Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat

In wheat, the deployment of marker-assisted selection has long been hampered by the lack of markers compatible with high-throughput cost-effective genotyping techniques. Recently, insertion site-based polymorphism (ISBP) markers have appeared as very powerful new tools for genomics and genetic studi...

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Bibliographic Details
Published in:Plant biotechnology journal 2010-02, Vol.8 (2), p.196-210
Main Authors: Paux, Etienne, Faure, Sébastien, Choulet, Frédéric, Roger, Delphine, Gauthier, Valérie, Martinant, Jean-Pierre, Sourdille, Pierre, Balfourier, François, Le Paslier, Marie-Christine, Chauveau, Aurélie, Cakir, Mehmet, Gandon, Béatrice, Feuillet, Catherine
Format: Article
Language:English
Subjects:
Base Sequence
Biological and medical sciences
Biotechnology
Chromosome Mapping
DNA, Plant - genetics
Fundamental and applied biological sciences. Psychology
Genome, Plant
Genomics - methods
Genotype
High-Throughput Screening Assays
Insertion site-based polymorphism
Life Sciences
mapping
marker-assisted selection
molecular marker
Molecular Sequence Data
polymorphism
Polymorphism, Single Nucleotide
Sequence Analysis, DNA - methods
Triticum - genetics
Vegetal Biology
wheat
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Summary:In wheat, the deployment of marker-assisted selection has long been hampered by the lack of markers compatible with high-throughput cost-effective genotyping techniques. Recently, insertion site-based polymorphism (ISBP) markers have appeared as very powerful new tools for genomics and genetic studies in hexaploid wheat. To demonstrate their possible use in wheat breeding programmes, we assessed their potential to meet the five main requirements for utilization in MAS: flexible and high-throughput detection methods, low quantity and quality of DNA required, low cost per assay, tight link to target loci and high level of polymorphism in breeding material. Toward this aim, we developed a programme, IsbpFinder, for the automated design of ISBP markers and adapted three detection methods (melting curve analysis, SNaPshot® Multiplex System and Illumina BeadArray technology) for high throughput and flexible detection of ISBP or ISBP-derived SNP markers. We demonstrate that the high level of polymorphism of the ISBPs combined with cost-effective genotyping methods can be used to efficiently saturate genetic maps, discriminate between elite cultivars, and design tightly linked diagnostic markers for virtually all target loci in the wheat genome. All together, our results suggest that ISBP markers have the potential to lead to a breakthrough in wheat marker-assisted selection.
ISSN:1467-7644
1467-7652
DOI:10.1111/j.1467-7652.2009.00477.x