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Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars

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Abstract

In this study, we developed 359 detection primers for single nucleotide polymorphisms (SNPs) previously discovered within intron sequences of wheat genes and used them to evaluate SNP polymorphism in common wheat (Triticum aestivum L.). These SNPs showed an average polymorphism information content (PIC) of 0.18 among 20 US elite wheat cultivars, representing seven market classes. This value increased to 0.23 when SNPs were pre-selected for polymorphisms among a diverse set of 13 hexaploid wheat accessions (excluding synthetic wheats) used in the wheat SNP discovery project (http://wheat.pw.usda.gov/SNP). PIC values for SNP markers in the D genome were approximately half of those for the A and B genomes. D genome SNPs also showed a larger PIC reduction relative to the other genomes (P < 0.05) when US cultivars were compared with the more diverse set of 13 wheat accessions. Within those accessions, D genome SNPs show a higher proportion of alleles with low minor allele frequencies (<0.125) than found in the other two genomes. These data suggest that the reduction of PIC values in the D genome was caused by differential loss of low frequency alleles during the population size bottleneck that accompanied the development of modern commercial cultivars. Additional SNP discovery efforts targeted to the D genome in elite wheat germplasm will likely be required to offset the lower diversity of this genome. With increasing SNP discovery projects and the development of high-throughput SNP assay technologies, it is anticipated that SNP markers will play an increasingly important role in wheat genetics and breeding applications.

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Abbreviations

EST:

Expressed sequence tag

FP:

Fluorescence polarization

HRS:

Hard red spring

HWS:

Hard white spring

HRW:

Hard red winter

HWW:

Hard White Winter

PIC:

Polymorphism information content

SSR:

Simple sequence repeat

SNP:

Single nucleotide polymorphism

SRW:

Soft red winter

SWS:

Soft white spring

SWW:

Soft white winter

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Acknowledgements

This research was supported in part by the funds from the U.S. Department of Agriculture, Cooperative State Research, Education and Extension Service, Coordinated Agricultural Project grant number 2006-55606-16629 and NSF Grant No. DBI-0321757. We thank Dr. Jan Dvorak for facilitating early access to the SNP data generated by the NSF project and for his useful suggestions and ideas and to Iago Lowe for his thorough revision of the manuscript.

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Authors and Affiliations

  1. USDA-ARS Biosciences Research Lab, 1605 Albrecht Blvd., Fargo, ND, 58105-5674, USA

    Shiaoman Chao

  2. Department of Plant Sciences, University of California, Davis, Davis, CA, 95616, USA

    Wenjun Zhang, Yaqin Ma, Ming-Cheng Luo & Jorge Dubcovsky

  3. Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA

    Eduard Akhunov

  4. Department of Plant and Soil Sciences, Montana State University, Bozeman, MT, 59717, USA

    Jamie Sherman

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  1. Shiaoman Chao
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  2. Wenjun Zhang
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  3. Eduard Akhunov
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  4. Jamie Sherman
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  5. Yaqin Ma
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  6. Ming-Cheng Luo
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  7. Jorge Dubcovsky
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Correspondence to Shiaoman Chao.

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Chao, S., Zhang, W., Akhunov, E. et al. Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars. Mol Breeding 23, 23–33 (2009). https://doi.org/10.1007/s11032-008-9210-6

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  • DOI: https://doi.org/10.1007/s11032-008-9210-6

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