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Melonek J, Duarte J, Martin J, Beuf L, Murigneux A, Varenne P, Comadran J, Specel S, Levadoux S, Bernath-Levin K, Torney F, Pichon JP, Perez P, Small I. The genetic basis of cytoplasmic male sterility and fertility restoration in wheat. Nat Commun 2021; 12:1036. [PMID: 33589621 PMCID: PMC7884431 DOI: 10.1038/s41467-021-21225-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/15/2021] [Indexed: 01/31/2023] Open
Abstract
Hybrid wheat varieties give higher yields than conventional lines but are difficult to produce due to a lack of effective control of male fertility in breeding lines. One promising system involves the Rf1 and Rf3 genes that restore fertility of wheat plants carrying Triticum timopheevii-type cytoplasmic male sterility (T-CMS). Here, by genetic mapping and comparative sequence analyses, we identify Rf1 and Rf3 candidates that can restore normal pollen production in transgenic wheat plants carrying T-CMS. We show that Rf1 and Rf3 bind to the mitochondrial orf279 transcript and induce cleavage, preventing expression of the CMS trait. The identification of restorer genes in wheat is an important step towards the development of hybrid wheat varieties based on a CMS-Rf system. The characterisation of their mode of action brings insights into the molecular basis of CMS and fertility restoration in plants.
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Affiliation(s)
- Joanna Melonek
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Jorge Duarte
- Groupe Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Jerome Martin
- Groupe Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Laurent Beuf
- Groupe Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Alain Murigneux
- Groupe Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Pierrick Varenne
- Groupe Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Jordi Comadran
- Groupe Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Sebastien Specel
- Groupe Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Sylvain Levadoux
- Groupe Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Kalia Bernath-Levin
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - François Torney
- Groupe Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | | | - Pascual Perez
- Groupe Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Ian Small
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia.
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2
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Xu X, Sharma R, Tondelli A, Russell J, Comadran J, Schnaithmann F, Pillen K, Kilian B, Cattivelli L, Thomas WTB, Flavell AJ. Genome-Wide Association Analysis of Grain Yield-Associated Traits in a Pan-European Barley Cultivar Collection. Plant Genome 2018; 11:170073. [PMID: 29505630 DOI: 10.3835/plantgenome2017.08.0073] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A collection of 379 Hordeum vulgare cultivars, comprising all combinations of spring and winter growth habits with two and six row ear type, was screened by genome wide association analysis to discover alleles controlling traits related to grain yield. Genotypes were obtained at 6,810 segregating gene-based single nucleotide polymorphism (SNP) loci and corresponding field trial data were obtained for eight traits related to grain yield at four European sites in three countries over two growth years. The combined data were analyzed and statistically significant associations between the traits and regions of the barley genomes were obtained. Combining this information with the high resolution gene map for barley allowed the identification of candidate genes underlying all scored traits and superposition of this information with the known genomics of grain trait genes in rice resulted in the assignation of 13 putative barley genes controlling grain traits in European cultivated barley. Several of these genes are associated with grain traits in both winter and spring barley.
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3
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Gilles LM, Khaled A, Laffaire JB, Chaignon S, Gendrot G, Laplaige J, Bergès H, Beydon G, Bayle V, Barret P, Comadran J, Martinant JP, Rogowsky PM, Widiez T. Loss of pollen-specific phospholipase NOT LIKE DAD triggers gynogenesis in maize. EMBO J 2017; 36:707-717. [PMID: 28228439 PMCID: PMC5350562 DOI: 10.15252/embj.201796603] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 02/08/2017] [Accepted: 02/09/2017] [Indexed: 12/27/2022] Open
Abstract
Gynogenesis is an asexual mode of reproduction common to animals and plants, in which stimuli from the sperm cell trigger the development of the unfertilized egg cell into a haploid embryo. Fine mapping restricted a major maize QTL (quantitative trait locus) responsible for the aptitude of inducer lines to trigger gynogenesis to a zone containing a single gene NOT LIKE DAD (NLD) coding for a patatin-like phospholipase A. In all surveyed inducer lines, NLD carries a 4-bp insertion leading to a predicted truncated protein. This frameshift mutation is responsible for haploid induction because complementation with wild-type NLD abolishes the haploid induction capacity. Activity of the NLD promoter is restricted to mature pollen and pollen tube. The translational NLD::citrine fusion protein likely localizes to the sperm cell plasma membrane. In Arabidopsis roots, the truncated protein is no longer localized to the plasma membrane, contrary to the wild-type NLD protein. In conclusion, an intact pollen-specific phospholipase is required for successful sexual reproduction and its targeted disruption may allow establishing powerful haploid breeding tools in numerous crops.
