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Ziems LA, Singh L, Dracatos PM, Dieters MJ, Sanchez-Garcia M, Amri A, Verma RPS, Park RF, Singh D. Characterization of Leaf Rust Resistance in International Barley Germplasm Using Genome-Wide Association Studies. Plants (Basel) 2023; 12:862. [PMID: 36840210 PMCID: PMC9963359 DOI: 10.3390/plants12040862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/09/2023] [Accepted: 02/11/2023] [Indexed: 06/18/2023]
Abstract
A panel of 114 genetically diverse barley lines were assessed in the greenhouse and field for resistance to the pathogen Puccinia hordei, the causal agent of barley leaf rust. Multi-pathotype tests revealed that 16.6% of the lines carried the all-stage resistance (ASR) gene Rph3, followed by Rph2 (4.4%), Rph1 (1.7%), Rph12 (1.7%) or Rph19 (1.7%). Five lines (4.4%) were postulated to carry the gene combinations Rph2+9.am, Rph2+19 and Rph8+19. Three lines (2.6%) were postulated to carry Rph15 based on seedling rust tests and genotyping with a marker linked closely to this gene. Based on greenhouse seedling tests and adult-plant field tests, 84 genotypes (73.7%) were identified as carrying APR, and genotyping with molecular markers linked closely to three known APR genes (Rph20, Rph23 and Rph24) revealed that 48 of the 84 genotypes (57.1%) likely carry novel (uncharacterized) sources of APR. Seven lines were found to carry known APR gene combinations (Rph20+Rph23, Rph23+Rph24 and Rph20+Rph24), and these lines had higher levels of field resistance compared to those carrying each of these three APR genes singly. GWAS identified 12 putative QTLs; strongly associated markers located on chromosomes 1H, 2H, 3H, 5H and 7H. Of these, the QTL on chromosome 7H had the largest effect on resistance response to P. hordei. Overall, these studies detected several potentially novel genomic regions associated with resistance. The findings provide useful information for breeders to support the utilization of these sources of resistance to diversify resistance to leaf rust in barley and increase resistance durability.
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Affiliation(s)
- Laura A. Ziems
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2570, Australia
| | - Lovepreet Singh
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2570, Australia
| | - Peter M. Dracatos
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2570, Australia
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Bundoora, VIC 3086, Australia
| | - Mark J. Dieters
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4067, Australia
| | - Miguel Sanchez-Garcia
- International Centre for Agriculture Research in Dry Areas (ICARDA), Rabat 10170, Morocco
| | - Ahmed Amri
- International Centre for Agriculture Research in Dry Areas (ICARDA), Rabat 10170, Morocco
| | - Ramesh Pal Singh Verma
- International Centre for Agriculture Research in Dry Areas (ICARDA), Rabat 10170, Morocco
- Indian Institute of Wheat and Barley Research, Karnal 132001, India
| | - Robert F. Park
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2570, Australia
| | - Davinder Singh
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2570, Australia
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Ziems LA, Franckowiak JD, Platz GJ, Mace ES, Park RF, Singh D, Jordan DR, Hickey LT. Investigating successive Australian barley breeding populations for stable resistance to leaf rust. Theor Appl Genet 2017; 130:2463-2477. [PMID: 28836114 DOI: 10.1007/s00122-017-2970-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/14/2017] [Indexed: 06/07/2023]
Abstract
Genome-wide association studies of barley breeding populations identified candidate minor genes for pairing with the adult plant resistance gene Rph20 to provide stable leaf rust resistance across environments. Stable resistance to barley leaf rust (BLR, caused by Puccinia hordei) was evaluated across environments in barley breeding populations (BPs). To identify genomic regions that can be combined with Rph20 to improve adult plant resistance (APR), two BPs genotyped with the Diversity Arrays Technology genotyping-by-sequencing platform (DArT-seq) were examined for reaction to BLR at both seedling and adult growth stages in Australian environments. An integrated consensus map comprising both first- and second-generation DArT platforms was used to integrate QTL information across two additional BPs, providing a total of four interrelated BPs and 15 phenotypic data sets. This enabled identification of key loci underpinning BLR resistance. The APR gene Rph20 was the only active resistance region consistently detected across BPs. Of the QTL identified, RphQ27 on chromosome 6HL was considered the best candidate for pairing with Rph20. RphQ27 did not align or share proximity with known genes and was detected in three of the four BPs. The combination of RphQ27 and Rph20 was of low frequency in the breeding material; however, strong resistance responses were observed for the lines carrying this pairing. This suggests that the candidate minor gene RphQ27 can interact additively with Rph20 to provide stable resistance to BLR across diverse environments.
