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Canaguier A, Grimplet J, Di Gaspero G, Scalabrin S, Duchêne E, Choisne N, Mohellibi N, Guichard C, Rombauts S, Le Clainche I, Bérard A, Chauveau A, Bounon R, Rustenholz C, Morgante M, Le Paslier MC, Brunel D, Adam-Blondon AF. A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3). Genom Data 2017; 14:56-62. [PMID: 28971018 PMCID: PMC5612791 DOI: 10.1016/j.gdata.2017.09.002] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/13/2017] [Accepted: 09/15/2017] [Indexed: 11/21/2022]
Affiliation(s)
- A Canaguier
- UMR GV, INRA, UEVE, ERL CNRS, 2 rue Gaston Crémieux, 91000 Evry, France.,EPGV US 1279, INRA, CEA, IG-CNG, Université Paris-Saclay, 91000 Evry, France
| | - J Grimplet
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño 26007, Spain
| | | | | | - E Duchêne
- SVQV, UMR 1131, INRA, Université de Strasbourg, 28 rue de Herrlisheim, 68000 Colmar, France
| | - N Choisne
- URGI, UR 1164, INRA, Université Paris-Saclay, route de Saint-Cyr, 78026 Versailles, France
| | - N Mohellibi
- URGI, UR 1164, INRA, Université Paris-Saclay, route de Saint-Cyr, 78026 Versailles, France
| | - C Guichard
- UMR GV, INRA, UEVE, ERL CNRS, 2 rue Gaston Crémieux, 91000 Evry, France.,IPS2, UMR 1403, INRA, Université Paris-Saclay, Rue de Noetzlin, bât. 630, 91190 Gif-sur-Yvette, France
| | - S Rombauts
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium
| | - I Le Clainche
- UMR GV, INRA, UEVE, ERL CNRS, 2 rue Gaston Crémieux, 91000 Evry, France.,EPGV US 1279, INRA, CEA, IG-CNG, Université Paris-Saclay, 91000 Evry, France
| | - A Bérard
- EPGV US 1279, INRA, CEA, IG-CNG, Université Paris-Saclay, 91000 Evry, France
| | - A Chauveau
- EPGV US 1279, INRA, CEA, IG-CNG, Université Paris-Saclay, 91000 Evry, France
| | - R Bounon
- UMR GV, INRA, UEVE, ERL CNRS, 2 rue Gaston Crémieux, 91000 Evry, France.,EPGV US 1279, INRA, CEA, IG-CNG, Université Paris-Saclay, 91000 Evry, France
| | - C Rustenholz
- SVQV, UMR 1131, INRA, Université de Strasbourg, 28 rue de Herrlisheim, 68000 Colmar, France
| | - M Morgante
- IGA, via J. Linussio 51, 33100 Udine, Italy
| | - M-C Le Paslier
- EPGV US 1279, INRA, CEA, IG-CNG, Université Paris-Saclay, 91000 Evry, France
| | - D Brunel
- EPGV US 1279, INRA, CEA, IG-CNG, Université Paris-Saclay, 91000 Evry, France
| | - A-F Adam-Blondon
- UMR GV, INRA, UEVE, ERL CNRS, 2 rue Gaston Crémieux, 91000 Evry, France.,URGI, UR 1164, INRA, Université Paris-Saclay, route de Saint-Cyr, 78026 Versailles, France
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2
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Adam-Blondon AF, Alaux M, Pommier C, Cantu D, Cheng ZM, Cramer GR, Davies C, Delrot S, Deluc L, Di Gaspero G, Grimplet J, Fennell A, Londo JP, Kersey P, Mattivi F, Naithani S, Neveu P, Nikolski M, Pezzotti M, Reisch BI, Töpfer R, Vivier MA, Ware D, Quesneville H. Towards an open grapevine information system. Hortic Res 2016; 3:16056. [PMID: 27917288 PMCID: PMC5120350 DOI: 10.1038/hortres.2016.56] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/10/2016] [Accepted: 10/21/2016] [Indexed: 05/26/2023]
Abstract
Viticulture, like other fields of agriculture, is currently facing important challenges that will be addressed only through sustained, dedicated and coordinated research. Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature, in many domains of study, including grapevine research, there is a need to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of these data. Considering the heterogeneous nature of the data produced, the transnational nature of the scientific community and the experience gained elsewhere, we have formed an open working group, in the framework of the International Grapevine Genome Program (www.vitaceae.org), to construct a coordinated federation of information systems holding grapevine data distributed around the world, providing an integrated set of interfaces supporting advanced data modeling, rich semantic integration and the next generation of data mining tools. To achieve this goal, it will be critical to develop, implement and adopt appropriate standards for data annotation and formatting. The development of this system, the GrapeIS, linking genotypes to phenotypes, and scientific research to agronomical and oeneological data, should provide new insights into grape biology, and allow the development of new varieties to meet the challenges of biotic and abiotic stress, environmental change, and consumer demand.
