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Delfan S, Bihamta MR, Dadrezaei ST, Abbasi A, Alipoor H. Exploring genomic regions involved in bread wheat resistance to leaf rust at seedling/adult stages by using GWAS analysis. BMC Genomics 2023; 24:83. [PMID: 36810004 PMCID: PMC9945389 DOI: 10.1186/s12864-022-09096-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 12/22/2022] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Global wheat productivity is seriously challenged by a range of rust pathogens, especially leaf rust derived from Puccinia triticina. Since the most efficient approach to control leaf rust is genetic resistance, many efforts have been made to uncover resistance genes; however, it demands an ongoing exploration for effective resistance sources because of the advent of novel virulent races. Thus, the current study was focused on detecting leaf rust resistance-related genomic loci against the P. triticina prevalent races by GWAS in a set of Iranian cultivars and landraces. RESULTS Evaluation of 320 Iranian bread wheat cultivars and landraces against four prevalent rust pathotypes of P. triticina (LR-99-2, LR-98-12, LR-98-22, and LR-97-12) indicated the diversity in wheat accessions responses to P. triticina. From GWAS results, 80 leaf rust resistance QTLs were located in the surrounding known QTLs/genes on almost chromosomes, except for 1D, 3D, 4D, and 7D. Of these, six MTAs (rs20781/rs20782 associated with resistance to LR-97-12; rs49543/rs52026 for LR-98-22; rs44885/rs44886 for LR-98-22/LR-98-1/LR-99-2) were found on genomic regions where no resistance genes previously reported, suggesting new loci conferring resistance to leaf rust. The GBLUP genomic prediction model appeared better than RR-BLUP and BRR, reflecting that GBLUP is a potent model for genomic selection in wheat accessions. CONCLUSIONS Overall, the newly identified MTAs as well as the highly resistant accessions in the recent work provide an opportunity towards improving leaf rust resistance.
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Affiliation(s)
- Saba Delfan
- grid.46072.370000 0004 0612 7950Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
| | - Mohammad Reza Bihamta
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran.
| | - Seyed Taha Dadrezaei
- grid.473705.20000 0001 0681 7351Department of Cereal Research, Seed and Plant Improvement Institute, Agricultural Research and Education Organization (AREEO), Karaj, Iran
| | - Alireza Abbasi
- grid.46072.370000 0004 0612 7950Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
| | - Hadi Alipoor
- grid.412763.50000 0004 0442 8645Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
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Wang Z, Jiang X, Zhang Y, Du Z, Feng J, Quan W, Ren J, Che M, Zhang Z. Identification and Validation of a Major Quantitative Trait Locus for Adult Plant Resistance Against Leaf Rust From the Chinese Wheat Landrace Bai Qimai. FRONTIERS IN PLANT SCIENCE 2022; 13:812002. [PMID: 35665144 PMCID: PMC9158542 DOI: 10.3389/fpls.2022.812002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/21/2022] [Indexed: 06/15/2023]
Abstract
Leaf rust caused by Puccinia triticina Eriks. (Pt) is a common disease of wheat worldwide. The Chinese wheat landrace Bai Qimai (BQM) has shown high resistance to leaf rust for a prolonged period of time; the infected leaves of BQM displayed high infection types (ITs), but they showed low disease severities at the adult plant stage. To find quantitative trait loci (QTL) for resistance to leaf rust, 186 recombinant inbred lines from the cross Nugaines × BQM were phenotyped for leaf rust response in multiple field environments under natural Pt infections and genotyped using the 90K wheat single nucleotide polymorphism (SNP) chip and simple sequence repeat (SSR) markers. A total of 2,397 polymorphic markers were used for QTL mapping, and a novel major QTL (QLr.cau-6DL) was detected on chromosome 6DL from BQM. The effectiveness of QLr.cau-6DL was validated using the three additional wheat populations (RL6058 × BQM, Aikang58 × BQM, and Jimai22 × BQM). QLr.cau-6DL could significantly reduce leaf rust severities across all tested environments and different genetic backgrounds, and its resistance was more effective than that of Lr34. Moreover, QLr.cau-6DL acted synergistically with Lr34 to confer strong resistance to leaf rust. We believe that QLr.cau-6DL should have high potential value in the breeding of wheat cultivars with leaf rust resistance.
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Affiliation(s)
- Zhen Wang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Xu Jiang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Yuzhu Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Ziyi Du
- School of Agroforestry & Medicine, Open University of China, Beijing, China
| | - Jing Feng
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Quan
- Beijing Engineering and Technique Research Center for Hybrid Wheat, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Junda Ren
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, China
| | - Mingzhe Che
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Zhongjun Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, China
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Vikas VK, Pradhan AK, Budhlakoti N, Mishra DC, Chandra T, Bhardwaj SC, Kumar S, Sivasamy M, Jayaprakash P, Nisha R, Shajitha P, Peter J, Geetha M, Mir RR, Singh K, Kumar S. Multi-locus genome-wide association studies (ML-GWAS) reveal novel genomic regions associated with seedling and adult plant stage leaf rust resistance in bread wheat (Triticum aestivum L.). Heredity (Edinb) 2022; 128:434-449. [PMID: 35418669 DOI: 10.1038/s41437-022-00525-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 01/02/2023] Open
Abstract
Leaf rust is one of the important diseases limiting global wheat production and productivity. To identify quantitative trait nucleotides (QTNs) or genomic regions associated with seedling and adult plant leaf rust resistance, multilocus genome-wide association studies (ML-GWAS) were performed on a panel of 400 diverse wheat genotypes using 35 K single-nucleotide polymorphism (SNP) genotyping assays and trait data of leaf rust resistance. Association analyses using six multi-locus GWAS models revealed a set of 201 significantly associated QTNs for seedling and 65 QTNs for adult plant resistance (APR), explaining 1.98-31.72% of the phenotypic variation for leaf rust. Among these QTNs, 51 reliable QTNs for seedling and 15 QTNs for APR were consistently detected in at least two GWAS models and were considered reliable QTNs. Three genomic regions were pleiotropic, each controlling two to three pathotype-specific seedling resistances to leaf rust. We also identified candidate genes, such as leucine-rich repeat receptor-like (LRR) protein kinases, P-loop containing nucleoside triphosphate hydrolase and serine-threonine/tyrosine-protein kinases (STPK), which have a role in pathogen recognition and disease resistance linked to the significantly associated genomic regions. The QTNs identified in this study can prove useful in wheat molecular breeding programs aimed at enhancing resistance to leaf rust and developing next-generation leaf rust-resistant varieties.
