, second, fifth, sixth, and seventh authors: Department of Plant, Soil, and Entomological Sciences, University of Idaho, Aberdeen; third author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul; fourth author: Department of Plant Sciences, University of California-Davis, Davis; eighth author: United States Department of Agriculture-Agricultural Research Service, Wheat Genetics, Quality, Physiology and Disease Research Unit, Pullman, WA 99164; and ninth author: Department of Plant Pathology, University of Minnesota, St. Paul
| | - James A Anderson
- First, second, fifth, sixth, and seventh authors: Department of Plant, Soil, and Entomological Sciences, University of Idaho, Aberdeen; third author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul; fourth author: Department of Plant Sciences, University of California-Davis, Davis; eighth author: United States Department of Agriculture-Agricultural Research Service, Wheat Genetics, Quality, Physiology and Disease Research Unit, Pullman, WA 99164; and ninth author: Department of Plant Pathology, University of Minnesota, St. Paul
| | - Junli Zhang
- First, second, fifth, sixth, and seventh authors: Department of Plant, Soil, and Entomological Sciences, University of Idaho, Aberdeen; third author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul; fourth author: Department of Plant Sciences, University of California-Davis, Davis; eighth author: United States Department of Agriculture-Agricultural Research Service, Wheat Genetics, Quality, Physiology and Disease Research Unit, Pullman, WA 99164; and ninth author: Department of Plant Pathology, University of Minnesota, St. Paul
| | - Weidong Zhao
- First, second, fifth, sixth, and seventh authors: Department of Plant, Soil, and Entomological Sciences, University of Idaho, Aberdeen; third author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul; fourth author: Department of Plant Sciences, University of California-Davis, Davis; eighth author: United States Department of Agriculture-Agricultural Research Service, Wheat Genetics, Quality, Physiology and Disease Research Unit, Pullman, WA 99164; and ninth author: Department of Plant Pathology, University of Minnesota, St. Paul
| | - Justin Wheeler
- First, second, fifth, sixth, and seventh authors: Department of Plant, Soil, and Entomological Sciences, University of Idaho, Aberdeen; third author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul; fourth author: Department of Plant Sciences, University of California-Davis, Davis; eighth author: United States Department of Agriculture-Agricultural Research Service, Wheat Genetics, Quality, Physiology and Disease Research Unit, Pullman, WA 99164; and ninth author: Department of Plant Pathology, University of Minnesota, St. Paul
| | - Natalie Klassen
- First, second, fifth, sixth, and seventh authors: Department of Plant, Soil, and Entomological Sciences, University of Idaho, Aberdeen; third author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul; fourth author: Department of Plant Sciences, University of California-Davis, Davis; eighth author: United States Department of Agriculture-Agricultural Research Service, Wheat Genetics, Quality, Physiology and Disease Research Unit, Pullman, WA 99164; and ninth author: Department of Plant Pathology, University of Minnesota, St. Paul
| | - Deven R See
- First, second, fifth, sixth, and seventh authors: Department of Plant, Soil, and Entomological Sciences, University of Idaho, Aberdeen; third author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul; fourth author: Department of Plant Sciences, University of California-Davis, Davis; eighth author: United States Department of Agriculture-Agricultural Research Service, Wheat Genetics, Quality, Physiology and Disease Research Unit, Pullman, WA 99164; and ninth author: Department of Plant Pathology, University of Minnesota, St. Paul
| | - Yanhong Dong
- First, second, fifth, sixth, and seventh authors: Department of Plant, Soil, and Entomological Sciences, University of Idaho, Aberdeen; third author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul; fourth author: Department of Plant Sciences, University of California-Davis, Davis; eighth author: United States Department of Agriculture-Agricultural Research Service, Wheat Genetics, Quality, Physiology and Disease Research Unit, Pullman, WA 99164; and ninth author: Department of Plant Pathology, University of Minnesota, St. Paul
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Muleta KT, Rouse MN, Rynearson S, Chen X, Buta BG, Pumphrey MO. Characterization of molecular diversity and genome-wide mapping of loci associated with resistance to stripe rust and stem rust in Ethiopian bread wheat accessions. BMC PLANT BIOLOGY 2017; 17:134. [PMID: 28778144 PMCID: PMC5545024 DOI: 10.1186/s12870-017-1082-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 07/21/2017] [Indexed: 05/06/2023]
