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Capo-chichi LJA, Elakhdar A, Kubo T, Nyachiro J, Juskiw P, Capettini F, Slaski JJ, Ramirez GH, Beattie AD. Genetic diversity and population structure assessment of Western Canadian barley cooperative trials. Front Plant Sci 2023; 13:1006719. [PMID: 36699829 PMCID: PMC9868428 DOI: 10.3389/fpls.2022.1006719] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Studying the population structure and genetic diversity of historical datasets is a proposed use for association analysis. This is particularly important when the dataset contains traits that are time-consuming or costly to measure. A set of 96 elite barley genotypes, developed from eight breeding programs of the Western Canadian Cooperative Trials were used in the current study. Genetic diversity, allelic variation, and linkage disequilibrium (LD) were investigated using 5063 high-quality SNP markers via the Illumina 9K Barley Infinium iSelect SNP assay. The distribution of SNPs markers across the barley genome ranged from 449 markers on chromosome 1H to 1111 markers on chromosome 5H. The average polymorphism information content (PIC) per locus was 0.275 and ranged from 0.094 to 0.375. Bayesian clustering in STRUCTURE and principal coordinate analysis revealed that the populations are differentiated primarily due to the different breeding program origins and ear-row type into five subpopulations. Analysis of molecular variance based on PhiPT values suggested that high values of genetic diversity were observed within populations and accounted for 90% of the total variance. Subpopulation 5 exhibited the most diversity with the highest values of the diversity indices, which represent the breeding program gene pool of AFC, AAFRD, AU, and BARI. With increasing genetic distance, the LD values, expressed as r2, declined to below the critical r2 = 0.18 after 3.91 cM, and the same pattern was observed on each chromosome. Our results identified an important pattern of genetic diversity among the Canadian barley panel that was proposed to be representative of target breeding programs and may have important implications for association mapping in the future. This highlight, that efforts to identify novel variability underlying this diversity may present practical breeding opportunities to develop new barley genotypes.
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Affiliation(s)
- Ludovic J. A. Capo-chichi
- Department of Renewable Resources, Faculty of Agriculture, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Ammar Elakhdar
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Field Crops Research Institute, Agricultural Research Center, Giza, Egypt
| | - Takahiko Kubo
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Joseph Nyachiro
- Field Crop Development Centre, Alberta Agriculture and Forestry, Lacombe, AB, Canada
| | - Patricia Juskiw
- Field Crop Development Centre, Alberta Agriculture and Forestry, Lacombe, AB, Canada
| | - Flavio Capettini
- Field Crop Development Centre, Alberta Agriculture and Forestry, Lacombe, AB, Canada
| | - Jan J. Slaski
- Ecosystems and Plant Sciences, InnoTech Alberta Inc., Vegreville, AB, Canada
| | - Guillermo Hernandez Ramirez
- Department of Renewable Resources, Faculty of Agriculture, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Aaron D. Beattie
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada
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Bouhlal O, Visioni A, Verma RPS, Kandil M, Gyawali S, Capettini F, Sanchez-Garcia M. CGIAR Barley Breeding Toolbox: A diversity panel to facilitate breeding and genomic research in the developing world. Front Plant Sci 2022; 13:1034322. [PMID: 36452106 PMCID: PMC9702823 DOI: 10.3389/fpls.2022.1034322] [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: 09/01/2022] [Accepted: 10/19/2022] [Indexed: 06/17/2023]
Abstract
Breeding programs in developing countries still cannot afford the new genotyping technologies, hindering their research. We aimed to assemble an Association Mapping panel to serve as CGIAR Barley Breeding Toolbox (CBBT), especially for the Developing World. The germplasm had to be representative of the one grown in the Developing World; with high genetic variability and be of public domain. For it, we genotyped with the Infinium iSelect 50K chip, a Global Barley Panel (GBP) of 530 genotypes representing a wide range of row-types, end-uses, growth habits, geographical origins and environments. 40,342 markers were polymorphic with an average polymorphism information content of 0.35 and 66% of them exceeding 0.25. The analysis of the population structure identified 8 subpopulations mostly linked to geographical origin, four of them with significant ICARDA origin. The 16 allele combinations at 4 major flowering genes (HvVRN-H3, HvPPD-H1, HvVRN-H1 and HvCEN) explained 11.07% genetic variation and were linked to the geographic origins of the lines. ICARDA material showed the widest diversity as revealed by the highest number of polymorphic loci (99.76% of all polymorphic SNPs in GBP), number of private alleles and the fact that ICARDA lines were present in all 8 subpopulations and carried all 16 allelic combinations. Due to their genetic diversity and their representativity of the germplasm adapted to the Developing World, ICARDA-derived lines and cultivated landraces were pre-selected to form the CBBT. Using the Mean of Transformed Kinships method, we assembled a panel capturing most of the allelic diversity in the GBP. The CBBT (N=250) preserves good balance between row-types and good representation of both phenology allelic combinations and subpopulations of the GBP. The CBBT and its genotypic data is available to researchers worldwide as a collaborative tool to underpin the genetic mechanisms of traits of interest for barley cultivation.