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Affiliation(s)
- V K Vikas
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, 643 231, India
| | | | - Neeraj Budhlakoti
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India.
| | | | - Tilak Chandra
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - S C Bhardwaj
- ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, Himachal Pradesh, 171002, India
| | - Subodh Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, Himachal Pradesh, 171002, India
| | - M Sivasamy
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, 643 231, India
| | - P Jayaprakash
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, 643 231, India
| | - R Nisha
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, 643 231, India
| | - P Shajitha
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, 643 231, India
| | - John Peter
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, 643 231, India
| | - M Geetha
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, 643 231, India
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Srinagar, India
| | - Kuldeep Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India.,Genetic Resource Division, ICRISAT, Patancheru, Hyderabad, India
| | - Sundeep Kumar
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India.
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Baranwal D, Cu S, Stangoulis J, Trethowan R, Bariana H, Bansal U. Identification of genomic regions conferring rust resistance and enhanced mineral accumulation in a HarvestPlus Association Mapping Panel of wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:865-882. [PMID: 34993553 DOI: 10.1007/s00122-021-04003-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/19/2021] [Indexed: 05/18/2023]
Abstract
New genomic regions for high accumulation of 10 minerals were identified. The 1B:1R and 2NS translocations enhanced concentrations of four and two minerals, respectively, in addition to disease resistance. Puccinia species, the causal agents of rust diseases of wheat, have the potential to cause total crop failures due their high evolutionary ability to acquire virulence for resistance genes deployed in commercial cultivars. Hence, the discovery of genetically diverse sources of rust resistance is essential. On the other hand, biofortification of wheat for essential nutrients, such as zinc (Zn) and iron (Fe), is also an objective in wheat improvement programs to tackle micronutrient deficiency. The development of rust-resistant and nutrient-concentrated wheat cultivars would be important for sustainable production and the fight against malnutrition. The HarvestPlus association mapping panel (HPAMP) that included nutrient-dense sources from diverse genetic backgrounds was genotyped using a 90 K Infinium SNP array and 13 markers linked with rust resistance genes. The HPAMP was used for genome-wide association mapping to identify genomic regions underpinning rust resistance and mineral accumulation. Twelve QTL for rust resistance and 53 for concentrations of 10 minerals were identified. Comparison of results from this study with the published QTL information revealed the detection of already known and some putatively new genes/QTL underpinning stripe rust and leaf rust resistance in this panel. Thirty-six new QTL for mineral concentration were identified on 17 chromosomes. Accessions carrying the 1B:1R translocation accumulated higher concentrations of Zn, Fe, Copper (Cu) and sulphur (S). The 2NS segment showed enhanced accumulation of grain Fe and Cu. Fifteen rust-resistant and biofortified accessions were identified for use as donor sources in breeding programs.
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Affiliation(s)
- Deepak Baranwal
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
- Department of Plant Breeding and Genetics, Bihar Agricultural University, Sabour, 813210, India
| | - Suong Cu
- College of Science & Engineering, Flinders University, Sturt Road, Bedford Park, South Australia, 5042, Australia
| | - James Stangoulis
- College of Science & Engineering, Flinders University, Sturt Road, Bedford Park, South Australia, 5042, Australia
| | - Richard Trethowan
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
| | - Harbans Bariana
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia.
| | - Urmil Bansal
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia.