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Affiliation(s)
- A-F Adam-Blondon
- URGI, UR1164 INRA, Université Paris-Saclay, Versailles 78026, France
| | - M Alaux
- URGI, UR1164 INRA, Université Paris-Saclay, Versailles 78026, France
| | - C Pommier
- URGI, UR1164 INRA, Université Paris-Saclay, Versailles 78026, France
| | - D Cantu
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
| | - Z-M Cheng
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
| | - GR Cramer
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
| | - C Davies
- CSIRO Agriculture and Food, Waite Campus, WIC West Building, PMB2, Glen Osmond, South Australia 5064, Australia
| | - S Delrot
- Université de Bordeaux, ISVV, EGFV, UMR 1287, F-33140 Villenave d’Ornon, France
| | - L Deluc
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - G Di Gaspero
- Istituto di Genomica Applicata, Udine 33100, Italy
| | - J Grimplet
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño 26006, Spain
| | - A Fennell
- Plant Science Department, South Dakota State University, BioSNTR, Brookings, SD 57007, USA
| | - JP Londo
- United States Department of Agriculture-Agricultural Research Service-Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - P Kersey
- European Molecular Biology Laboratory, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - F Mattivi
- Dipartimento Qualità Alimentare e Nutrizione, Centro Ricerca ed Innovazione Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Italia
| | - S Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - P Neveu
- UMR Mistea, INRA, Montpellier 34060, France
| | - M Nikolski
- University of Bordeaux, CBiB, Bordeaux 33000, France
- University of Bordeaux, CNRS/LaBRI, Talence 33405, France
| | - M Pezzotti
- Department of Biotechnology, Università degli Studi di Verona, Verona 37134, Italy
| | - BI Reisch
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - R Töpfer
- JKI Institute for Grapevine Breeding Geilweilerhof, Siebeldingen 76833, Germany
| | - MA Vivier
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch University, Stellenbosch, Matieland 7602, South Africa
| | - D Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- US Department of Agriculture-Agricultural Research Service, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14853, USA
| | - H Quesneville
- URGI, UR1164 INRA, Université Paris-Saclay, Versailles 78026, France
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Di Gaspero G, Cipriani G, Adam-Blondon AF, Testolin R. Linkage maps of grapevine displaying the chromosomal locations of 420 microsatellite markers and 82 markers for R-gene candidates. Theor Appl Genet 2007; 114:1249-63. [PMID: 17380315 DOI: 10.1007/s00122-007-0516-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Accepted: 01/28/2007] [Indexed: 05/14/2023]
Abstract
Genetic maps functionally oriented towards disease resistance have been constructed in grapevine by analysing with a simultaneous maximum-likelihood estimation of linkage 502 markers including microsatellites and resistance gene analogs (RGAs). Mapping material consisted of two pseudo-testcrosses, 'Chardonnay' x 'Bianca' and 'Cabernet Sauvignon' x '20/3' where the seed parents were Vitis vinifera genotypes and the male parents were Vitis hybrids carrying resistance to mildew diseases. Individual maps included 320-364 markers each. The simultaneous use of two mapping crosses made with two pairs of distantly related parents allowed mapping as much as 91% of the markers tested. The integrated map included 420 Simple Sequence Repeat (SSR) markers that identified 536 SSR loci and 82 RGA markers that identified 173 RGA loci. This map consisted of 19 linkage groups (LGs) corresponding to the grape haploid chromosome number, had a total length of 1,676 cM and a mean distance between adjacent loci of 3.6 cM. Single-locus SSR markers were randomly distributed over the map (CD = 1.12). RGA markers were found in 18 of the 19 LGs but most of them (83%) were clustered on seven LGs, namely groups 3, 7, 9, 12, 13, 18 and 19. Several RGA clusters mapped to chromosomal regions where phenotypic traits of resistance to fungal diseases such as downy mildew and powdery mildew, bacterial diseases such as Pierce's disease, and pests such as dagger and root-knot nematode, were previously mapped in different segregating populations. The high number of RGA markers integrated into this new map will help find markers linked to genetic determinants of different pest and disease resistances in grape.
