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Karaiskou N, Buggiotti L, Leder E, Primmer CR. High degree of transferability of 86 newly developed zebra finch EST-linked microsatellite markers in 8 bird species. ACTA ACUST UNITED AC 2008; 99:688-93. [PMID: 18583388 DOI: 10.1093/jhered/esn052] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
High-resolution analysis for population genetic and functional studies requires the use of large numbers of polymorphic markers. The recent increase of available genetic tools is facilitated by the use of publicly available expressed sequence tag (EST) sequence databases that are a valuable resource for identifying gene-linked markers. In the present study, we applied bioinformatics analyses to identify microsatellite markers present in EST sequences from a zebra finch (Taeniopgia guttata) EST database and we explore the success of cross-species amplification of EST-linked microsatellite markers in 7 passerine and 1 nonpasserine species. Eighty-six zebra finch EST-linked microsatellite loci were screened for polymorphism revealing a high amplification success rate and adequate levels of polymorphism (33.3-51%) for relatively closely related species, whereas success decreased in the most distantly related species to zebra finch. EST-linked microsatellites appear to be more highly transferable between taxa than anonymous microsatellites as they revealed higher amplification and polymorphism success between different families indicating that they will be a useful source of gene-linked polymorphic markers in a broad range of avian species.
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Affiliation(s)
- Nikoletta Karaiskou
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, PO Box 54 124, Thessaloniki, Macedonia, Greece
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252
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Lewers KS, Saski CA, Cuthbertson BJ, Henry DC, Staton ME, Main DS, Dhanaraj AL, Rowland LJ, Tomkins JP. A blackberry (Rubus L.) expressed sequence tag library for the development of simple sequence repeat markers. BMC PLANT BIOLOGY 2008; 8:69. [PMID: 18570660 PMCID: PMC2474608 DOI: 10.1186/1471-2229-8-69] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2008] [Accepted: 06/20/2008] [Indexed: 05/03/2023]
Abstract
BACKGROUND The recent development of novel repeat-fruiting types of blackberry (Rubus L.) cultivars, combined with a long history of morphological marker-assisted selection for thornlessness by blackberry breeders, has given rise to increased interest in using molecular markers to facilitate blackberry breeding. Yet no genetic maps, molecular markers, or even sequences exist specifically for cultivated blackberry. The purpose of this study is to begin development of these tools by generating and annotating the first blackberry expressed sequence tag (EST) library, designing primers from the ESTs to amplify regions containing simple sequence repeats (SSR), and testing the usefulness of a subset of the EST-SSRs with two blackberry cultivars. RESULTS A cDNA library of 18,432 clones was generated from expanding leaf tissue of the cultivar Merton Thornless, a progenitor of many thornless commercial cultivars. Among the most abundantly expressed of the 3,000 genes annotated were those involved with energy, cell structure, and defense. From individual sequences containing SSRs, 673 primer pairs were designed. Of a randomly chosen set of 33 primer pairs tested with two blackberry cultivars, 10 detected an average of 1.9 polymorphic PCR products. CONCLUSION This rate predicts that this library may yield as many as 940 SSR primer pairs detecting 1,786 polymorphisms. This may be sufficient to generate a genetic map that can be used to associate molecular markers with phenotypic traits, making possible molecular marker-assisted breeding to compliment existing morphological marker-assisted breeding in blackberry.
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Affiliation(s)
- Kim S Lewers
- USDA-ARS, Beltsville Agricultural Research Center, Genetic Improvement of Fruits and Vegetables Lab, Bldg. 010A, BARC-West, 10300 Baltimore Ave., Beltsville, MD 20705-2350, USA
| | - Chris A Saski
- Clemson University Genomics Institute, 51 New Cherry St., 304 Biosystems Research Complex, Clemson University, Clemson, SC 29634, USA
| | - Brandon J Cuthbertson
- Clemson University Genomics Institute, 51 New Cherry St., 304 Biosystems Research Complex, Clemson University, Clemson, SC 29634, USA
- National Institutes of Health/National Institute of Environmental Health Sciences, Laboratory of Signal Transduction, Peptide Hormone Action Group, 111 TW Alexander Drive, PO Box 12233, MD F3-04 Research Triangle Park, NC 27709-2233, USA
| | - David C Henry
- Clemson University Genomics Institute, 51 New Cherry St., 304 Biosystems Research Complex, Clemson University, Clemson, SC 29634, USA
| | - Meg E Staton
- Clemson University Genomics Institute, 51 New Cherry St., 304 Biosystems Research Complex, Clemson University, Clemson, SC 29634, USA
| | - Dorrie S Main
- Clemson University Genomics Institute, 51 New Cherry St., 304 Biosystems Research Complex, Clemson University, Clemson, SC 29634, USA
- Center for Integrated Biotechnology, Dept of Horticulture and Landscape Architecture, Washington State University, 45 Johnson Hall, Pullman, WA 99164-6414, USA
| | - Anik L Dhanaraj
- USDA-ARS, Beltsville Agricultural Research Center, Genetic Improvement of Fruits and Vegetables Lab, Bldg. 010A, BARC-West, 10300 Baltimore Ave., Beltsville, MD 20705-2350, USA
- Monsanto Research Centre, Biotech Product Support, 44/2A Bellary Road, NH-7, Hebbal, Bangalore 560 092, India
| | - Lisa J Rowland
- USDA-ARS, Beltsville Agricultural Research Center, Genetic Improvement of Fruits and Vegetables Lab, Bldg. 010A, BARC-West, 10300 Baltimore Ave., Beltsville, MD 20705-2350, USA