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Zhang Y, Wang Z, Quan W, Zhang X, Feng J, Ren J, Jiang X, Zhang Z. Mapping of a QTL with major effect on reducing leaf rust severity at the adult plant growth stage on chromosome 2BL in wheat landrace Hongmazha. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1363-1376. [PMID: 33550471 DOI: 10.1007/s00122-021-03776-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
A major QTL (QLr.cau-2BL) for APR to leaf rust was detected on 2BL; an SSR marker was developed to closely link with QLr.cau-2BL and validated for effectiveness of MAS. The wheat landrace Hongmazha (HMZ) possesses adult plant resistance (APR) to leaf rust. To detect and validate quantitative trait locus (QTL) for the APR, four wheat populations were assessed for leaf rust severity in a total of eight field and greenhouse experiments. The mapping population Aquileja × HMZ (120 recombinant inbred lines, RILs) was genotyped using 90 K SNP markers. A major QTL (QLr.cau-2BL) was detected between the markers IWB3854 and IWB21922 on chromosome 2BL. IWB3854 and IWB21922 were positioned at approximately 531.14 Mb and 616.48 Mb, respectively, on 2BL of IWGSC RefSeq v1.0 physical map. Based on the sequences between 531.14 and 616.48 Mb on 2BL of IWGSC RefSeq v1.0, 415 simple sequence repeat (SSR) markers were developed. These markers and 28 previously published SSR makers were screened; the resulted polymorphic markers were used to genotype the relatively larger population RL6058 × HMZ (371 RILs). QLr.cau-2BL was mapped within a 1.5 cM interval on 2BL map of RL6058 × HMZ, and a marker (Ta2BL_ssr7) was identified to closely link with QLr.cau-2BL. Effectiveness of selection for QLr.cau-2BL based on Ta2BL_ssr7 was validated using two populations (RL6058 × HMZ F2:3 and Jimai22 × HMZ BC4F2:3). In addition, polymorphism at Ta2BL_ssr7 was detected among a panel of 282 commercial wheat cultivars. We believe, therefore, that Ta2BL_ssr7 should be useful for introducing QLr.cau-2BL into commercial wheat cultivars and for accumulating QLr.cau-2BL with other APR QTL.
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Affiliation(s)
- Yibin Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Zhen Wang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Wei Quan
- Beijing Engineering and Technique Research Center for Hybrid Wheat, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, People's Republic of China.
| | - Xiang Zhang
- National Fisheries Technology Extension Center, Beijing, 100125, People's Republic of China
| | - Jing Feng
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Junda Ren
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Xu Jiang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Zhongjun Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, People's Republic of China.
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Kolmer JA, Turner MK, Rouse MN, Anderson JA. Adult Plant Leaf Rust Resistance in AC Taber Wheat Maps to Chromosomes 2BS and 3BS. PHYTOPATHOLOGY 2021; 111:380-385. [PMID: 32734813 DOI: 10.1094/phyto-03-20-0074-r] [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: 06/11/2023]
Abstract
AC Taber is a hard red spring wheat cultivar that has had long-lasting resistance to the leaf rust fungus Puccinia triticina. The objective of this study was to determine the chromosome location of the leaf rust resistance genes in AC Taber. The leaf rust-susceptible cultivar Thatcher was crossed with AC Taber to develop an F6 recombinant inbred line (RIL) population. The RILs and parents were evaluated for segregation of leaf rust resistance in five field plot tests and in two seedling tests to race BBBDB of P. triticina. A genetic map of the RIL population was developed using 90,000 single nucleotide polymorphism markers with the Illumina Infinium iSelect 90K wheat bead array. Quantitative trait loci (QTLs) with significant effects for lower leaf rust severity in the field plot tests were found on chromosomes 2BS and 3BS. The same QTLs also had significant effects for lower infection type in seedlings to leaf rust race BBBDB. The gene on 2BS was the adult plant resistance gene Lr13, and the gene on 3BS mapped to the same region as the adult plant resistance gene Lr74 and other QTLs for leaf rust resistance. Kompetitive allele-specific PCR assay markers linked to the 2BS and 3BS regions were developed and should be useful for marker-based selection of these genes.
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Affiliation(s)
- J A Kolmer
- Cereal Disease Laboratory, U.S. Department of Agriculture Agricultural Research Service, St. Paul, MN 55108
| | - M K Turner
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
| | - M N Rouse
- Cereal Disease Laboratory, U.S. Department of Agriculture Agricultural Research Service, St. Paul, MN 55108
| | - J A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
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Rollar S, Serfling A, Geyer M, Hartl L, Mohler V, Ordon F. QTL mapping of adult plant and seedling resistance to leaf rust (Puccinia triticina Eriks.) in a multiparent advanced generation intercross (MAGIC) wheat population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:37-51. [PMID: 33201290 PMCID: PMC7813716 DOI: 10.1007/s00122-020-03657-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 07/28/2020] [Indexed: 05/22/2023]
Abstract
The Bavarian MAGIC Wheat population, comprising 394 F6:8 recombinant inbred lines was phenotyped for Puccinia triticina resistance in multi-years' field trials at three locations and in a controlled environment seedling test. Simple intervall mapping revealed 19 QTL, corresponding to 11 distinct chromosomal regions. The biotrophic rust fungus Puccinia triticina is one of the most important wheat pathogens with the potential to cause yield losses up to 70%. Growing resistant cultivars is the most cost-effective and environmentally friendly way to encounter this problem. The emergence of leaf rust races being virulent against common resistance genes increases the demand for wheat varieties with novel resistances. In the past decade, the use of complex experimental populations, like multiparent advanced generation intercross (MAGIC) populations, has risen and offers great advantages for mapping resistances. The genetic diversity of multiple parents, which has been recombined over several generations, leads to a broad phenotypic diversity, suitable for high-resolution mapping of quantitative traits. In this study, interval mapping was performed to map quantitative trait loci (QTL) for leaf rust resistance in the Bavarian MAGIC Wheat population, comprising 394 F6:8 recombinant inbred lines (RILs). Phenotypic evaluation of the RILs for adult plant resistance was carried out in field trials at three locations and two years, as well as in a controlled-environment seedling inoculation test. In total, interval mapping revealed 19 QTL, which corresponded to 11 distinct chromosomal regions controlling leaf rust resistance. Six of these regions may represent putative new QTL. Due to the elite parental material, RILs identified to be resistant to leaf rust can be easily introduced in breeding programs.