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Affiliation(s)
- Laurine M Gilles
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon ENS de Lyon UCB Lyon 1 CNRS, INRA, Lyon, France
- Limagrain Europe SAS, Research Centre, Chappes, France
| | - Abdelsabour Khaled
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon ENS de Lyon UCB Lyon 1 CNRS, INRA, Lyon, France
- Department of Genetics, Faculty of Agriculture, Sohag University, Sohag, Egypt
| | | | - Sandrine Chaignon
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon ENS de Lyon UCB Lyon 1 CNRS, INRA, Lyon, France
| | - Ghislaine Gendrot
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon ENS de Lyon UCB Lyon 1 CNRS, INRA, Lyon, France
| | - Jérôme Laplaige
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon ENS de Lyon UCB Lyon 1 CNRS, INRA, Lyon, France
| | - Hélène Bergès
- INRA, US1258 Centre National des Ressources Génomiques Végétales, Auzeville, France
| | - Genséric Beydon
- INRA, US1258 Centre National des Ressources Génomiques Végétales, Auzeville, France
| | - Vincent Bayle
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon ENS de Lyon UCB Lyon 1 CNRS, INRA, Lyon, France
| | - Pierre Barret
- INRA, UMR1095 Génétique, Diversité, Ecophysiologie des Céréales, Clermont-Ferrand, France
| | | | | | - Peter M Rogowsky
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon ENS de Lyon UCB Lyon 1 CNRS, INRA, Lyon, France
| | - Thomas Widiez
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon ENS de Lyon UCB Lyon 1 CNRS, INRA, Lyon, France
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Abstract
Genomic selection in crop breeding introduces modeling challenges not found in animal studies. These include the need to accommodate replicate plants for each line, consider spatial variation in field trials, address line by environment interactions, and capture nonadditive effects. Here, we propose a flexible single-stage genomic selection approach that resolves these issues. Our linear mixed model incorporates spatial variation through environment-specific terms, and also randomization-based design terms. It considers marker, and marker by environment interactions using ridge regression best linear unbiased prediction to extend genomic selection to multiple environments. Since the approach uses the raw data from line replicates, the line genetic variation is partitioned into marker and nonmarker residual genetic variation (i.e., additive and nonadditive effects). This results in a more precise estimate of marker genetic effects. Using barley height data from trials, in 2 different years, of up to 477 cultivars, we demonstrate that our new genomic selection model improves predictions compared to current models. Analyzing single trials revealed improvements in predictive ability of up to 5.7%. For the multiple environment trial (MET) model, combining both year trials improved predictive ability up to 11.4% compared to a single environment analysis. Benefits were significant even when fewer markers were used. Compared to a single-year standard model run with 3490 markers, our partitioned MET model achieved the same predictive ability using between 500 and 1000 markers depending on the trial. Our approach can be used to increase accuracy and confidence in the selection of the best lines for breeding and/or, to reduce costs by using fewer markers.