Abstract
BACKGROUND The narrow genetic basis of resistance in modern wheat cultivars and the strong selection response of pathogen populations have been responsible for periodic and devastating epidemics of the wheat rust diseases. Characterizing new sources of resistance and incorporating multiple genes into elite cultivars is the most widely accepted current mechanism to achieve durable varietal performance against changes in pathogen virulence. Here, we report a high-density molecular characterization and genome-wide association study (GWAS) of stripe rust and stem rust resistance in 190 Ethiopian bread wheat lines based on phenotypic data from multi-environment field trials and seedling resistance screening experiments. A total of 24,281 single nucleotide polymorphism (SNP) markers filtered from the wheat 90 K iSelect genotyping assay was used to survey Ethiopian germplasm for population structure, genetic diversity and marker-trait associations. RESULTS Upon screening for field resistance to stripe rust in the Pacific Northwest of the United States and Ethiopia over multiple growing seasons, and against multiple races of stripe rust and stem rust at seedling stage, eight accessions displayed resistance to all tested races of stem rust and field resistance to stripe rust in all environments. Our GWAS results show 15 loci were significantly associated with seedling and adult plant resistance to stripe rust at false discovery rate (FDR)-adjusted probability (P) <0.10. GWAS also detected 9 additional genomic regions significantly associated (FDR-adjusted P < 0.10) with seedling resistance to stem rust in the Ethiopian wheat accessions. Many of the identified resistance loci were mapped close to previously identified rust resistance genes; however, three loci on the short arms of chromosomes 5A and 7B for stripe rust resistance and two on chromosomes 3B and 7B for stem rust resistance may be novel. CONCLUSION Our results demonstrate that considerable genetic variation resides within the landrace accessions that can be utilized to broaden the genetic base of rust resistance in wheat breeding germplasm. The molecular markers identified in this study should be useful in efficiently targeting the associated resistance loci in marker-assisted breeding for rust resistance in Ethiopia and other countries.
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Affiliation(s)
- Kebede T Muleta
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Matthew N Rouse
- USDA-ARS Cereal Disease Laboratory, Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Sheri Rynearson
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Xianming Chen
- USDA-ARS, Wheat Health, Genetics, and Quality Research Unit, and Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, Pullman, WA, 99164-6430, USA
| | - Bedada G Buta
- Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, P. O. Box 489, Assela, Ethiopia
| | - Michael O Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA.
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Kumar J, Gupta DS, Gupta S, Dubey S, Gupta P, Kumar S. Quantitative trait loci from identification to exploitation for crop improvement. PLANT CELL REPORTS 2017; 36:1187-1213. [PMID: 28352970 DOI: 10.1007/s00299-017-2127-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/09/2017] [Indexed: 05/24/2023]
Abstract
Advancement in the field of genetics and genomics after the discovery of Mendel's laws of inheritance has led to map the genes controlling qualitative and quantitative traits in crop plant species. Mapping of genomic regions controlling the variation of quantitatively inherited traits has become routine after the advent of different types of molecular markers. Recently, the next generation sequencing methods have accelerated the research on QTL analysis. These efforts have led to the identification of more closely linked molecular markers with gene/QTLs and also identified markers even within gene/QTL controlling the trait of interest. Efforts have also been made towards cloning gene/QTLs or identification of potential candidate genes responsible for a trait. Further new concepts like crop QTLome and QTL prioritization have accelerated precise application of QTLs for genetic improvement of complex traits. In the past years, efforts have also been made in exploitation of a number of QTL for improving grain yield or other agronomic traits in various crops through markers assisted selection leading to cultivation of these improved varieties at farmers' field. In present article, we reviewed QTLs from their identification to exploitation in plant breeding programs and also reviewed that how improved cultivars developed through introgression of QTLs have improved the yield productivity in many crops.
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Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India.