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Affiliation(s)
- Sandra Rollar
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin Baur‑Straße 27, 06484 Quedlinburg, Germany
| | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin Baur‑Straße 27, 06484 Quedlinburg, Germany
| | - Manuel Geyer
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 8, Freising, Germany
| | - Lorenz Hartl
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 8, Freising, Germany
| | - Volker Mohler
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 8, Freising, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin Baur‑Straße 27, 06484 Quedlinburg, Germany
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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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9
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Leonova IN, Skolotneva ES, Salina EA. Genome-wide association study of leaf rust resistance in Russian spring wheat varieties. BMC PLANT BIOLOGY 2020; 20:135. [PMID: 33050873 PMCID: PMC7557001 DOI: 10.1186/s12870-020-02333-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/06/2020] [Indexed: 05/29/2023]
Abstract
BACKGROUND Leaf rust (Puccinia triticina Eriks.) is one of the most dangerous diseases of common wheat worldwide. Three approaches: genome-wide association study (GWAS), marker-assisted selection (MAS) and phytopathological evaluation in field, were used for assessment of the genetic diversity of Russian spring wheat varieties on leaf rust resistance loci and for identification of associated molecular markers. RESULTS The collection, consisting of 100 Russian varieties of spring wheat, was evaluated over three seasons for resistance to the native population of leaf rust specific to the West Siberian region of Russia. The results indicated that most cultivars showed high susceptibility to P. triticina, with severity ratings (SR) of 60S-90S, however some cultivars showed a high level of leaf rust resistance (SR < 20MR-R). Based on the results of genome-wide association studies (GWAS) performed using the wheat 15 K genotyping array, 20 SNPs located on chromosomes 6D, 6A, 6B, 5A, 1B, 2A, 2B and 7A were revealed to be associated with leaf rust resistance. Genotyping with markers developed for known leaf rust resistance genes showed that most of the varieties contain genes Lr1, Lr3a, Lr9, Lr10, Lr17a, Lr20, Lr26 and Lr34, which are not currently effective against the pathogen. In the genome of three wheat varieties, gene Lr6Ai = 2 inherited from Th. intermedium was detected, which provides complete protection against the rust pathogen. It has been suggested that the QTL mapped to the chromosome 5AS of wheat cultivar Tulaikovskaya-zolotistaya, Tulaikovskaya-10, Samsar, and Volgouralskaya may be a new, previously undescribed locus conferring resistance to leaf rust. Obtained results also indicate that chromosome 1BL of the varieties Sonata, Otrada-Sibiri, Tertsiya, Omskaya-23, Tulaikovskaya-1, Obskaya-14, and Sirena may contain an unknown locus that provides a resistance response to local population. CONCLUSIONS This study provides new insights into the genetic basis of resistance to leaf rust in Russian spring wheat varieties. The SNPs significantly associated with leaf rust resistance can be used for the development and application of diagnostic markers in marker-assisted selection schemes.
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Affiliation(s)
- Irina N. Leonova
- The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - Ekaterina S. Skolotneva
- The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - Elena A. Salina
- Kurchatov Genomics Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090 Russia
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10
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Joukhadar R, Hollaway G, Shi F, Kant S, Forrest K, Wong D, Petkowski J, Pasam R, Tibbits J, Bariana H, Bansal U, Spangenberg G, Daetwyler H, Gendall T, Hayden M. Genome-wide association reveals a complex architecture for rust resistance in 2300 worldwide bread wheat accessions screened under various Australian conditions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2695-2712. [PMID: 32504212 DOI: 10.1007/s00122-020-03626-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 05/25/2020] [Indexed: 05/13/2023]
Abstract
We utilized 2300 wheat accessions including worldwide landraces, cultivars and primary synthetic-derived germplasm with three Australian cultivars: Annuello, Yitpi and Correll, to investigate field-based resistance to leaf (Lr) rust, stem (Sr) rust and stripe (Yr) rust diseases across a range of Australian wheat agri-production zones. Generally, the resistance in the modern Australian cultivars, synthetic derivatives, South and North American materials outperformed other geographical subpopulations. Different environments for each trait showed significant correlations, with average r values of 0.53, 0.23 and 0.66 for Lr, Sr and Yr, respectively. Single-trait genome-wide association studies (GWAS) revealed several environment-specific and multi-environment quantitative trait loci (QTL). Multi-trait GWAS confirmed a cluster of Yr QTL on chromosome 3B within a 4.4-cM region. Linkage disequilibrium and comparative mapping showed that at least three Yr QTL exist within the 3B cluster including the durable rust resistance gene Yr30. An Sr/Lr QTL on chromosome 3D was found mainly in the synthetic-derived germplasm from Annuello background which is known to carry the Agropyron elongatum 3D translocation involving the Sr24/Lr24 resistance locus. Interestingly, estimating the SNP effects using a BayesR method showed that the correlation among the highest 1% of QTL effects across environments (excluding GWAS QTL) had significant correlations, with average r values of 0.26, 0.16 and 0.55 for Lr, Sr and Yr, respectively. These results indicate the importance of small effect QTL in achieving durable rust resistance which can be captured using genomic selection.
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Affiliation(s)
- Reem Joukhadar
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, Australia.