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Affiliation(s)
- Helena Oakey
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
| | - Brian Cullis
- National Institute for Applied Statistics Research Australia, University of Wollongong, NSW, 2522, Australia
| | - Robin Thompson
- Rothamsted Research, Harpenden, Hertfordshire AL5 3JQ, UK
| | - Jordi Comadran
- Department of Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
| | - Claire Halpin
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
| | - Robbie Waugh
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK Department of Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
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5
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Muñoz-Amatriaín M, Cuesta-Marcos A, Endelman JB, Comadran J, Bonman JM, Bockelman HE, Chao S, Russell J, Waugh R, Hayes PM, Muehlbauer GJ. The USDA barley core collection: genetic diversity, population structure, and potential for genome-wide association studies. PLoS One 2014; 9:e94688. [PMID: 24732668 PMCID: PMC3986206 DOI: 10.1371/journal.pone.0094688] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/18/2014] [Indexed: 11/18/2022] Open
Abstract
New sources of genetic diversity must be incorporated into plant breeding programs if they are to continue increasing grain yield and quality, and tolerance to abiotic and biotic stresses. Germplasm collections provide a source of genetic and phenotypic diversity, but characterization of these resources is required to increase their utility for breeding programs. We used a barley SNP iSelect platform with 7,842 SNPs to genotype 2,417 barley accessions sampled from the USDA National Small Grains Collection of 33,176 accessions. Most of the accessions in this core collection are categorized as landraces or cultivars/breeding lines and were obtained from more than 100 countries. Both STRUCTURE and principal component analysis identified five major subpopulations within the core collection, mainly differentiated by geographical origin and spike row number (an inflorescence architecture trait). Different patterns of linkage disequilibrium (LD) were found across the barley genome and many regions of high LD contained traits involved in domestication and breeding selection. The genotype data were used to define 'mini-core' sets of accessions capturing the majority of the allelic diversity present in the core collection. These 'mini-core' sets can be used for evaluating traits that are difficult or expensive to score. Genome-wide association studies (GWAS) of 'hull cover', 'spike row number', and 'heading date' demonstrate the utility of the core collection for locating genetic factors determining important phenotypes. The GWAS results were referenced to a new barley consensus map containing 5,665 SNPs. Our results demonstrate that GWAS and high-density SNP genotyping are effective tools for plant breeders interested in accessing genetic diversity in large germplasm collections.
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Affiliation(s)
- María Muñoz-Amatriaín
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Alfonso Cuesta-Marcos
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America
| | - Jeffrey B. Endelman
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Jordi Comadran
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - John M. Bonman
- USDA-ARS, Small Grains and Potato Germplasm Research Unit, Aberdeen, Idaho, United States of America
| | - Harold E. Bockelman
- USDA-ARS, Small Grains and Potato Germplasm Research Unit, Aberdeen, Idaho, United States of America
| | - Shiaoman Chao
- USDA-ARS, Biosciences Research Lab, Fargo, North Dakota, United States of America
| | - Joanne Russell
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Robbie Waugh
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Patrick M. Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America
| | - Gary J. Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota, United States of America
- * E-mail:
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6
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Oakey H, Shafiei R, Comadran J, Uzrek N, Cullis B, Gomez LD, Whitehead C, McQueen-Mason SJ, Waugh R, Halpin C. Identification of crop cultivars with consistently high lignocellulosic sugar release requires the use of appropriate statistical design and modelling. Biotechnol Biofuels 2013; 6:185. [PMID: 24359577 PMCID: PMC3878416 DOI: 10.1186/1754-6834-6-185] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 12/06/2013] [Indexed: 05/09/2023]
Abstract
BACKGROUND In this study, a multi-parent population of barley cultivars was grown in the field for two consecutive years and then straw saccharification (sugar release by enzymes) was subsequently analysed in the laboratory to identify the cultivars with the highest consistent sugar yield. This experiment was used to assess the benefit of accounting for both the multi-phase and multi-environment aspects of large-scale phenotyping experiments with field-grown germplasm through sound statistical design and analysis. RESULTS Complementary designs at both the field and laboratory phases of the experiment ensured that non-genetic sources of variation could be separated from the genetic variation of cultivars, which was the main target of the study. The field phase included biological replication and plot randomisation. The laboratory phase employed re-randomisation and technical replication of samples within a batch, with a subset of cultivars chosen as duplicates that were randomly allocated across batches. The resulting data was analysed using a linear mixed model that incorporated field and laboratory variation and a cultivar by trial interaction, and ensured that the cultivar means were more accurately represented than if the non-genetic variation was ignored. The heritability detected was more than doubled in each year of the trial by accounting for the non-genetic variation in the analysis, clearly showing the benefit of this design and approach. CONCLUSIONS The importance of accounting for both field and laboratory variation, as well as the cultivar by trial interaction, by fitting a single statistical model (multi-environment trial, MET, model), was evidenced by the changes in list of the top 40 cultivars showing the highest sugar yields. Failure to account for this interaction resulted in only eight cultivars that were consistently in the top 40 in different years. The correspondence between the rankings of cultivars was much higher at 25 in the MET model. This approach is suited to any multi-phase and multi-environment population-based genetic experiment.