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Affiliation(s)
- G Di Gaspero
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze 208, 33100, Udine, Italy.
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Doligez A, Adam-Blondon AF, Cipriani G, Di Gaspero G, Laucou V, Merdinoglu D, Meredith CP, Riaz S, Roux C, This P. An integrated SSR map of grapevine based on five mapping populations. Theor Appl Genet 2006; 113:369-82. [PMID: 16799809 DOI: 10.1007/s00122-006-0295-1] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2005] [Accepted: 04/19/2006] [Indexed: 05/10/2023]
Abstract
A grapevine (mainly Vitis vinifera L., 2n = 38) composite genetic map was constructed with CarthaGene using segregation data from five full-sib populations of 46, 95, 114, 139 and 153 individuals, to determine the relative position of a large set of molecular markers. This consensus map comprised 515 loci (502 SSRs and 13 other type PCR-based markers), amplified using 439 primer pairs (426 SSRs and 13 others) with 50.1% common markers shared by at least two crosses. Out of all loci, 257, 85, 74, 69 and 30 were mapped in 1, 2, 3, 4 and 5 individual mapping populations, respectively. Marker order was generally well conserved between maps of individual populations, with only a few significant differences in the recombination rate of marker pairs between two or more populations. The total length of the integrated map was 1,647 cM Kosambi covering 19 linkage groups, with a mean distance between neighbour loci of 3.3 cM. A framework-integrated map was also built, with marker order supported by a LOD of 2.0. It included 257 loci spanning 1,485 cM Kosambi with a mean inter-locus distance of 6.2 cM over 19 linkage groups. These integrated maps are the most comprehensive SSR-based maps available so far in grapevine and will serve either for choosing markers evenly scattered over the whole genome or for selecting markers that cover particular regions of interest. The framework map is also a useful starting point for the integration of the V. vinifera physical and genetic maps.
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Affiliation(s)
- A Doligez
- INRA, UMR DGPC 1097, équipe Génétique Vigne, bâtiment 6, 2 place Viala, 34060, Montpellier Cedex 1, France.
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5
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Barker CL, Donald T, Pauquet J, Ratnaparkhe MB, Bouquet A, Adam-Blondon AF, Thomas MR, Dry I. Genetic and physical mapping of the grapevine powdery mildew resistance gene, Run1, using a bacterial artificial chromosome library. Theor Appl Genet 2005; 111:370-7. [PMID: 15902396 DOI: 10.1007/s00122-005-2030-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2005] [Accepted: 04/06/2005] [Indexed: 05/02/2023]
Abstract
Resistance to grapevine powdery mildew is controlled by Run1, a single dominant gene present in the wild grapevine species, Muscadinia rotundifolia, but absent from the cultivated species, Vitis vinifera. Run1 has been introgressed into V. vinifera using a pseudo-backcross strategy, and genetic markers have previously been identified that are linked to the resistance locus. Here we describe the construction of comprehensive genetic and physical maps spanning the resistance locus that will enable future positional cloning of the resistance gene. Physical mapping was performed using a bacterial artificial chromosome (BAC) library constructed using genomic DNA extracted from a resistant V. vinifera individual carrying Run1 within an introgression. BAC contig assembly has enabled 20 new genetic markers to be identified that are closely linked to Run1, and the position of the resistance locus has been refined, locating the gene between the simple sequence repeat (SSR) marker, VMC4f3.1, and the BAC end sequence-derived marker, CB292.294. This region contains two multigene families of resistance gene analogues (RGA). A comparison of physical and genetic mapping data indicates that recombination is severely repressed in the vicinity of Run1, possibly due to divergent sequence contained within the introgressed fragment from M. rotundifolia that carries the Run1 gene.