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia.
| | - Grant Hollaway
- Agriculture Victoria, Natimuk Road, Horsham, VIC, 3401, Australia
| | - Fan Shi
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, Australia
| | - Surya Kant
- Agriculture Victoria, Natimuk Road, Horsham, VIC, 3401, Australia
| | - Kerrie Forrest
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, Australia
| | - Debbie Wong
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, Australia
| | - Joanna Petkowski
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, Australia
| | - Raj Pasam
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, Australia
| | - Josquin Tibbits
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, Australia
| | - Harbans Bariana
- Faculty of Agriculture and Environment, Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia
| | - Urmil Bansal
- Faculty of Agriculture and Environment, Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia
| | - German Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Hans Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Tony Gendall
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Matthew Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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11
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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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12
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Ramakrishnan SM, Sidhu JS, Ali S, Kaur N, Wu J, Sehgal SK. Molecular characterization of bacterial leaf streak resistance in hard winter wheat. PeerJ 2019; 7:e7276. [PMID: 31341737 PMCID: PMC6637926 DOI: 10.7717/peerj.7276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/07/2019] [Indexed: 11/20/2022] Open
Abstract
Bacterial leaf streak (BLS) caused by Xanthomonas campestris pv. translucens is one of the major bacterial diseases threatening wheat production in the United States Northern Great Plains (NGP) region. It is a sporadic but widespread wheat disease that can cause significant loss in grain yield and quality. Identification and characterization of genomic regions in wheat that confer resistance to BLS will help track resistance genes/QTLs in future wheat breeding. In this study, we evaluated a hard winter wheat association mapping panel (HWWAMP) containing 299 hard winter wheat lines from the US hard winter wheat growing region for their reactions to BLS. We observed a range of BLS responses among the lines, importantly, we identified ten genotypes that showed a resistant reaction both in greenhouse and field evaluation. -Genome-wide association analysis with 15,990 SNPs was conducted using an exponentially compressed mixed linear model. Five genomic regions (p < 0.001) that regulate the resistance to BLS were identified on chromosomes 1AL, 1BS, 3AL, 4AL, and 7AS. The QTLs Q.bls.sdsu-1AL, Q.bls.sdsu-1BS, Q.bls.sdsu-3AL, Q.bls.sdsu-4AL, and Q.bls.sdsu-7AS explain a total of 42% of the variation. In silico analysis of sequences in the candidate regions on chromosomes 1AL, 1BS, 3AL, 4AL, and 7AS identified 10, 25, 22, eight, and nine genes, respectively with known plant defense-related functions. Comparative analysis with rice showed two syntenic regions in rice that harbor genes for bacterial leaf streak resistance. The ten BLS resistant genotypes and SNP markers linked to the QTLs identified in our study could facilitate breeding for BLS resistance in winter wheat.
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Affiliation(s)
- Sai Mukund Ramakrishnan
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Jagdeep Singh Sidhu
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Shaukat Ali
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Navjot Kaur
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Jixiang Wu
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Sunish K. Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
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13
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Pinto da Silva GB, Zanella CM, Martinelli JA, Chaves MS, Hiebert CW, McCallum BD, Boyd LA. Quantitative Trait Loci Conferring Leaf Rust Resistance in Hexaploid Wheat. PHYTOPATHOLOGY 2018; 108:1344-1354. [PMID: 30211634 DOI: 10.1094/phyto-06-18-0208-rvw] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Leaf rust, caused by the fungal pathogen Puccinia triticina, is a major threat to wheat production in many wheat-growing regions of the world. The introduction of leaf rust resistance genes into elite wheat germplasm is the preferred method of disease control, being environmentally friendly and crucial to sustained wheat production. Consequently, there is considerable value in identifying and characterizing new sources of leaf rust resistance. While many major, qualitative leaf rust resistance genes have been identified in wheat, a growing number of valuable sources of quantitative resistance have been reported. Here we review the progress made in the genetic identification of quantitative trait loci (QTL) for leaf rust resistance detected primarily in field analyses, i.e., adult plant resistance. Over the past 50 years, leaf rust resistance loci have been assigned to genomic locations through chromosome analyses and genetic mapping in biparental mapping populations, studies that represent 79 different wheat leaf rust resistance donor lines. In addition, seven association mapping studies have identified adult plant and seedling leaf rust resistance marker trait associations in over 4,000 wheat genotypes. Adult plant leaf rust resistance QTL have been found on all 21 chromosomes of hexaploid wheat, with the B genome carrying the greatest number of QTL. The group 2 chromosomes are also particularly rich in leaf rust resistance QTL. The A genome has the lowest number of QTL for leaf rust resistance. Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
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Affiliation(s)
- Gerarda Beatriz Pinto da Silva
- First and third author: Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 7712. Porto Alegre, RS, Brazil; second and seventh authors: NIAB, Huntingdon Road, Cambridge, CB3 0LE, UK; fourth author: Empresa Brasileira de Pesquisa Agropecuária-Embrapa Clima Temperado, Rodovia BR-392, Km 78, Pelotas, RS, Brazil; and fifth and sixth authors: Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB R6M 1Y5, Canada