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Affiliation(s)
- Outmane Bouhlal
- Biodiversity and Crop Improvement Program (BCIP), International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
- Team of Anthropogenetics and Biotechnologies, Faculty of Sciences, Chouaib Doukkali University, El-Jadida, Morocco
| | - Andrea Visioni
- Biodiversity and Crop Improvement Program (BCIP), International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | | | - Mostafa Kandil
- Team of Anthropogenetics and Biotechnologies, Faculty of Sciences, Chouaib Doukkali University, El-Jadida, Morocco
| | | | | | - Miguel Sanchez-Garcia
- Biodiversity and Crop Improvement Program (BCIP), International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
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Muñoz-Amatriaín M, Hernandez J, Herb D, Baenziger PS, Bochard AM, Capettini F, Casas A, Cuesta-Marcos A, Einfeldt C, Fisk S, Genty A, Helgerson L, Herz M, Hu G, Igartua E, Karsai I, Nakamura T, Sato K, Smith K, Stockinger E, Thomas W, Hayes P. Perspectives on Low Temperature Tolerance and Vernalization Sensitivity in Barley: Prospects for Facultative Growth Habit. Front Plant Sci 2020; 11:585927. [PMID: 33469459 PMCID: PMC7814503 DOI: 10.3389/fpls.2020.585927] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/01/2020] [Indexed: 05/13/2023]
Abstract
One option to achieving greater resiliency for barley production in the face of climate change is to explore the potential of winter and facultative growth habits: for both types, low temperature tolerance (LTT) and vernalization sensitivity are key traits. Sensitivity to short-day photoperiod is a desirable attribute for facultative types. In order to broaden our understanding of the genetics of these phenotypes, we mapped quantitative trait loci (QTLs) and identified candidate genes using a genome-wide association studies (GWAS) panel composed of 882 barley accessions that was genotyped with the Illumina 9K single-nucleotide polymorphism (SNP) chip. Fifteen loci including 5 known and 10 novel QTL/genes were identified for LTT-assessed as winter survival in 10 field tests and mapped using a GWAS meta-analysis. FR-H1, FR-H2, and FR-H3 were major drivers of LTT, and candidate genes were identified for FR-H3. The principal determinants of vernalization sensitivity were VRN-H1, VRN-H2, and PPD-H1. VRN-H2 deletions conferred insensitive or intermediate sensitivity to vernalization. A subset of accessions with maximum LTT were identified as a resource for allele mining and further characterization. Facultative types comprised a small portion of the GWAS panel but may be useful for developing germplasm with this growth habit.