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Affiliation(s)
- C L Barker
- CSIRO Plant Industry, Glen Osmond, SA, Australia.
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Adam-Blondon AF, Bernole A, Faes G, Lamoureux D, Pateyron S, Grando MS, Caboche M, Velasco R, Chalhoub B. Construction and characterization of BAC libraries from major grapevine cultivars. Theor Appl Genet 2005; 110:1363-71. [PMID: 15834699 DOI: 10.1007/s00122-005-1924-9] [Citation(s) in RCA: 31] [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: 10/27/2004] [Accepted: 01/05/2005] [Indexed: 05/20/2023]
Abstract
Genome projects were initiated on grapevine (Vitis vinifera L., 2n=38, genome size 475 Mb) through the successful construction of four bacterial artificial chromosome (BAC) libraries from three major cultivars, Cabernet Sauvignon (Cabernet S), Syrah and two different clones of Pinot Noir (Pinot N). Depending on the library, the genome coverage represented 4.5-14.8 genome equivalents with clones having a mean insert size of 93-158 kb. BAC pools suitable for PCR screening were constructed for two of these BAC libraries [Cabernet S and Pinot N clone (cl) 115] and subsequently used to confirm the genome coverage of both libraries by PCR anchoring of 74 genetic markers sampled from the 19 linkage groups. For ten of these markers, two bands on separate BAC pools were differentiated that could correspond either to different alleles or to a duplication of the locus being studied. Finally, a preliminary assessment of the correspondence between genetic and physical distances was made through the anchoring of all the markers mapped along linkage group 1 of the V. vinifera genetic map. A pair of markers, 2.1 cM apart, anchored the same BAC clones, which allowed us to estimate that 1 cM corresponded in this particular region to a maximum length of 130 kb.
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Affiliation(s)
- A-F Adam-Blondon
- Unité Mixte de Recherches sur les Génomes des Végétaux, INRA, 2 rue Gaston Crémieux, 5708 91 057, Evry Cedex, France.
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Adam-Blondon AF, Roux C, Claux D, Butterlin G, Merdinoglu D, This P. Mapping 245 SSR markers on the Vitis vinifera genome: a tool for grape genetics. Theor Appl Genet 2004; 109:1017-27. [PMID: 15184982 DOI: 10.1007/s00122-004-1704-y] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2003] [Accepted: 04/02/2004] [Indexed: 05/08/2023]
Abstract
The aim of the present work was to develop a microsatellite marker-based map of the Vitis vinifera genome (n=19), useful for genetic studies in this perennial heterozygous species, as SSR markers are highly transferable co-dominant markers. A total of 346 primer pairs were tested on the two parents (Syrah and Grenache) of a full sib population of 96 individuals (S x G population), successfully amplifying 310 markers. Of these, 88.4% markers were heterozygous for at least one of the two parents. A total of 292 primer pairs were then tested on Riesling, the parent of the RS1 population derived from selfing (96 individuals), successfully amplifying 299 markers among which 207 (62.9%) were heterozygous. Only 6.7% of the markers were homozygous in all three genotypes, stressing the interest of such markers in grape genetics. Four maps were constructed based on the segregation of 245 SSR markers in the two populations. The Syrah map was constructed from the segregations of 177 markers that could be ordered into 19 linkage groups (total length 1,172.2 cM). The Grenache map was constructed with the segregations of 178 markers that could be ordered into 18 linkage groups (total length 1,360.6 cM). The consensus S x G map was constructed with the segregations of 220 markers that were ordered into 19 linkage groups (total length 1,406.1 cM). One hundred and eleven markers were scored on the RS1 population, among them 27 that were not mapped using the S x G map. Out of these 111 markers, 110 allowed to us to construct a map of a total length of 1,191.7 cM. Using these four maps, the genome length of V. vinifera was estimated to be around 2,200 cM. The present work allowed us to map 123 new SSR markers on the V. vinifera genome that had not been ordered in a previous SSR-based map (Riaz et al. 2004), representing an average of 6.5 new markers per linkage group. Any new SSR marker mapped is of great potential usefulness for many applications such as the transfer of well-scattered markers to other maps for QTL detection, the use of markers in specific regions for the fine mapping of genes/QTL, or for the choice of markers for MAS.