| | - Camila Martini Zanella
- First and third author: Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 7712. Porto Alegre, RS, Brazil; second and seventh authors: NIAB, Huntingdon Road, Cambridge, CB3 0LE, UK; fourth author: Empresa Brasileira de Pesquisa Agropecuária-Embrapa Clima Temperado, Rodovia BR-392, Km 78, Pelotas, RS, Brazil; and fifth and sixth authors: Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB R6M 1Y5, Canada
| | - José Antônio Martinelli
- First and third author: Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 7712. Porto Alegre, RS, Brazil; second and seventh authors: NIAB, Huntingdon Road, Cambridge, CB3 0LE, UK; fourth author: Empresa Brasileira de Pesquisa Agropecuária-Embrapa Clima Temperado, Rodovia BR-392, Km 78, Pelotas, RS, Brazil; and fifth and sixth authors: Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB R6M 1Y5, Canada
| | - Márcia Soares Chaves
- First and third author: Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 7712. Porto Alegre, RS, Brazil; second and seventh authors: NIAB, Huntingdon Road, Cambridge, CB3 0LE, UK; fourth author: Empresa Brasileira de Pesquisa Agropecuária-Embrapa Clima Temperado, Rodovia BR-392, Km 78, Pelotas, RS, Brazil; and fifth and sixth authors: Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB R6M 1Y5, Canada
| | - Colin W Hiebert
- First and third author: Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 7712. Porto Alegre, RS, Brazil; second and seventh authors: NIAB, Huntingdon Road, Cambridge, CB3 0LE, UK; fourth author: Empresa Brasileira de Pesquisa Agropecuária-Embrapa Clima Temperado, Rodovia BR-392, Km 78, Pelotas, RS, Brazil; and fifth and sixth authors: Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB R6M 1Y5, Canada
| | - Brent D McCallum
- First and third author: Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 7712. Porto Alegre, RS, Brazil; second and seventh authors: NIAB, Huntingdon Road, Cambridge, CB3 0LE, UK; fourth author: Empresa Brasileira de Pesquisa Agropecuária-Embrapa Clima Temperado, Rodovia BR-392, Km 78, Pelotas, RS, Brazil; and fifth and sixth authors: Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB R6M 1Y5, Canada
| | - Lesley Ann Boyd
- First and third author: Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 7712. Porto Alegre, RS, Brazil; second and seventh authors: NIAB, Huntingdon Road, Cambridge, CB3 0LE, UK; fourth author: Empresa Brasileira de Pesquisa Agropecuária-Embrapa Clima Temperado, Rodovia BR-392, Km 78, Pelotas, RS, Brazil; and fifth and sixth authors: Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB R6M 1Y5, Canada
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14
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Zatybekov A, Abugalieva S, Didorenko S, Rsaliyev A, Turuspekov Y. GWAS of a soybean breeding collection from South East and South Kazakhstan for resistance to fungal diseases. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.392] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Soybean (Glycine max(L.) Merr) is an essential food, feed, and technical culture. In Kazakhstan the area under soybean is increasing every year, helping to solve the problem of protein deficiency in human nutrition and animal feeding. One of the main problems of soybean production is fungal diseases causing yields losses of up to 30 %. Modern genomic studies can be applied to facilitate efficient breeding research for improvement of soybean fungal disease tolerance. Therefore, the objective of this genome-wide association study (GWAS) was analysis of a soybean collection consisting of 182 accessions in relation to fungal diseases in the conditions of South East and South Kazakhstan. Field evaluation of the soybean collection suggested thatFusariumspp. andCercospora sojinaaffected plants in the South region (RIBSP), andSeptoria glycines– in the South East region (KRIAPP). The major objective of the study was identification of QTL associated with resistance to fusarium root rot (FUS), frogeye leaf spot (FLS), and brown spot (BS). GWAS using 4 442 SNP (single nucleotide polymorphism) markers of Illumina iSelect array allowed for identification of fifteen marker trait associations (MTA) resistant to the three diseases at two different stages of growth. Two QTL both for FUS (chromosomes 13 and 17) and BS (chromosomes 14 and 17) were genetically mapped, including one presumably novel QTL for BS (chromosome 17). Also, five presumably novel QTL for FLS were genetically mapped on chromosomes 2, 7, and 15. The results can be used for improvement of the local breeding projects based on marker-assisted selection approach.
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15
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Kolmer JA, Bernardo A, Bai G, Hayden MJ, Chao S. Adult Plant Leaf Rust Resistance Derived from Toropi Wheat is Conditioned by Lr78 and Three Minor QTL. PHYTOPATHOLOGY 2018; 108:246-253. [PMID: 28990484 DOI: 10.1094/phyto-07-17-0254-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Leaf rust caused by Puccinia triticina is an important disease of wheat in many regions worldwide. Durable or long-lasting leaf rust resistance has been difficult to achieve because populations of P. triticina are highly variable for virulence to race-specific resistance genes, and respond to selection by resistance genes in released wheat cultivars. The wheat cultivar Toropi, developed and grown in Brazil, was noted to have long-lasting leaf rust resistance that was effective only in adult plants. The objectives of this study were to determine the chromosome location of the leaf rust resistance genes derived from Toropi in two populations of recombinant inbred lines in a partial Thatcher wheat background. In the first population, a single gene with major effects on chromosome 5DS that mapped 2.2 centimorgans distal to IWA6289, strongly reduced leaf rust severity in all 3 years of field plot tests. This gene for adult plant leaf rust resistance was designated as Lr78. In the second population, quantitative trait loci (QTL) with small effects on chromosomes 1BL, 3BS, and 4BS were found. These QTL expressed inconsistently over 4 years of field plot tests. The adult plant leaf rust resistance derived from Toropi involved a complex combination of QTL with large and small effects.
