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Large SNP arrays for genotyping in crop plants

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Abstract

Genotyping with large numbers of molecular markers is now an indispensable tool within plant genetics and breeding. Especially through the identification of large numbers of single nucleotide polymorphism (SNP) markers using the novel high-throughput sequencing technologies, it is now possible to reliably identify many thousands of SNPs at many different loci in a given plant genome. For a number of important crop plants, SNP markers are now being used to design genotyping arrays containing thousands of markers spread over the entire genome and to analyse large numbers of samples. In this article, we discuss aspects that should be considered during the design of such large genotyping arrays and the analysis of individuals. The fact that crop plants are also often autopolyploid or allopolyploid is given due consideration. Furthermore, we outline some potential applications of large genotyping arrays including high-density genetic mapping, characterization (fingerprinting) of genetic material and breeding-related aspects such as association studies and genomic selection.

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Abbreviations

GBS:

genotyping by sequencing

LD:

linkage disequilibrium

NGS:

next-generation sequencing

PIC:

Polymorphism Information Content

QTL:

quantitatively inherited traits

SNP:

single nucleotide polymorphism

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Acknowledgements

The authors acknowledge the assistance of the technical staff at TraitGenetics during SNP marker development and the analysis of many samples using genotyping arrays. Research in the area of large-scale genotyping at TraitGenetics has in part been funded by grants from the German Federal Ministry of Education and Research (BMBF).

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Authors and Affiliations

  1. TraitGenetics GmbH, Am Schwabeplan 1b, D-06466, Gatersleben, Germany

    Martin W Ganal, Andreas Polley, Eva-Maria Graner, Joerg Plieske, Ralf Wieseke, Hartmut Luerssen & Gregor Durstewitz

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  1. Martin W Ganal
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  2. Andreas Polley
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  3. Eva-Maria Graner
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  4. Joerg Plieske
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  5. Ralf Wieseke
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  6. Hartmut Luerssen
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  7. Gregor Durstewitz
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Corresponding author

Correspondence to Martin W Ganal.

Additional information

[Ganal MW, Polley A, Graner E-M, Plieske J, Wieseke R, Luerssen H and Durstewitz G 2012 Large SNP arrays for genotyping in crop plants. J. Biosci. 37 1–8] DOI 10.1007/s12038-012-9225-3

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Ganal, M.W., Polley, A., Graner, EM. et al. Large SNP arrays for genotyping in crop plants. J Biosci 37, 821–828 (2012). https://doi.org/10.1007/s12038-012-9225-3

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  • DOI: https://doi.org/10.1007/s12038-012-9225-3

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