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sunanda Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sonali Dubey
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Priyanka Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat-Institutes, B.P. 6299, Rabat, Morocco
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Lucas SJ, Salantur A, Yazar S, Budak H. High-throughput SNP genotyping of modern and wild emmer wheat for yield and root morphology using a combined association and linkage analysis. Funct Integr Genomics 2017; 17:667-685. [PMID: 28550605 DOI: 10.1007/s10142-017-0563-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 05/11/2017] [Accepted: 05/12/2017] [Indexed: 11/24/2022]
Abstract
Durum wheat (Triticum turgidum var. durum Desf.) is a major world crop that is grown primarily in areas of the world that experience periodic drought, and therefore, breeding climate-resilient durum wheat is a priority. High-throughput single nucleotide polymorphism (SNP) genotyping techniques have greatly increased the power of linkage and association mapping analyses for bread wheat, but as yet there is no durum wheat-specific platform available. In this study, we evaluate the new 384HT Wheat Breeders Array for its usefulness in tetraploid wheat breeding by genotyping a breeding population of F6 hybrids, derived from multiple crosses between T. durum cultivars and wild and cultivated emmer wheat accessions. Using a combined linkage and association mapping approach, we generated a genetic map including 1345 SNP markers, and identified markers linked to 6 QTLs for coleoptile length (2), heading date (1), anthocyanin accumulation (1) and osmotic stress tolerance (2). We also developed a straightforward approach for combining genetic data from multiple families of limited size that will be useful for evaluating and mapping pre-existing breeding material.
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Affiliation(s)
- Stuart J Lucas
- SU Nanotechnology Research and Application Centre, Sabanci University, 34956, Tuzla, İstanbul, Turkey.
| | - Ayten Salantur
- Breeding and Genetics, Field Crops Central Research Institute, Ankara, Turkey
| | - Selami Yazar
- Breeding and Genetics, Field Crops Central Research Institute, Ankara, Turkey
| | - Hikmet Budak
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey. .,412 Leon Johnson Hall, Cereal Genomics Lab, Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA.
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35
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Babiker EM, Gordon TC, Bonman JM, Chao S, Rouse MN, Jin Y, Newcomb M, Wanyera R, Bhavani S. Genetic Loci Conditioning Adult Plant Resistance to the Ug99 Race Group and Seedling Resistance to Races TRTTF and TTTTF of the Stem Rust Pathogen in Wheat Landrace CItr 15026. PLANT DISEASE 2017; 101:496-501. [PMID: 30677344 DOI: 10.1094/pdis-10-16-1447-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Wheat landrace CItr 15026 previously showed adult plant resistance (APR) to the Ug99 stem rust race group in Kenya and seedling resistance to Puccinia graminis f. sp. tritici races QFCSC, TTTTF, and TRTTF. CItr 15026 was crossed to susceptible accessions LMPG-6 and Red Bobs, and 180 double haploid (DH) lines and 140 recombinant inbred lines (RIL), respectively, were developed. The 90K wheat iSelect single-nucleotide polymorphism platform was used to genotype the parents and populations. Parents and 180 DH lines were evaluated in the field in Kenya for three seasons. A major quantitative trait locus (QTL) for APR was consistently detected on chromosome arm 6AS. This QTL was further detected in the RIL population screened in Kenya for one season. Parents, F1, and the two populations were tested as seedlings against races TRTTF and TTTTF. In addition, the DH population was tested against race QFCSC. Goodness-of-fit tests indicated that the TRTTF resistance in CItr 15026 was controlled by two complementary genes whereas the TTTTF and QFCSC resistance was conditioned by one dominant gene. The TRTTF resistance loci mapped to chromosome arms 6AS and 6DS, whereas the TTTTF and QFCSC resistance locus mapped to the same region on 6DS as the TRTTF resistance. The APR identified in CItr 15026 should be useful in developing cultivars with durable stem rust resistance.