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Affiliation(s)
- María Muñoz-Amatriaín
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
- *Correspondence: María Muñoz-Amatriaín,
| | - Javier Hernandez
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
- Javier Hernandez,
| | - Dustin Herb
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
| | - P. Stephen Baenziger
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | | | - Flavio Capettini
- Field Crop Development Centre, Alberta Agriculture and Forestry, Lacombe, AB, Canada
| | - Ana Casas
- Consejo Superior de Investigaciones Científicas (CSIC), Aula Dei Experimental Station, Zaragoza, Spain
| | | | | | - Scott Fisk
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
| | - Amelie Genty
- Secobra Recherches, Centre de Bois Henry, Maule, France
| | - Laura Helgerson
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
| | - Markus Herz
- Bavarian State Research Center for Agriculture, Institute for Crop Science, Freising, Germany
| | - Gongshe Hu
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Aberdeen, ID, United States
| | - Ernesto Igartua
- Consejo Superior de Investigaciones Científicas (CSIC), Aula Dei Experimental Station, Zaragoza, Spain
| | - Ildiko Karsai
- Department of Molecular Breeding, Center for Agricultural Research, Martonvásár, Hungary
| | - Toshiki Nakamura
- Division of Field Crops and Horticulture Research Tohoku Agricultural Research Center National Agriculture and Food Research Organization (NARO), Morioka, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Kevin Smith
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
| | - Eric Stockinger
- Department of Horticulture and Crop Science, The Ohio State University/Ohio Agricultural Research and Development Center (OARDC), Wooster, OH, United States
| | - William Thomas
- The James Hutton Institute (JHI), Invergowrie, United Kingdom
| | - Patrick Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
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Daba S, Horsley R, Schwarz P, Chao S, Capettini F, Mohammadi M. Association and genome analyses to propose putative candidate genes for malt quality traits. J Sci Food Agric 2019; 99:2775-2785. [PMID: 30430569 DOI: 10.1002/jsfa.9485] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 07/25/2018] [Revised: 10/25/2018] [Accepted: 11/11/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND We studied the genetics of nine malt quality traits using association genetics in a panel of North Dakota, ICARDA, and Ethiopian barley lines. Grain samples harvested from Bekoji in 2011 and 2012 were used. RESULTS The mapping panel revealed strong population structure explained by inflorescence-type, geographic origin, and breeding history. North Dakota germplasm were superior in malt quality traits and they can be donors to improve malt quality properties. We identified 106 marker-trait associations (MTAs) for the nine traits, representing 81 genomic regions across all barley chromosomes. Chromosomes 3H, 5H, and 7H contained most of the MTAs (58.5%). Nearly 18.5% of these genomic regions contained two to three malt quality traits. Within ±250 kb of 81 genomic regions, we recovered 348 barley genes, with some potential impacting malt quality. These include invertase, β-fructofuranosidase, α-glucosidase, serine carboxypeptidase, and bidirectional sugar transporter SWEET14-like protein. Eighteen of these genes were also previously reported in the Hordeum Toolbox, and 17 of them highly expressed during the germination process. CONCLUSION The results from this study invite further follow-up functional characterization experiments to relate the genes with individual malt quality traits with higher confidence. It also provides germplasm resources for malt barley improvement. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Sintayehu Daba
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
| | - Richard Horsley
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Paul Schwarz
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Shaoman Chao
- USDA-ARS, Cereal Crop Research Unit, Fargo, ND, USA
| | - Flavio Capettini
- Alberta Agriculture and Forestry, Field Crop Development Center, Lacombe, AB, Canada
| | - Mohsen Mohammadi
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
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Gutiérrez L, Germán S, Pereyra S, Hayes PM, Pérez CA, Capettini F, Locatelli A, Berberian NM, Falconi EE, Estrada R, Fros D, Gonza V, Altamirano H, Huerta-Espino J, Neyra E, Orjeda G, Sandoval-Islas S, Singh R, Turkington K, Castro AJ. Multi-environment multi-QTL association mapping identifies disease resistance QTL in barley germplasm from Latin America. Theor Appl Genet 2015; 128:501-16. [PMID: 25548806 DOI: 10.1007/s00122-014-2448-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 12/17/2014] [Indexed: 05/12/2023]
Abstract
Multi-environment multi-QTL mixed models were used in a GWAS context to identify QTL for disease resistance. The use of mega-environments aided the interpretation of environment-specific and general QTL. Diseases represent a major constraint for barley (Hordeum vulgare L.) production in Latin America. Spot blotch (caused by Cochliobolus sativus), stripe rust (caused by Puccinia striiformis f.sp. hordei) and leaf rust (caused by Puccinia hordei) are three of the most important diseases that affect the crop in the region. Since fungicide application is not an economically or environmentally sound solution, the development of durably resistant varieties is a priority for breeding programs. Therefore, new resistance sources are needed. The objective of this work was to detect genomic regions associated with field level plant resistance to spot blotch, stripe rust, and leaf rust in Latin American germplasm. Disease severities measured in multi-environment trials across the Americas and 1,096 SNPs in a population of 360 genotypes were used to identify genomic regions associated with disease resistance. Optimized experimental design and spatial modeling were used in each trial to estimate genotypic means. Genome-Wide Association Mapping (GWAS) in each environment was used to detect Quantitative Trait Loci (QTL). All significant environment-specific QTL were subsequently included in a multi-environment-multi-QTL (MEMQ) model. Geographical origin and inflorescence type were the main determinants of population structure. Spot blotch severity was low to intermediate while leaf and stripe rust severity was high in all environments. Mega-environments were defined by locations for spot blotch and leaf rust. Significant marker-trait associations for spot blotch (9 QTL), leaf (6 QTL) and stripe rust (7 QTL) and both global and environment-specific QTL were detected that will be useful for future breeding efforts.
