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Development and test of 21 multiplex PCRs composed of SSRs spanning most of the apple genome |
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| Authors: | A. Patocchi F. Fernández-Fernández K. Evans D. Gobbin F. Rezzonico A. Boudichevskaia F. Dunemann M. Stankiewicz-Kosyl F. Mathis-Jeanneteau C. E. Durel L. Gianfranceschi F. Costa C. Toller V. Cova D. Mott M. Komjanc E. Barbaro L. Kodde E. Rikkerink C. Gessler W. E. van de Weg |
| Affiliation: | 1. Plant Pathology, Institute of Integrative Biology (IBZ), ETH Zurich, 8092, Zurich, Switzerland 11. Agroscope Changins-W?denswil Research station, Plant protection, Phytopathology, Schloss, B. O. 185, 8820, W?denswil, Switzerland 2. East Malling Research, New Road, East Malling, Kent, ME19 6BJ, England, UK 3. Bundesforschungsinstitut für Kulturpflanzen, Julius Kühn-Institut (JKI), Pillnitzer Platz 3a, 01326, Dresden, Germany 4. Laboratory of Basic Research in Horticulture, Faculty of Horticulture and Landscape Architecture, Warsaw Agricultural University (WAU), ul. Nowoursynowska 166, 02-787, Warsaw, Poland 5. UMR1259 Genetics and Horticulture (GenHort), Institut National de la Recherche Agronomique (INRA), BP 60057, 49071, Beaucouzé, France 6. Department of Biomolecular Sciences and Biotechnology, University of Milan, Via Celoria 26, 20133, Milan, Italy 7. Department of Fruit Tree and Woody Plant Sciences, University of Bologna, 40127, Bologna, Italy 8. Istituto Agrario di San Michele all’Adige, 38010, San Michele all’Adige, Trento, Italy 9. Department of Biodiversity and Breeding, Plant Research International, P.O. Box 16, 6700 AA, Wageningen, The Netherlands 10. The Horticulture and Food Research Institute of New Zealand Ltd, Mt Albert Research Center, Private Bag, 92169, Auckland, New Zealand |
| Abstract: | A series of 21 multiplex (MP) polymerase chain reactions containing simple sequence repeat (SSR) markers spanning most of the apple genome has been developed. Eighty-eight SSR markers, well distributed over all 17 linkage groups (LGs), have been selected. Eighty-four of them were included in 21 different MPs while four could not be included in any MPs. The 21 MPs were then used to genotype approximately 2,000 DNA samples from the European High-quality Disease-Resistant Apples for a Sustainable agriculture project. Two SSRs (CH01d03 and NZAL08) were discarded at an early stage as they did not produce stable amplifications in the MPs, while the scoring of the multilocus (ML) SSR Hi07d11 and CN44794 was too complex for large-scale genotyping. The testing of the remaining 80 SSRs over a large number of different genotypes allowed: (1) a better estimation of their level of polymorphism; as well as of (2) the size range of the alleles amplified; (3) the identification of additional unmapped loci of some ML SSRs; (4) the development of methods to assign alleles to the different loci of ML SSRs and (5) conditions at which an SSR previously described as ML would amplify alleles of a single locus to be determined. These data resulted in the selection of 75 SSRs out of the 80 that are well suited and recommended for large genotyping projects. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. |
| Keywords: | SSR Multiplex PCR Genotyping Malus |
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