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Affiliation(s)
- Helena Oakey
- Division of Plant Sciences, College of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Reza Shafiei
- Division of Plant Sciences, College of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Jordi Comadran
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA Scotland, UK
| | - Nicola Uzrek
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA Scotland, UK
| | - Brian Cullis
- National Institute for Applied Statistics Research Australia, University of Wollongong, Wollongong, NSW 2522, Australia
- Computational Informatics, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT 2600, Australia
| | - Leonardo D Gomez
- Biology Department, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York YO10 5DD, UK
| | - Caragh Whitehead
- Biology Department, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York YO10 5DD, UK
| | - Simon J McQueen-Mason
- Biology Department, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York YO10 5DD, UK
| | - Robbie Waugh
- Division of Plant Sciences, College of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA Scotland, UK
| | - Claire Halpin
- Division of Plant Sciences, College of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
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7
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Visioni A, Tondelli A, Francia E, Pswarayi A, Malosetti M, Russell J, Thomas W, Waugh R, Pecchioni N, Romagosa I, Comadran J. Genome-wide association mapping of frost tolerance in barley (Hordeum vulgare L.). BMC Genomics 2013; 14:424. [PMID: 23802597 PMCID: PMC3701572 DOI: 10.1186/1471-2164-14-424] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 06/12/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Frost tolerance is a key trait with economic and agronomic importance in barley because it is a major component of winter hardiness, and therefore limits the geographical distribution of the crop and the effective transfer of quality traits between spring and winter crop types. Three main frost tolerance QTL (Fr-H1, Fr-H2 and Fr-H3) have been identified from bi-parental genetic mapping but it can be argued that those mapping populations only capture a portion of the genetic diversity of the species. A genetically broad dataset consisting of 184 genotypes, representative of the barley gene pool cultivated in the Mediterranean basin over an extended time period, was genotyped with 1536 SNP markers. Frost tolerance phenotype scores were collected from two trial sites, Foradada (Spain) and Fiorenzuola (Italy) and combined with the genotypic data in genome wide association analyses (GWAS) using Eigenstrat and kinship approaches to account for population structure. RESULTS GWAS analyses identified twelve and seven positive SNP associations at Foradada and Fiorenzuola, respectively, using Eigenstrat and six and four, respectively, using kinship. Linkage disequilibrium analyses of the significant SNP associations showed they are genetically independent. In the kinship analysis, two of the significant SNP associations were tightly linked to the Fr-H2 and HvBmy loci on chromosomes 5H and 4HL, respectively. The other significant kinship associations were located in genomic regions that have not previously been associated with cold stress. CONCLUSIONS Haplotype analysis revealed that most of the significant SNP loci are fixed in the winter or facultative types, while they are freely segregating within the un-adapted spring barley genepool. Although there is a major interest in detecting new variation to improve frost tolerance of available winter and facultative types, from a GWAS perspective, working within the un-adapted spring germplasm pool is an attractive alternative strategy which would minimize statistical issues, simplify the interpretation of the data and identify phenology independent genetic determinants of frost tolerance.
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Affiliation(s)
- Andrea Visioni
- Centre UdL-IRTA, Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida, Lleida, Spain
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8
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Comadran J, Kilian B, Russell J, Ramsay L, Stein N, Ganal M, Shaw P, Bayer M, Thomas W, Marshall D, Hedley P, Tondelli A, Pecchioni N, Francia E, Korzun V, Walther A, Waugh R. Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley. Nat Genet 2012; 44:1388-92. [PMID: 23160098 DOI: 10.1038/ng.2447] [Citation(s) in RCA: 278] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 09/27/2012] [Indexed: 01/13/2023]
Abstract
As early farming spread from the Fertile Crescent in the Near East around 10,000 years before the present, domesticated crops encountered considerable ecological and environmental change. Spring-sown crops that flowered without the need for an extended period of cold to promote flowering and day length-insensitive crops able to exploit the longer, cooler days of higher latitudes emerged and became established. To investigate the genetic consequences of adaptation to these new environments, we identified signatures of divergent selection in the highly differentiated modern-day spring and winter barleys. In one genetically divergent region, we identify a natural variant of the barley homolog of Antirrhinum CENTRORADIALIS (HvCEN) as a contributor to successful environmental adaptation. The distribution of HvCEN alleles in a large collection of wild and landrace accessions indicates that this involved selection and enrichment of preexisting genetic variants rather than the acquisition of mutations after domestication.