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Affiliation(s)
- Lucia Gutiérrez
- Departmento de Biometria, Estadistica y Computo, Facultad de Agronomía, Universidad de la República, Garzón 780, Montevideo, Uruguay,
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Vales MI, Schön CC, Capettini F, Chen XM, Corey AE, Mather DE, Mundt CC, Richardson KL, Sandoval-Islas JS, Utz HF, Hayes PM. Effect of population size on the estimation of QTL: a test using resistance to barley stripe rust. Theor Appl Genet 2005; 111:1260-70. [PMID: 16179997 DOI: 10.1007/s00122-005-0043-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Accepted: 07/06/2005] [Indexed: 05/04/2023]
Abstract
The limited population sizes used in many quantitative trait locus (QTL) detection experiments can lead to underestimation of QTL number, overestimation of QTL effects, and failure to quantify QTL interactions. We used the barley/barley stripe rust pathosystem to evaluate the effect of population size on the estimation of QTL parameters. We generated a large (n = 409) population of doubled haploid lines derived from the cross of two inbred lines, BCD47 and Baronesse. This population was evaluated for barley stripe rust severity in the Toluca Valley, Mexico, and in Washington State, USA, under field conditions. BCD47 was the principal donor of resistance QTL alleles, but the susceptible parent also contributed some resistance alleles. The major QTL, located on the long arm of chromosome 4H, close to the Mlo gene, accounted for up to 34% of the phenotypic variance. Subpopulations of different sizes were generated using three methods-resampling, selective genotyping, and selective phenotyping-to evaluate the effect of population size on the estimation of QTL parameters. In all cases, the number of QTL detected increased with population size. QTL with large effects were detected even in small populations, but QTL with small effects were detected only by increasing population size. Selective genotyping and/or selective phenotyping approaches could be effective strategies for reducing the costs associated with conducting QTL analysis in large populations. The method of choice will depend on the relative costs of genotyping versus phenotyping.
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Affiliation(s)
- M I Vales
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331-3002, USA.
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Vales MI, Schön CC, Capettini F, Chen XM, Corey AE, Mather DE, Mundt CC, Richardson KL, Sandoval-Islas JS, Utz HF, Hayes PM. Effect of population size on the estimation of QTL: a test using resistance to barley stripe rust. Theor Appl Genet 2005; 111:1260-1270. [PMID: 16179997 DOI: 10.1007/s00122-524005-0043-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Accepted: 07/06/2005] [Indexed: 05/24/2023]
Abstract
The limited population sizes used in many quantitative trait locus (QTL) detection experiments can lead to underestimation of QTL number, overestimation of QTL effects, and failure to quantify QTL interactions. We used the barley/barley stripe rust pathosystem to evaluate the effect of population size on the estimation of QTL parameters. We generated a large (n = 409) population of doubled haploid lines derived from the cross of two inbred lines, BCD47 and Baronesse. This population was evaluated for barley stripe rust severity in the Toluca Valley, Mexico, and in Washington State, USA, under field conditions. BCD47 was the principal donor of resistance QTL alleles, but the susceptible parent also contributed some resistance alleles. The major QTL, located on the long arm of chromosome 4H, close to the Mlo gene, accounted for up to 34% of the phenotypic variance. Subpopulations of different sizes were generated using three methods-resampling, selective genotyping, and selective phenotyping-to evaluate the effect of population size on the estimation of QTL parameters. In all cases, the number of QTL detected increased with population size. QTL with large effects were detected even in small populations, but QTL with small effects were detected only by increasing population size. Selective genotyping and/or selective phenotyping approaches could be effective strategies for reducing the costs associated with conducting QTL analysis in large populations. The method of choice will depend on the relative costs of genotyping versus phenotyping.