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Affiliation(s)
- J A Kolmer
- First author: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Cereal Disease Laboratory, St. Paul, MN 55108; second author: Department of Plant Pathology, Kansas State University, Manhattan 66506; third author: USDA-ARS Hard Red Winter Wheat Genetics Research, Manhattan, KS 66506; fourth author: Department of Economic Development, Jobs, Transport and Resources, AgriBio Center, LaTrobe University, Bundorra, Victoria 3083, Australia; and fifth author: USDA, Cereal Crops Research Unit, Fargo ND 58102
| | - A Bernardo
- First author: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Cereal Disease Laboratory, St. Paul, MN 55108; second author: Department of Plant Pathology, Kansas State University, Manhattan 66506; third author: USDA-ARS Hard Red Winter Wheat Genetics Research, Manhattan, KS 66506; fourth author: Department of Economic Development, Jobs, Transport and Resources, AgriBio Center, LaTrobe University, Bundorra, Victoria 3083, Australia; and fifth author: USDA, Cereal Crops Research Unit, Fargo ND 58102
| | - G Bai
- First author: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Cereal Disease Laboratory, St. Paul, MN 55108; second author: Department of Plant Pathology, Kansas State University, Manhattan 66506; third author: USDA-ARS Hard Red Winter Wheat Genetics Research, Manhattan, KS 66506; fourth author: Department of Economic Development, Jobs, Transport and Resources, AgriBio Center, LaTrobe University, Bundorra, Victoria 3083, Australia; and fifth author: USDA, Cereal Crops Research Unit, Fargo ND 58102
| | - M J Hayden
- First author: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Cereal Disease Laboratory, St. Paul, MN 55108; second author: Department of Plant Pathology, Kansas State University, Manhattan 66506; third author: USDA-ARS Hard Red Winter Wheat Genetics Research, Manhattan, KS 66506; fourth author: Department of Economic Development, Jobs, Transport and Resources, AgriBio Center, LaTrobe University, Bundorra, Victoria 3083, Australia; and fifth author: USDA, Cereal Crops Research Unit, Fargo ND 58102
| | - S Chao
- First author: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Cereal Disease Laboratory, St. Paul, MN 55108; second author: Department of Plant Pathology, Kansas State University, Manhattan 66506; third author: USDA-ARS Hard Red Winter Wheat Genetics Research, Manhattan, KS 66506; fourth author: Department of Economic Development, Jobs, Transport and Resources, AgriBio Center, LaTrobe University, Bundorra, Victoria 3083, Australia; and fifth author: USDA, Cereal Crops Research Unit, Fargo ND 58102
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16
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Riaz A, Athiyannan N, Periyannan SK, Afanasenko O, Mitrofanova OP, Platz GJ, Aitken EAB, Snowdon RJ, Lagudah ES, Hickey LT, Voss-Fels KP. Unlocking new alleles for leaf rust resistance in the Vavilov wheat collection. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:127-144. [PMID: 28980023 DOI: 10.1007/s00122-017-2990-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/21/2017] [Indexed: 05/06/2023]
Abstract
Thirteen potentially new leaf rust resistance loci were identified in a Vavilov wheat diversity panel. We demonstrated the potential of allele stacking to strengthen resistance against this important pathogen. Leaf rust (LR) caused by Puccinia triticina is an important disease of wheat (Triticum aestivum L.), and the deployment of genetically resistant cultivars is the most viable strategy to minimise yield losses. In this study, we evaluated a diversity panel of 295 bread wheat accessions from the N. I. Vavilov Institute of Plant Genetic Resources (St Petersburg, Russia) for LR resistance and performed genome-wide association studies (GWAS) using 10,748 polymorphic DArT-seq markers. The diversity panel was evaluated at seedling and adult plant growth stages using three P. triticina pathotypes prevalent in Australia. GWAS was applied to 11 phenotypic data sets which identified a total of 52 significant marker-trait associations representing 31 quantitative trait loci (QTL). Among them, 29 QTL were associated with adult plant resistance (APR). Of the 31 QTL, 13 were considered potentially new loci, whereas 4 co-located with previously catalogued Lr genes and 14 aligned to regions reported in other GWAS and genomic prediction studies. One seedling LR resistance QTL located on chromosome 3A showed pronounced levels of linkage disequilibrium among markers (r 2 = 0.7), suggested a high allelic fixation. Subsequent haplotype analysis for this region found seven haplotype variants, of which two were strongly associated with LR resistance at seedling stage. Similarly, analysis of an APR QTL on chromosome 7B revealed 22 variants, of which 4 were associated with resistance at the adult plant stage. Furthermore, most of the tested lines in the diversity panel carried 10 or more combined resistance-associated marker alleles, highlighting the potential of allele stacking for long-lasting resistance.
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Affiliation(s)
- Adnan Riaz
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Naveenkumar Athiyannan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, ACT, Australia
| | - Sambasivam K Periyannan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, ACT, Australia
| | - Olga Afanasenko
- Department of Plant Resistance to Diseases, All-Russian Research Institute for Plant Protection, St Petersburg, Russia
| | - Olga P Mitrofanova
- N. I. Vavilov Institute of Plant Genetic Resources, St Petersburg, Russia
| | - Gregory J Platz
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, Australia
| | - Elizabeth A B Aitken
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Evans S Lagudah
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, ACT, Australia
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia.
| | - Kai P Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia.
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany.