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Affiliation(s)
- Jordi Comadran
- Cell and Molecular Sciences Group, The James Hutton Institute, Invergowrie, Dundee, UK
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9
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Farré A, Cuadrado A, Lacasa-Benito I, Cistué L, Schubert I, Comadran J, Jansen J, Romagosa I. Genetic characterization of a reciprocal translocation present in a widely grown barley variety. Mol Breed 2012; 30:1109-1119. [PMID: 22924020 PMCID: PMC3410021 DOI: 10.1007/s11032-011-9698-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 12/27/2011] [Indexed: 05/30/2023]
Abstract
Artificially induced translocation stocks have been used to physically map the barley genome; however, natural translocations are extremely uncommon in cultivated genotypes. Albacete is a barley variety widely grown in recent decades in Spain and carrying a reciprocal translocation which obviously does not affect its agronomical fitness. This translocation has been characterized by a combination of cytological and molecular genetic approaches. Firstly, recombination frequencies between markers on chromosomes 1H and 3H were estimated to determine the boundaries of the reciprocal interchange. Secondly, 1H-3H wheat barley telosome addition lines were used to assign selected markers to chromosome arms. Thirdly, fluorescence in situ hybridization (FISH) with rDNA probes (5S and 18S-5.8S-26S) and microsatellite probes [(ACT)(5), (AAG)(5) and (CAG)(5)] was used to determine the locations of the translocation breakpoints more precisely. Fourthly, fine-mapping of the regions around the translocation breakpoints was used to increase the marker density for comparative genomics. The results obtained in this study indicate that the translocation is quite large with breakpoints located on the long arms of chromosomes 1H and 3H, between the pericentromeric (AAG)(5) bands and above the (ACT)(5) interstitial distal bands, resulting in the reciprocal translocation 1HS.1HL-3HL and 3HS.3HL-1HL. The gene content around the translocation breakpoints could be inferred from syntenic relationships observed among different species from the grass family Poaceae (rice, Sorghum and Brachypodium) and was estimated at approximately 1,100 and 710 gene models for 1H and 3H, respectively. Duplicated segments between chromosomes Os01 and Os05 in rice derived from ancestral duplications within the grass family overlap with the translocation breakpoints on chromosomes 1H and 3H in the barley variety Albacete.
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Affiliation(s)
- A. Farré
- Department of Plant Production and Forest Science, University of Lleida, Lleida, Spain
- Biometris, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - A. Cuadrado
- Department of Cell Biology and Genetics, University of Alcalá de Henares, Alcalá de Henares, Spain
| | - I. Lacasa-Benito
- Department of Plant Production and Forest Science, University of Lleida, Lleida, Spain
| | - L. Cistué
- Estación Experimental de Aula Dei, CSIC, Zaragoza, Spain
| | - I. Schubert
- Department of Cytogenetics, Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - J. Comadran
- Genetics Programme, The James Hutton Institute, Dundee, Scotland, UK
| | - J. Jansen
- Biometris, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - I. Romagosa
- Department of Plant Production and Forest Science, University of Lleida, Lleida, Spain
- Centre UdL-IRTA, University of Lleida, Lleida, Spain
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Wang M, Jiang N, Jia T, Leach L, Cockram J, Comadran J, Shaw P, Waugh R, Luo Z. Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars. Theor Appl Genet 2012; 124:233-46. [PMID: 21915710 DOI: 10.1007/s00122-011-1697-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 08/29/2011] [Indexed: 05/18/2023]
Abstract
Genome-wide association study (GWAS) has become an obvious general approach for studying traits of agricultural importance in higher plants, especially crops. Here, we present a GWAS of 32 morphologic and 10 agronomic traits in a collection of 615 barley cultivars genotyped by genome-wide polymorphisms from a recently developed barley oligonucleotide pool assay. Strong population structure effect related to mixed sampling based on seasonal growth habit and ear row number is present in this barley collection. Comparison of seven statistical approaches in a genome-wide scan for significant associations with or without correction for confounding by population structure, revealed that in reducing false positive rates while maintaining statistical power, a mixed linear model solution outperforms genomic control, structured association, stepwise regression control and principal components adjustment. The present study reports significant associations for sixteen morphologic and nine agronomic traits and demonstrates the power and feasibility of applying GWAS to explore complex traits in highly structured plant samples.