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Affiliation(s)
- M I Vales
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331-3002, USA.
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Castro AJ, Capettini F, Corey AE, Filichkina T, Hayes PM, Kleinhofs A, Kudrna D, Richardson K, Sandoval-Islas S, Rossi C, Vivar H. Mapping and pyramiding of qualitative and quantitative resistance to stripe rust in barley. Theor Appl Genet 2003; 107:922-30. [PMID: 12845434 DOI: 10.1007/s00122-003-1329-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2002] [Accepted: 03/06/2003] [Indexed: 05/19/2023]
Abstract
The identification and location of sources of genetic resistance to plant diseases are important contributions to the development of resistant varieties. The combination of different sources and types of resistance in the same genotype should assist in the development of durably resistant varieties. Using a doubled haploid (DH), mapping population of barley, we mapped a qualitative resistance gene ( Rpsx) to barley stripe rust in the accession CI10587 (PI 243183) to the long arm of chromosome 1(7H). We combined the Rpsx gene, through a series of crosses, with three mapped and validated barley stripe rust resistance QTL alleles located on chromosomes 4(4H) (QTL4), 5(1H) (QTL5), and 7(5H) (QTL7). Three different barley DH populations were developed from these crosses, two combining Rpsx with QTL4 and QTL7, and the third combining Rpsx with QTL5. Disease severity testing in four environments and QTL mapping analyses confirmed the effects and locations of Rpsx, QTL4, and QTL5, thereby validating the original estimates of QTL location and effect. QTL alleles on chromosomes 4(4H) and 5(1H) were effective in decreasing disease severity in the absence of the resistance allele at Rpsx. Quantitative resistance effects were mainly additive, although magnitude interactions were detected. Our results indicate that combining qualitative and quantitative resistance in the same genotype is feasible. However, the durability of such resistance pyramids will require challenge from virulent isolates, which currently are not reported in North America.
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Affiliation(s)
- A J Castro
- Departamento de Producción Vegetal, Est. Exp. "Dr. Mario A. Cassinoni", Facultad de Agronomía, Universidad de la República, Ruta 3 Km.373, Paysandú 60000, Uruguay
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de la Pena RC, Smith KP, Capettini F, Muehlbauer GJ, Gallo-Meagher M, Dill-Macky R, Somers DA, Rasmusson DC. Quantitative trait loci associated with resistance to Fusarium head blight and kernel discoloration in barley. Theor Appl Genet 1999; 99:561-9. [PMID: 22665190 DOI: 10.1007/s001220051269] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Resistance to Fusarium head blight (FHB), deoxynivalenol (DON) accumulation, and kernel discoloration (KD) in barley are difficult traits to introgress into elite varieties because current screening methods are laborious and disease levels are strongly influenced by environment. To improve breeding strategies directed toward enhancing these traits, we identified genomic regions containing quantitative trait loci (QTLs) associated with resistance to FHB, DON accumulation, and KD in a breeding population of F(4:7) lines using restriction fragment length polymorphic (RFLP) markers. We evaluated 101 F(4:7) lines, derived from a cross between the cultivar Chevron and an elite breeding line, M69, for each of the traits in three or four environments. We used 94 previously mapped RFLP markers to create a linkage map. Using composite interval mapping, we identified 10, 11, and 4 QTLs associated with resistance to FHB, DON accumulation, and KD, respectively. Markers flanking these QTLs should be useful for introgressing resistance to FHB, DON accumulation, and KD into elite barley cultivars.
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Affiliation(s)
- R C de la Pena
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, 55108, XX
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