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Affiliation(s)
- E M Babiker
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Small Grains and Potato Germplasm Research Unit, Aberdeen, ID 83210
| | - T C Gordon
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Small Grains and Potato Germplasm Research Unit, Aberdeen, ID 83210
| | - J M Bonman
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Small Grains and Potato Germplasm Research Unit, Aberdeen, ID 83210
| | - S Chao
- USDA-ARS, Cereal Crops Research, Fargo, ND 58102
| | - M N Rouse
- USDA-ARS, Cereal Disease Laboratory, St. Paul, MN 55108
| | - Y Jin
- USDA-ARS, Cereal Disease Laboratory, St. Paul, MN 55108
| | - M Newcomb
- School of Plant Sciences, University of Arizona, Maricopa
| | - R Wanyera
- Kenya Agricultural and Livestock Research Organization, Njoro 20107, Kenya
| | - S Bhavani
- International Maize and Wheat Improvement Center, Nairobi, Kenya
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36
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Hiebert CW, Rouse MN, Nirmala J, Fetch T. Genetic Mapping of Stem Rust Resistance to Puccinia graminis f. sp. tritici Race TRTTF in the Canadian Wheat Cultivar Harvest. PHYTOPATHOLOGY 2017; 107:192-197. [PMID: 27705664 DOI: 10.1094/phyto-05-16-0186-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Stem rust, caused by Puccinia graminis f. sp. tritici, is a destructive disease of wheat that can be controlled by deploying effective stem rust resistance (Sr) genes. Highly virulent races of P. graminis f. sp. tritici in Africa have been detected and characterized. These include race TRTTF and the Ug99 group of races such as TTKSK. Several Canadian and U.S. spring wheat cultivars, including the widely grown Canadian cultivar 'Harvest', are resistant to TRTTF. However, the genetic basis of resistance to TRTTF in Canadian and U.S. spring wheat cultivars is unknown. The objectives of this study were to determine the number of Sr genes involved in TRTTF resistance in Harvest, genetically map the resistance with DNA markers, and use markers to assess the distribution of that resistance in a panel of Canadian cultivars. A doubled haploid (DH) population was produced from the cross LMPG-6S/Harvest. The DH population was tested with race TRTTF at the seedling stage. Of 92 DH progeny evaluated, 46 were resistant and 46 were susceptible which perfectly fit a 1:1 ratio indicating a single Sr gene was responsible for conferring resistance to TRTTF in Harvest. Mapping with single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers placed the resistance gene distally on the chromosome 6AS genetic map, which corresponded to the location reported for Sr8. SSR marker gwm459 and 30 cosegregating SNP markers showed the closest linkage, mapping 2.2 cM proximal to the Sr gene. Gene Sr8a confers resistance to TRTTF and may account for the resistance in Harvest. Testing a panel of Canadian wheat cultivars with four SNP markers closely linked to resistance to TRTTF suggested that the resistance present in Harvest is present in many Canadian cultivars. Two of these SNP markers were also predictive of TRTTF resistance in a panel of 241 spring wheat lines from the United States, Canada, and Mexico.
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Affiliation(s)
- Colin W Hiebert
- First author: Agriculture and Agri-Food Canada, Morden Research and Development Centre, 100, Morden, MB R6M 1Y5, Canada; second and third authors: U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory and Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108; and fourth author: Agriculture and Agri-Food Canada, Brandon Research and Development Centre, Brandon, MB R7A 5Y3, Canada
| | - Matthew N Rouse
- First author: Agriculture and Agri-Food Canada, Morden Research and Development Centre, 100, Morden, MB R6M 1Y5, Canada; second and third authors: U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory and Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108; and fourth author: Agriculture and Agri-Food Canada, Brandon Research and Development Centre, Brandon, MB R7A 5Y3, Canada
| | - Jayaveeramuthu Nirmala
- First author: Agriculture and Agri-Food Canada, Morden Research and Development Centre, 100, Morden, MB R6M 1Y5, Canada; second and third authors: U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory and Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108; and fourth author: Agriculture and Agri-Food Canada, Brandon Research and Development Centre, Brandon, MB R7A 5Y3, Canada
| | - Tom Fetch
- First author: Agriculture and Agri-Food Canada, Morden Research and Development Centre, 100, Morden, MB R6M 1Y5, Canada; second and third authors: U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory and Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108; and fourth author: Agriculture and Agri-Food Canada, Brandon Research and Development Centre, Brandon, MB R7A 5Y3, Canada
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Nirmala J, Chao S, Olivera P, Babiker EM, Abeyo B, Tadesse Z, Imtiaz M, Talbert L, Blake NK, Akhunov E, Pumphrey MO, Jin Y, Rouse MN. Markers Linked to Wheat Stem Rust Resistance Gene Sr11 Effective to Puccinia graminis f. sp. tritici Race TKTTF. PHYTOPATHOLOGY 2016; 106:1352-1358. [PMID: 27359266 DOI: 10.1094/phyto-04-16-0165-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Wheat stem rust, caused by Puccinia graminis f. sp. tritici, can cause severe yield losses on susceptible wheat varieties and cultivars. Although stem rust can be controlled by the use of genetic resistance, population dynamics of P. graminis f. sp. tritici can frequently lead to defeat of wheat stem rust resistance genes. P. graminis f. sp. tritici race TKTTF caused a severe epidemic in Ethiopia on Ug99-resistant 'Digalu' in 2013 and 2014. The gene Sr11 confers resistance to race TKTTF and is present in 'Gabo 56'. We identified seven single-nucleotide polymorphism (SNP) markers linked to Sr11 from a cross between Gabo 56 and 'Chinese Spring' exploiting a 90K Infinium iSelect Custom beadchip. Five SNP markers were validated on a 'Berkut'/'Scalavatis' population that segregated for Sr11, using KBioscience competitive allele-specific polymerase chain reaction (KASP) assays. Two of the SNP markers, KASP_6BL_IWB10724 and KASP_6BL_IWB72471, were predictive of Sr11 among wheat genetic stocks, cultivars, and breeding lines from North America, Ethiopia, and Pakistan. These markers can be utilized to select for Sr11 in wheat breeding and to detect the presence of Sr11 in uncharacterized germplasm.