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17
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Zatybekov A, Abugalieva S, Didorenko S, Gerasimova Y, Sidorik I, Anuarbek S, Turuspekov Y. GWAS of agronomic traits in soybean collection included in breeding pool in Kazakhstan. BMC PLANT BIOLOGY 2017; 17:179. [PMID: 29143671 PMCID: PMC5688460 DOI: 10.1186/s12870-017-1125-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
BACKGROUND In recent years soybean is becoming one of the most important oilseed crops in Kazakhstan. Only within the last ten years (2006-2016), the area under soybean is expanded from 45 thousand hectares (ha) in 2006 to 120 thousand ha in 2016. The general trend of soybean expansion is from south-eastern to eastern and northern regions of the country, where average temperatures are lower and growing seasons are shorter. These new soybean growing territories were poorly examined in terms of general effects on productivity level among the diverse sample of soybean accessions. In this study, phenotypic data were collected in three separate regions of Kazakhstan and entire soybean sample was genotyped for identification of marker-trait associations (MTA). RESULTS In this study, the collection of 113 accessions representing five different regions of the World was planted in 2015-2016 in northern, eastern, and south-eastern regions of Kazakhstan. It was observed that North American accessions showed the highest yield in four out of six trials especially in Northern Kazakhstan in both years. The entire sample was genotyped with 6 K SNP Illumina array. 4442 SNPs found to be polymorphic and were used for whole genome genotyping purposes. Obtained SNP markers data and field data were used for GWAS (genome-wide association study). 30 SNPs appear to be very significant in 42 MTAs in six studied environments. CONCLUSIONS The study confirms the efficiency of GWAS for the identification of molecular markers which tag important agronomic traits. Overall thirty SNP markers associated with time to flowering and maturation, plant height, number of fertile nodes, seeds per plant and yield were identified. Physical locations of 32 identified out of 42 total MTAs coincide well with positions of known analogous QTLs. This result indicates importance of revealed MTAs for soybean growing regions in Kazakhstan. Obtained results would serve as required prerequisite for forming and realization of specific breeding programs towards effective adaptation and increased productivity of soybean in three different regions of Kazakhstan.
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Affiliation(s)
- Alibek Zatybekov
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan 050040
| | - Saule Abugalieva
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan 050040
| | - Svetlana Didorenko
- Kazakh Research Institute of Agriculture, Almalybak vil., Almaty region Kazakhstan 040909
| | - Yelena Gerasimova
- East Kazakhstan Research Institute of Agriculture, Solnechnyi vil., Ust-Kamenogorsk region Kazakhstan 070518
| | - Ivan Sidorik
- Kostanai Research Institute of Agriculture, Zarechnoe vil., Kostanai region Kazakhstan 111108
| | - Shynar Anuarbek
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan 050040
| | - Yerlan Turuspekov
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan 050040
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Turuspekov Y, Baibulatova A, Yermekbayev K, Tokhetova L, Chudinov V, Sereda G, Ganal M, Griffiths S, Abugalieva S. GWAS for plant growth stages and yield components in spring wheat (Triticum aestivum L.) harvested in three regions of Kazakhstan. BMC PLANT BIOLOGY 2017; 17:190. [PMID: 29143598 PMCID: PMC5688510 DOI: 10.1186/s12870-017-1131-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
BACKGROUND Spring wheat is the largest agricultural crop grown in Kazakhstan with an annual sowing area of 12 million hectares in 2016. Annually, the country harvests around 15 million tons of high quality grain. Despite environmental stress factors it is predicted that the use of new technologies may lead to increases in productivity from current levels of 1.5 to up to 3 tons per hectare. One way of improving wheat productivity is by the application of new genomic oriented approaches in plant breeding projects. Genome wide association studies (GWAS) are emerging as powerful tools for the understanding of the inheritance of complex traits via utilization of high throughput genotyping technologies and phenotypic assessments of plant collections. In this study, phenotyping and genotyping data on 194 spring wheat accessions from Kazakhstan, Russia, Europe, and CIMMYT were assessed for the identification of marker-trait associations (MTA) of agronomic traits by using GWAS. RESULTS Field trials in Northern, Central and Southern regions of Kazakhstan using 194 spring wheat accessions revealed strong correlations of yield with booting date, plant height, biomass, number of spikes per plant, and number of kernels per spike. The accessions from Europe and CIMMYT showed high breeding potential for Southern and Central regions of the country in comparison with the performance of the local varieties. The GGE biplot method, using average yield per plant, suggested a clear separation of accessions into their three breeding origins in relationship to the three environments in which they were evaluated. The genetic variation in the three groups of accessions was further studied using 3245 polymorphic SNP (single nucleotide polymorphism) markers. The application of Principal Coordinate analysis clearly grouped the 194 accessions into three clades according to their breeding origins. GWAS on data from nine field trials allowed the identification of 114 MTAs for 12 different agronomic traits. CONCLUSIONS Field evaluation of foreign germplasm revealed its poor yield performance in Northern Kazakhstan, which is the main wheat growing region in the country. However, it was found that EU and CIMMYT germplasm has high breeding potential to improve yield performance in Central and Southern regions. The use of Principal Coordinate analysis clearly separated the panel into three distinct groups according to their breeding origin. GWAS based on use of the TASSEL 5.0 package allowed the identification of 114 MTAs for twelve agronomic traits. The study identifies a network of key genes for improvement of yield productivity in wheat growing regions of Kazakhstan.
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Affiliation(s)
- Yerlan Turuspekov
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan 050040
| | - Aida Baibulatova
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan 050040
| | - Kanat Yermekbayev
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan 050040
| | - Laura Tokhetova
- Kazakh Rice Research Institute, Kyzylorda, Kazakhstan 120016
| | | | - Grigoriy Sereda
- Karaganda Research Institute of Agriculture, Karaganda region, Kazakhstan 100435
| | | | - Simon Griffiths
- John Innes Centre, Norwich Research Park, Norwich, NR47UH UK
| | - Saule Abugalieva
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan 050040
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