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Affiliation(s)
- Minghui Wang
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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11
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Comadran J, Russell JR, Booth A, Pswarayi A, Ceccarelli S, Grando S, Stanca AM, Pecchioni N, Akar T, Al-Yassin A, Benbelkacem A, Ouabbou H, Bort J, van Eeuwijk FA, Thomas WTB, Romagosa I. Mixed model association scans of multi-environmental trial data reveal major loci controlling yield and yield related traits in Hordeum vulgare in Mediterranean environments. Theor Appl Genet 2011; 122:1363-73. [PMID: 21279625 PMCID: PMC3075395 DOI: 10.1007/s00122-011-1537-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 01/06/2011] [Indexed: 05/05/2023]
Abstract
An association panel consisting of 185 accessions representative of the barley germplasm cultivated in the Mediterranean basin was used to localise quantitative trait loci (QTL) controlling grain yield and yield related traits. The germplasm set was genotyped with 1,536 SNP markers and tested for associations with phenotypic data gathered over 2 years for a total of 24 year × location combinations under a broad range of environmental conditions. Analysis of multi-environmental trial (MET) data by fitting a mixed model with kinship estimates detected from two to seven QTL for the major components of yield including 1000 kernel weight, grains per spike and spikes per m(2), as well as heading date, harvest index and plant height. Several of the associations involved SNPs tightly linked to known major genes determining spike morphology in barley (vrs1 and int-c). Similarly, the largest QTL for heading date co-locates with SNPs linked with eam6, a major locus for heading date in barley for autumn sown conditions. Co-localization of several QTL related to yield components traits suggest that major developmental loci may be linked to most of the associations. This study highlights the potential of association genetics to identify genetic variants controlling complex traits.
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Comadran J, Ramsay L, MacKenzie K, Hayes P, Close TJ, Muehlbauer G, Stein N, Waugh R. Patterns of polymorphism and linkage disequilibrium in cultivated barley. Theor Appl Genet 2011; 122:523-31. [PMID: 21076812 PMCID: PMC3026706 DOI: 10.1007/s00122-010-1466-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Accepted: 09/30/2010] [Indexed: 05/18/2023]
Abstract
We carried out a genome-wide analysis of polymorphism (4,596 SNP loci across 190 elite cultivated accessions) chosen to represent the available genetic variation in current elite North West European and North American barley germplasm. Population sub-structure, patterns of diversity and linkage disequilibrium varied considerably across the seven barley chromosomes. Gene-rich and rarely recombining haplotype blocks that may represent up to 60% of the physical length of barley chromosomes extended across the 'genetic centromeres'. By positioning 2,132 bi-parentally mapped SNP markers with minimum allele frequencies higher than 0.10 by association mapping, 87.3% were located to within 5 cM of their original genetic map position. We show that at this current marker density genetically diverse populations of relatively small size are sufficient to fine map simple traits, providing they are not strongly stratified within the sample, fall outside the genetic centromeres and population sub-structure is effectively controlled in the analysis. Our results have important implications for association mapping, positional cloning, physical mapping and practical plant breeding in barley and other major world cereals including wheat and rye that exhibit comparable genome and genetic features.
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Affiliation(s)
- Jordi Comadran
- Genetics Programme, Scottish Crop Research Institute, Dundee, DD2 5DA Scotland, UK
| | - Luke Ramsay
- Genetics Programme, Scottish Crop Research Institute, Dundee, DD2 5DA Scotland, UK
| | | | - Patrick Hayes
- Oregon State University, Barley Project Crop Science Bldg. 30th and Campus Way, Corvallis, OR 97333 USA
| | - Timothy J. Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA
| | - Gary Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108-6026 USA
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
| | - Robbie Waugh
- Genetics Programme, Scottish Crop Research Institute, Dundee, DD2 5DA Scotland, UK
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Ramsay L, Comadran J, Druka A, Marshall DF, Thomas WTB, Macaulay M, MacKenzie K, Simpson C, Fuller J, Bonar N, Hayes PM, Lundqvist U, Franckowiak JD, Close TJ, Muehlbauer GJ, Waugh R. INTERMEDIUM-C, a modifier of lateral spikelet fertility in barley, is an ortholog of the maize domestication gene TEOSINTE BRANCHED 1. Nat Genet 2011; 43:169-72. [PMID: 21217754 DOI: 10.1038/ng.745] [Citation(s) in RCA: 182] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 12/10/2010] [Indexed: 01/06/2023]
Abstract
The domestication of cereals has involved common changes in morphological features, such as seed size, seed retention and modification of vegetative and inflorescence architecture that ultimately contributed to an increase in harvested yield. In barley, this process has resulted in two different cultivated types, two-rowed and six-rowed forms, both derived from the wild two-rowed ancestor, with archaeo-botanical evidence indicating the origin of six-rowed barley early in the domestication of the species, some 8,600-8,000 years ago. Variation at SIX-ROWED SPIKE 1 (VRS1) is sufficient to control this phenotype. However, phenotypes imposed by VRS1 alleles are modified by alleles at the INTERMEDIUM-C (INT-C) locus. Here we show that INT-C is an ortholog of the maize domestication gene TEOSINTE BRANCHED 1 (TB1) and identify 17 coding mutations in barley TB1 correlated with lateral spikelet fertility phenotypes.