| | - Jeff P Tomkins
- Clemson University Genomics Institute, 51 New Cherry St., 304 Biosystems Research Complex, Clemson University, Clemson, SC 29634, USA
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253
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Mathimaran N, Falquet L, Ineichen K, Picard C, Redecker D, Boller T, Wiemken A. Microsatellites for disentangling underground networks: Strain-specific identification of Glomus intraradices, an arbuscular mycorrhizal fungus. Fungal Genet Biol 2008; 45:812-7. [DOI: 10.1016/j.fgb.2008.02.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 02/22/2008] [Accepted: 02/25/2008] [Indexed: 11/28/2022]
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256
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Karrenberg S, Widmer A. Ecologically relevant genetic variation from a non-Arabidopsis perspective. CURRENT OPINION IN PLANT BIOLOGY 2008; 11:156-162. [PMID: 18329951 DOI: 10.1016/j.pbi.2008.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Revised: 01/18/2008] [Accepted: 01/21/2008] [Indexed: 05/26/2023]
Abstract
Ecologically relevant genetic variation occurs in genes harbouring alleles that are adaptive in some environments but not in others. Analysis of this type of genetic variation in model organisms has made substantial progress, and is now being expanded to other species in order to better cover the diversity of plant life. Recent advances in connecting ecological and molecular studies in non-model species have been made with regard to edaphic and climatic adaptation, plant reproduction, life-history parameters and biotic interactions. New research avenues that increase biological complexity and ecological relevance by integrating ecological experiments with population genetic and functional genomic approaches provide new insights into the genetic basis of ecologically relevant variation.
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Affiliation(s)
- Sophie Karrenberg
- ETH Zurich, Institute of Integrative Biology, Plant Ecological Genetics, Universitaetstr. 16, 8092 Zurich, Switzerland
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258
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Peleg Z, Saranga Y, Krugman T, Abbo S, Nevo E, Fahima T. Allelic diversity associated with aridity gradient in wild emmer wheat populations. PLANT, CELL & ENVIRONMENT 2008; 31:39-49. [PMID: 17908203 DOI: 10.1111/j.1365-3040.2007.01731.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The association between allelic diversity and ecogeographical variables was studied in natural populations of wild emmer wheat [Triticum turgidum ssp. dicoccoides (Körn.) Thell.], the tetraploid progenitor of cultivated wheat. Patterns of allelic diversity in 54 microsatellite loci were analyzed in a collection of 145 wild emmer wheat accessions representing 25 populations that were sampled across naturally occurring aridity gradient in Israel and surrounding regions. The obtained results revealed that 56% of the genetic variation resided among accessions within populations, while only 44% of the variation resided between populations. An unweighted pair-group method analysis (UPGMA) tree constructed based on the microsatellite allelic diversity divided the 25 populations into six major groups. Several groups were comprised of populations that were collected in ecologically similar but geographically remote habitats. Furthermore, genetic differentiation between populations was independent of the geographical distances. An interesting evolutionary phenomenon is highlighted by the unimodal relationship between allelic diversity and annual rainfall (r = 0.74, P < 0.0002), indicating higher allelic diversity in populations originated from habitats with intermediate environmental stress (i.e. rainfall 350-550 mm year(-1)). These results show for the first time that the 'intermediate-disturbance hypothesis', explaining biological diversity at the ecosystem level, also dominates the genetic diversity within a single species, the lowest hierarchical element of the biological diversity.
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Affiliation(s)
- Zvi Peleg
- The Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 31905, Israel
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259
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Mathimaran N, Falquet L, Ineichen K, Picard C, Redecker D, Wiemken A, Boller T. Unexpected vagaries of microsatellite loci in Glomus intraradices: length polymorphisms are rarely caused by variation in repeat number only. THE NEW PHYTOLOGIST 2008; 180:568-570. [PMID: 19138227 DOI: 10.1111/j.1469-8137.2008.02649.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Natarajan Mathimaran
- Zurich-Basel Plant Science Center, Botanisches Institut der Universität Basel, Hebelstrasse 1, CH-4056 Basel, Switzerland
| | - Laurent Falquet
- Swiss Institute of Bioinformatics, University of Lausanne, Quartier Sorge - Bâtiment Génopode, 1015 Lausanne, Switzerland
| | - Kurt Ineichen
- Zurich-Basel Plant Science Center, Botanisches Institut der Universität Basel, Hebelstrasse 1, CH-4056 Basel, Switzerland
| | - Cyril Picard
- Swiss Institute of Bioinformatics, University of Lausanne, Quartier Sorge - Bâtiment Génopode, 1015 Lausanne, Switzerland
| | - Dirk Redecker
- Zurich-Basel Plant Science Center, Botanisches Institut der Universität Basel, Hebelstrasse 1, CH-4056 Basel, Switzerland
| | - Andres Wiemken
- Zurich-Basel Plant Science Center, Botanisches Institut der Universität Basel, Hebelstrasse 1, CH-4056 Basel, Switzerland
| | - Thomas Boller
- Zurich-Basel Plant Science Center, Botanisches Institut der Universität Basel, Hebelstrasse 1, CH-4056 Basel, Switzerland
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