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Affiliation(s)
- Jayaveeramuthu Nirmala
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Shiaoman Chao
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Pablo Olivera
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Ebrahiem M Babiker
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Bekele Abeyo
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Zerihun Tadesse
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Muhammad Imtiaz
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Luther Talbert
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Nancy K Blake
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Eduard Akhunov
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Michael O Pumphrey
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Yue Jin
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
| | - Matthew N Rouse
- First, twelfth, and thirteenth authors: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), St. Paul, MN 55108; second author: Cereal Crops Research, USDA-ARS, Fargo, ND, 58102; third, twelfth, and thirteenth authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; fourth author: Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210; fifth author: International Maize and Wheat Improvement Center (CIMMYT)-Ethiopia, Addis Ababa, Ethiopia; sixth author: Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Kulumsa, Ethiopia; seventh author: CIMMYT-Pakistan, Islamabad, Pakistan; eighth and ninth authors: Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717; tenth author: Department of Plant Pathology, Kansas State University, Manhattan 66506; and eleventh author: Department of Crop and Soil Sciences, Washington State University, Pullman, 99164
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Bulli P, Zhang J, Chao S, Chen X, Pumphrey M. Genetic Architecture of Resistance to Stripe Rust in a Global Winter Wheat Germplasm Collection. G3 (BETHESDA, MD.) 2016; 6:2237-53. [PMID: 27226168 PMCID: PMC4978880 DOI: 10.1534/g3.116.028407] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/16/2016] [Indexed: 12/30/2022]
Abstract
Virulence shifts in populations of Puccinia striiformis f. sp. tritici (Pst), the causal pathogen of wheat stripe rust, are a major challenge to resistance breeding. The majority of known resistance genes are already ineffective against current races of Pst, necessitating the identification and introgression of new sources of resistance. Germplasm core collections that reflect the range of genetic and phenotypic diversity of crop species are ideal platforms for examining the genetic architecture of complex traits such as resistance to stripe rust. We report the results of genetic characterization and genome-wide association analysis (GWAS) for resistance to stripe rust in a core subset of 1175 accessions in the National Small Grains Collection (NSGC) winter wheat germplasm collection, based on genotyping with the wheat 9K single nucleotide polymorphism (SNP) iSelect assay and phenotyping of seedling and adult plants under natural disease epidemics in four environments. High correlations among the field data translated into high heritability values within and across locations. Population structure was evident when accessions were grouped by stripe rust reaction. GWAS identified 127 resistance loci that were effective across at least two environments, including 20 with significant genome-wide adjusted P-values. Based on relative map positions of previously reported genes and QTL, five of the QTL with significant genome-wide adjusted P-values in this study represent potentially new loci. This study provides an overview of the diversity of Pst resistance in the NSGC winter wheat germplasm core collection, which can be exploited for diversification of stripe rust resistance in breeding programs.