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Affiliation(s)
- Luke Ramsay
- Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee, Scotland, UK
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Waugh R, Marshall D, Thomas B, Comadran J, Russell J, Close T, Stein N, Hayes P, Muehlbauer G, Cockram J, O’Sullivan D, Mackay I, Flavell A, AGOUEB, BarleyCAP, Ramsay L. Whole-genome association mapping in elite inbred crop varietiesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”. Genome 2010; 53:967-72. [DOI: 10.1139/g10-078] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have previously shown that linkage disequilibrium (LD) in the elite cultivated barley ( Hordeum vulgare ) gene pool extends, on average, for <1–5 cM. Based on this information, we have developed a platform for whole genome association studies that comprises a collection of elite lines that we have characterized at 3060 genome-wide single nucleotide polymorphism (SNP) marker loci. Interrogating this data set shows that significant population substructure is present within the elite gene pool and that diversity and LD vary considerably across each of the seven barley chromosomes. However, we also show that a subpopulation comprised of only the two-rowed spring germplasm is less structured and well suited to whole genome association studies without the need for extensive statistical intervention to account for structure. At the current marker density, the two-rowed spring population is suited for fine mapping simple traits that are located outside of the genetic centromeres with a resolution that is sufficient for candidate gene identification by exploiting conservation of synteny with fully sequenced model genomes and the emerging barley physical map.
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Affiliation(s)
- Robbie Waugh
- Genetics, Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Gatersleben, Germany
- Barley Project, 109 Crop Science Building, Oregon State University, Corvallis, OR 97333, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108-6026, USA
| | - David Marshall
- Genetics, Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Gatersleben, Germany
- Barley Project, 109 Crop Science Building, Oregon State University, Corvallis, OR 97333, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108-6026, USA
| | - Bill Thomas
- Genetics, Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Gatersleben, Germany
- Barley Project, 109 Crop Science Building, Oregon State University, Corvallis, OR 97333, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108-6026, USA
| | - Jordi Comadran
- Genetics, Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Gatersleben, Germany
- Barley Project, 109 Crop Science Building, Oregon State University, Corvallis, OR 97333, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108-6026, USA
| | - Joanne Russell
- Genetics, Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Gatersleben, Germany
- Barley Project, 109 Crop Science Building, Oregon State University, Corvallis, OR 97333, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108-6026, USA
| | - Tim Close
- Genetics, Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Gatersleben, Germany
- Barley Project, 109 Crop Science Building, Oregon State University, Corvallis, OR 97333, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108-6026, USA
| | - Nils Stein
- Genetics, Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Gatersleben, Germany
- Barley Project, 109 Crop Science Building, Oregon State University, Corvallis, OR 97333, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108-6026, USA
| | - Pat Hayes
- Genetics, Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Gatersleben, Germany
- Barley Project, 109 Crop Science Building, Oregon State University, Corvallis, OR 97333, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108-6026, USA
| | - Gary Muehlbauer
- Genetics, Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Gatersleben, Germany
- Barley Project, 109 Crop Science Building, Oregon State University, Corvallis, OR 97333, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108-6026, USA
| | - James Cockram
- Genetics, Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Gatersleben, Germany
- Barley Project, 109 Crop Science Building, Oregon State University, Corvallis, OR 97333, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108-6026, USA
| | - Donal O’Sullivan
- Genetics, Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Gatersleben, Germany
- Barley Project, 109 Crop Science Building, Oregon State University, Corvallis, OR 97333, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108-6026, USA
| | - Ian Mackay
- Genetics, Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Gatersleben, Germany
- Barley Project, 109 Crop Science Building, Oregon State University, Corvallis, OR 97333, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108-6026, USA
| | - Andrew Flavell
- Genetics, Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Gatersleben, Germany
- Barley Project, 109 Crop Science Building, Oregon State University, Corvallis, OR 97333, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108-6026, USA