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Geffroy V, Creusot F, Falquet J, Sévignac M, Adam-Blondon AF, Bannerot H, Gepts P, Dron M. A family of LRR sequences in the vicinity of the Co-2 locus for anthracnose resistance in Phaseolus vulgaris and its potential use in marker-assisted selection. Theor Appl Genet 1998; 96:494-502. [PMID: 24710889 DOI: 10.1007/s001220050766] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Molecular markers offer new opportunities for breeding for disease resistance. Resistance gene pyramiding in a single cultivar, as a strategy for durable resistance, can be facilitated by marker-assisted selection (MAS). A RAPD marker, ROH20(450), linked to the Mesoamerican Co-2 anthracnose resistance gene, was previously transformed into a SCAR marker, SCH20. In the present paper we have further characterized the relevance of the SCH20 SCAR marker in different genetic backgrounds. Since this SCAR marker was found to be useful mainly in the Andean gene pool, we identified a new PCR-based marker (SCAreoli) for indirect scoring of the presence of the Co-2 gene. The SCAreoli SCAR marker is polymorphic in the Mesoamerican as well as in the Andean gene pool and should be useful in MAS. We also report that PvH20, the cloned sequence corresponding to the 450-bp RAPD marker ROH20(450), contains six imperfect leucine-rich repeats, and reveals a family of related sequences in the vicinity of the Co-2 locus. These results are discussed in the context of the recent cloning of some plant resistance genes.
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Affiliation(s)
- V Geffroy
- LPPM, IBP, Bât, 630, Université Paris Sud, 91405 ORSAY Cedex, France E-mail: , FR
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Abstract
A bean genetic map was developed to locate resistance genes against anthracnose and genes involved in plant defense mechanisms. One hundred and fifty-seven markers (51 restriction fragment length polymorphism, 100 random amplified polymorphic DNA, 2 sequence characterized amplified regions, and 4 morphological markers) were used to construct a genetic map covering 567.5 cM of the bean genome. Morphological markers consisted in two resistance genes towards anthracnose (Are and RVI), a dominant gene for nuclear male sterility (Ms8) and a pod-shape character (SGou). This map was established by using a backcross population (BC1) of 128 individuals, derived from a cross between two European bean genotypes: Ms8EO2 and Corel. Nine percent of the markers showed segregation distortions and mapped to three regions. Clusters of 2-10 markers were observed in every linkage group. The possible origin of these clusters is discussed. Nineteen markers shared with a previously published bean linkage map allowed us to establish a preliminary correspondence between the two maps. Finally, seven genes involved in plant defense mechanisms were located on this map.
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Affiliation(s)
- A F Adam-Blondon
- Département de Biologie Moléculaire Végétale, Université Paris-Sud, Orsay, France
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10
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Adam-Blondon AF, Sévignac M, Bannerot H, Dron M. SCAR, RAPD and RFLP markers linked to a dominant gene (Are) conferring resistance to anthracnose in common bean. Theor Appl Genet 1994; 88:865-70. [PMID: 24186190 DOI: 10.1007/bf01253998] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/1993] [Accepted: 12/21/1993] [Indexed: 05/20/2023]
Abstract
Anthracnose, caused by the fungusColletotrichum lindemuthianum, is a severe disease of common bean (Phaseolus vulgaris L.) controlled, in Europe, by a single dominant gene,Are. Four pairs of near-isogenic lines (NILs) were constructed, in which theAre gene was introgressed into different genetic backgrounds. These pairs of NILs were used to search for DNA markers linked to the resistance gene. Nine molecular markers, five RAPDs and four RFLPs, were found to discriminate between the resistant and the susceptible members of these NILs. A backcross progeny of 120 individuals was analysed to map these markers in relation to theAre locus. Five out of the nine markers were shown to be linked to theAre gene within a distance of 12.0 cM. The most tightly linked, a RAPD marker, was used to generate a pair of primers that specifically amplify this RAPD (sequence characterized amplified region, SCAR).
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Affiliation(s)
- A F Adam-Blondon
- Dépt Biol Mol Végétale, Bat 430, Université Paris Sud, 91405, Orsay Cedex, France
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