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Affiliation(s)
- Peter Bulli
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
| | - Junli Zhang
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Shiaoman Chao
- USDA-ARS Genotyping Laboratory, Biosciences Research Laboratory, Fargo, North Dakota 58102
| | - Xianming Chen
- USDA-ARS, Wheat Health, Genetics and Quality Research Unit, Washington State University, Pullman, Washington 99164 Department of Plant Pathology, Washington State University, Pullman, Washington 99164
| | - Michael Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
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Bajgain P, Rouse MN, Tsilo TJ, Macharia GK, Bhavani S, Jin Y, Anderson JA. Nested Association Mapping of Stem Rust Resistance in Wheat Using Genotyping by Sequencing. PLoS One 2016; 11:e0155760. [PMID: 27186883 PMCID: PMC4870046 DOI: 10.1371/journal.pone.0155760] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 05/04/2016] [Indexed: 11/19/2022] Open
Abstract
We combined the recently developed genotyping by sequencing (GBS) method with joint mapping (also known as nested association mapping) to dissect and understand the genetic architecture controlling stem rust resistance in wheat (Triticum aestivum). Ten stem rust resistant wheat varieties were crossed to the susceptible line LMPG-6 to generate F6 recombinant inbred lines. The recombinant inbred line populations were phenotyped in Kenya, South Africa, and St. Paul, Minnesota, USA. By joint mapping of the 10 populations, we identified 59 minor and medium-effect QTL (explained phenotypic variance range of 1% - 20%) on 20 chromosomes that contributed towards adult plant resistance to North American Pgt races as well as the highly virulent Ug99 race group. Fifteen of the 59 QTL were detected in multiple environments. No epistatic relationship was detected among the QTL. While these numerous small- to medium-effect QTL are shared among the families, the founder parents were found to have different allelic effects for the QTL. Fourteen QTL identified by joint mapping were also detected in single-population mapping. As these QTL were mapped using SNP markers with known locations on the physical chromosomes, the genomic regions identified with QTL could be explored more in depth to discover candidate genes for stem rust resistance. The use of GBS-derived de novo SNPs in mapping resistance to stem rust shown in this study could be used as a model to conduct similar marker-trait association studies in other plant species.
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Affiliation(s)
- Prabin Bajgain
- Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN 47907, United States of America
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN 55108, United States of America
| | - Matthew N. Rouse
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Cereal Disease Laboratory, St. Paul, MN 55108, United States of America
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, United States of America
| | - Toi J. Tsilo
- Agricultural Research Council – Small Grain Institute, Bethlehem, 9700, Free State, South Africa
| | - Godwin K. Macharia
- Kenya Agricultural and Livestock Research Organization (KALRO), Njoro, Kenya
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue, Gigiri, Nairobi, Kenya
| | - Yue Jin
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Cereal Disease Laboratory, St. Paul, MN 55108, United States of America
| | - James A. Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN 55108, United States of America
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Gao L, Turner MK, Chao S, Kolmer J, Anderson JA. Genome Wide Association Study of Seedling and Adult Plant Leaf Rust Resistance in Elite Spring Wheat Breeding Lines. PLoS One 2016; 11:e0148671. [PMID: 26849364 PMCID: PMC4744023 DOI: 10.1371/journal.pone.0148671] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/21/2016] [Indexed: 11/26/2022] Open
Abstract
Leaf rust is an important disease, threatening wheat production annually. Identification of resistance genes or QTLs for effective field resistance could greatly enhance our ability to breed durably resistant varieties. We applied a genome wide association study (GWAS) approach to identify resistance genes or QTLs in 338 spring wheat breeding lines from public and private sectors that were predominately developed in the Americas. A total of 46 QTLs were identified for field and seedling traits and approximately 20–30 confer field resistance in varying degrees. The 10 QTLs accounting for the most variation in field resistance explained 26–30% of the total variation (depending on traits: percent severity, coefficient of infection or response type). Similarly, the 10 QTLs accounting for most of the variation in seedling resistance to different races explained 24–34% of the variation, after correcting for population structure. Two potentially novel QTLs (QLr.umn-1AL, QLr.umn-4AS) were identified. Identification of novel genes or QTLs and validation of previously identified genes or QTLs for seedling and especially adult plant resistance will enhance understanding of leaf rust resistance and assist breeding for resistant wheat varieties. We also developed computer programs to automate field and seedling rust phenotype data conversions. This is the first GWAS study of leaf rust resistance in elite wheat breeding lines genotyped with high density 90K SNP arrays.