| | - AGOUEB
- Genetics, Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Gatersleben, Germany
- Barley Project, 109 Crop Science Building, Oregon State University, Corvallis, OR 97333, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108-6026, USA
| | - BarleyCAP
- Genetics, Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Gatersleben, Germany
- Barley Project, 109 Crop Science Building, Oregon State University, Corvallis, OR 97333, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108-6026, USA
| | - Luke Ramsay
- Genetics, Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, 06466, Gatersleben, Germany
- Barley Project, 109 Crop Science Building, Oregon State University, Corvallis, OR 97333, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108-6026, USA
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Moragues M, Comadran J, Waugh R, Milne I, Flavell AJ, Russell JR. Effects of ascertainment bias and marker number on estimations of barley diversity from high-throughput SNP genotype data. Theor Appl Genet 2010; 120:1525-34. [PMID: 20157694 DOI: 10.1007/s00122-010-1273-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 01/19/2010] [Indexed: 05/25/2023]
Abstract
The capability of molecular markers to provide information of genetic structure is influenced by their number and the way they are chosen. This study evaluates the effects of single nucleotide polymorphism (SNP) number and selection strategy on estimates of germplasm diversity and population structure for different types of barley germplasm, namely cultivar and landrace. One hundred and sixty-nine barley landraces from Syria and Jordan and 171 European barley cultivars were genotyped with 1536 SNPs. Different subsets of 384 and 96 SNPs were selected from the 1536 set, based on their ability to detect diversity in landraces or cultivated barley in addition to corresponding randomly chosen subsets. All SNP sets except the landrace-optimised subsets underestimated the diversity present in the landrace germplasm, and all subsets of SNP gave similar estimates for cultivar germplasm. All marker subsets gave qualitatively similar estimates of the population structure in both germplasm sets, but the 96 SNP sets showed much lower data resolution values than the larger SNP sets. From these data we deduce that pre-selecting markers for their diversity in a germplasm set is very worthwhile in terms of the quality of data obtained. Second, we suggest that a properly chosen 384 SNP subset gives a good combination of power and economy for germplasm characterization, whereas the rather modest gain from using 1536 SNPs does not justify the increased cost and 96 markers give unacceptably low performance. Lastly, we propose a specific 384 SNP subset as a standard genotyping tool for middle-eastern landrace barley.
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Affiliation(s)
- M Moragues
- Division of Plant Sciences, University of Dundee at SCRI, Dundee, UK
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16
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Comadran J, Thomas WTB, van Eeuwijk FA, Ceccarelli S, Grando S, Stanca AM, Pecchioni N, Akar T, Al-Yassin A, Benbelkacem A, Ouabbou H, Bort J, Romagosa I, Hackett CA, Russell JR. Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin. Theor Appl Genet 2009; 119:175-87. [PMID: 19415228 DOI: 10.1007/s00122-009-1027-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 03/25/2009] [Indexed: 05/18/2023]
Abstract
Population structure and genome-wide linkage disequilibrium (LD) were investigated in 192 Hordeum vulgare accessions providing a comprehensive coverage of past and present barley breeding in the Mediterranean basin, using 50 nuclear microsatellite and 1,130 DArT((R)) markers. Both clustering and principal coordinate analyses clearly sub-divided the sample into five distinct groups centred on key ancestors and regions of origin of the germplasm. For given genetic distances, large variation in LD values was observed, ranging from closely linked markers completely at equilibrium to marker pairs at 50 cM separation still showing significant LD. Mean LD values across the whole population sample decayed below r (2) of 0.15 after 3.2 cM. By assaying 1,130 genome-wide DArT((R)) markers, we demonstrated that, after accounting for population substructure, current genome coverage of 1 marker per 1.5 cM except for chromosome 4H with 1 marker per 3.62 cM is sufficient for whole genome association scans. We show, by identifying associations with powdery mildew that map in genomic regions known to have resistance loci, that associations can be detected in strongly stratified samples provided population structure is effectively controlled in the analysis. The population we describe is, therefore, shown to be a valuable resource, which can be used in basic and applied research in barley.
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Affiliation(s)
- Jordi Comadran
- Genetics Programme, Scottish Crop Research Institute (SCRI), Invergowrie, Dundee, Scotland, UK.
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