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Affiliation(s)
- L A Ziems
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.
| | - J D Franckowiak
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, 55108, USA
| | - G J Platz
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - E S Mace
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - R F Park
- The University of Sydney, Plant Breeding Institute, Narellan, NSW, 2567, Australia
| | - D Singh
- The University of Sydney, Plant Breeding Institute, Narellan, NSW, 2567, Australia
| | - D R Jordan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - L T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
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Ziems LA, Hickey LT, Platz GJ, Franckowiak JD, Dracatos PM, Singh D, Park RF. Characterization of Rph24: A Gene Conferring Adult Plant Resistance to Puccinia hordei in Barley. Phytopathology 2017; 107:834-841. [PMID: 28430019 DOI: 10.1094/phyto-08-16-0295-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We identified Rph24 as a locus in barley (Hordeum vulgare L.) controlling adult plant resistance (APR) to leaf rust, caused by Puccinia hordei. The locus was previously reported as a quantitative trait locus in barley line ND24260-1 and named qRphND. We crossed ND24260-1 to the leaf-rust-susceptible standard Gus and determined inheritance patterns in the progeny. For the comparative marker frequency analysis (MFA), resistant and susceptible tails of the F2 were genotyped with Diversity Arrays Technology genotyping-by-sequencing (DArT-Seq) markers. The Rph24 locus was positioned at 55.5 centimorgans on chromosome 6H on the DArT-Seq consensus map. Evaluation of F2:3 families confirmed that a single locus from ND24260-1 conferred partial resistance. The haploblock strongly associated with the Rph24 locus was used to estimate the allele frequency in a collection of 282 international barley cultivars. Rph24 was frequently paired with APR locus Rph20 in cultivars displaying high levels of APR to leaf rust. The markers identified in this study for Rph24 should be useful for marker-assisted selection.
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Affiliation(s)
- Laura A Ziems
- First and second authors: The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, QLD 4072, Australia; third author: Department of Agriculture and Fisheries, Hermitage Research Facility, 604 Yangan Rd, Warwick, QLD 4370, Australia; fourth author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108; and fifth and sixth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW 2167, Australia
| | - Lee T Hickey
- First and second authors: The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, QLD 4072, Australia; third author: Department of Agriculture and Fisheries, Hermitage Research Facility, 604 Yangan Rd, Warwick, QLD 4370, Australia; fourth author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108; and fifth and sixth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW 2167, Australia
| | - Gregory J Platz
- First and second authors: The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, QLD 4072, Australia; third author: Department of Agriculture and Fisheries, Hermitage Research Facility, 604 Yangan Rd, Warwick, QLD 4370, Australia; fourth author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108; and fifth and sixth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW 2167, Australia
| | - Jerome D Franckowiak
- First and second authors: The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, QLD 4072, Australia; third author: Department of Agriculture and Fisheries, Hermitage Research Facility, 604 Yangan Rd, Warwick, QLD 4370, Australia; fourth author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108; and fifth and sixth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW 2167, Australia
| | - Peter M Dracatos
- First and second authors: The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, QLD 4072, Australia; third author: Department of Agriculture and Fisheries, Hermitage Research Facility, 604 Yangan Rd, Warwick, QLD 4370, Australia; fourth author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108; and fifth and sixth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW 2167, Australia
| | - Davinder Singh
- First and second authors: The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, QLD 4072, Australia; third author: Department of Agriculture and Fisheries, Hermitage Research Facility, 604 Yangan Rd, Warwick, QLD 4370, Australia; fourth author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108; and fifth and sixth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW 2167, Australia
| | - Robert F Park
- First and second authors: The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, QLD 4072, Australia; third author: Department of Agriculture and Fisheries, Hermitage Research Facility, 604 Yangan Rd, Warwick, QLD 4370, Australia; fourth author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108; and fifth and sixth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW 2167, Australia
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Ziems LA, Hickey LT, Hunt CH, Mace ES, Platz GJ, Franckowiak JD, Jordan DR. Association mapping of resistance to Puccinia hordei in Australian barley breeding germplasm. Theor Appl Genet 2014; 127:1199-212. [PMID: 24626954 DOI: 10.1007/s00122-014-2291-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 02/17/2014] [Indexed: 05/08/2023]
Abstract
"To find stable resistance using association mapping tools, QTL with major and minor effects on leaf rust reactions were identified in barley breeding lines by assessing seedlings and adult plants." Three hundred and sixty (360) elite barley (Hordeum vulgare L.) breeding lines from the Northern Region Barley Breeding Program in Australia were genotyped with 3,244 polymorphic diversity arrays technology markers and the results used to map quantitative trait loci (QTL) conferring a reaction to leaf rust (Puccinia hordei Otth). The F3:5 (Stage 2) lines were derived or sourced from different geographic origins or hubs of international barley breeding ventures representing two breeding cycles (2009 and 2011 trials) and were evaluated across eight environments for infection type at both seedling and adult plant stages. Association mapping was performed using mean scores for disease reaction, accounting for family effects using the eigenvalues from a matrix of genotype correlations. In this study, 15 QTL were detected; 5 QTL co-located with catalogued leaf rust resistance genes (Rph1, Rph3/19, Rph8/14/15, Rph20, Rph21), 6 QTL aligned with previously reported genomic regions and 4 QTL (3 on chromosome 1H and 1 on 7H) were novel. The adult plant resistance gene Rph20 was identified across the majority of environments and pathotypes. The QTL detected in this study offer opportunities for breeding for more durable resistance to leaf rust through pyramiding multiple genomic regions via marker-assisted selection.
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Affiliation(s)
- L A Ziems
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia,
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