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Affiliation(s)
- Liangliang Gao
- University of Minnesota, Department of Agronomy and Plant Genetics, St. Paul, MN, 55108, United States of America
| | - M. Kathryn Turner
- University of Minnesota, Department of Agronomy and Plant Genetics, St. Paul, MN, 55108, United States of America
| | - Shiaoman Chao
- USDA-ARS Biosciences Research Lab, Fargo, ND, 58102, United States of America
| | - James Kolmer
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN, 55108, United States of America
- University of Minnesota, Department of Plant Pathology, St. Paul, MN, 55108, United States of America
- * E-mail: (JAA); (JK)
| | - James A. Anderson
- University of Minnesota, Department of Agronomy and Plant Genetics, St. Paul, MN, 55108, United States of America
- * E-mail: (JAA); (JK)
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Bajgain P, Rouse MN, Bulli P, Bhavani S, Gordon T, Wanyera R, Njau PN, Legesse W, Anderson JA, Pumphrey MO. Erratum to: Association mapping of North American spring wheat breeding germplasm reveals loci conferring resistance to Ug99 and other African stem rust races. BMC PLANT BIOLOGY 2016; 16:24. [PMID: 26786273 PMCID: PMC4719385 DOI: 10.1186/s12870-015-0684-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 12/14/2015] [Indexed: 05/05/2023]
Affiliation(s)
- P Bajgain
- Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, 47907, IN, USA.
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, 55108, MN, USA.
| | - M N Rouse
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Cereal Disease Laboratory, St. Paul, 55108, MN, USA
- Department of Plant Pathology, University of Minnesota, St. Paul, 55108, MN, USA
| | - P Bulli
- Department of Crop and Soil Sciences, Washington State University, Pullman, 99164, WA, USA
| | - S Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue, Gigiri, Nairobi, Kenya
| | - T Gordon
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Aberdeen, 83210, ID, USA
| | - R Wanyera
- Kenya Agricultural and Livestock Research Organization (KALRO), Njoro, Kenya
| | - P N Njau
- Kenya Agricultural and Livestock Research Organization (KALRO), Njoro, Kenya
| | - W Legesse
- Ethiopian Institute of Agricultural Research (EIAR), Pawe, Ethiopia
| | - J A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, 55108, MN, USA.
| | - M O Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, 99164, WA, USA
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Gao L, Turner MK, Chao S, Kolmer J, Anderson JA. Genome Wide Association Study of Seedling and Adult Plant Leaf Rust Resistance in Elite Spring Wheat Breeding Lines. PLoS One 2016. [PMID: 26849364 DOI: 10.1371/journal.pgen.148671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
Leaf rust is an important disease, threatening wheat production annually. Identification of resistance genes or QTLs for effective field resistance could greatly enhance our ability to breed durably resistant varieties. We applied a genome wide association study (GWAS) approach to identify resistance genes or QTLs in 338 spring wheat breeding lines from public and private sectors that were predominately developed in the Americas. A total of 46 QTLs were identified for field and seedling traits and approximately 20-30 confer field resistance in varying degrees. The 10 QTLs accounting for the most variation in field resistance explained 26-30% of the total variation (depending on traits: percent severity, coefficient of infection or response type). Similarly, the 10 QTLs accounting for most of the variation in seedling resistance to different races explained 24-34% of the variation, after correcting for population structure. Two potentially novel QTLs (QLr.umn-1AL, QLr.umn-4AS) were identified. Identification of novel genes or QTLs and validation of previously identified genes or QTLs for seedling and especially adult plant resistance will enhance understanding of leaf rust resistance and assist breeding for resistant wheat varieties. We also developed computer programs to automate field and seedling rust phenotype data conversions. This is the first GWAS study of leaf rust resistance in elite wheat breeding lines genotyped with high density 90K SNP arrays.
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Affiliation(s)
- Liangliang Gao
- University of Minnesota, Department of Agronomy and Plant Genetics, St. Paul, MN, 55108, United States of America
| | - M Kathryn Turner
- University of Minnesota, Department of Agronomy and Plant Genetics, St. Paul, MN, 55108, United States of America
| | - Shiaoman Chao
- USDA-ARS Biosciences Research Lab, Fargo, ND, 58102, United States of America
| | - James Kolmer
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN, 55108, United States of America
- University of Minnesota, Department of Plant Pathology, St. Paul, MN, 55108, United States of America
| | - James A Anderson
- University of Minnesota, Department of Agronomy and Plant Genetics, St. Paul, MN, 55108, United States of America
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