Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome
Despite a substantial investment in the development of panels of single nucleotide polymorphism (SNP) markers, the simple sequence repeat (SSR) technology with a limited multiplexing capability remains a standard, even for applications requiring whole-genome information. Diversity arrays technology (DArT) types hundreds to thousands of genomic loci in parallel, as previously demonstrated in a number diploid plant species. Here we show that DArT performs similarly well for the hexaploid genome of bread wheat (Triticum aestivum L.). The methodology previously used to generate DArT fingerprints of barley also generated a large number of high-quality markers in wheat (99.8% allele-calling concordance and approximately 95% call rate). The genetic relationships among bread wheat cultivars revealed by DArT coincided with knowledge generated with other methods, and even closely related cultivars could be distinguished. To verify the Mendelian behaviour of DArT markers, we typed a set of 90 Cranbrook × Halberd doubled haploid lines for which a framework (FW) map comprising a total of 339 SSR, restriction fragment length polymorphism (RFLP) and amplified fragment length polymorphism (AFLP) markers was available. We added an equal number of DArT markers to this data set and also incorporated 71 sequence tagged microsatellite (STM) markers. A comparison of logarithm of the odds (LOD) scores, call rates and the degree of genome coverage indicated that the quality and information content of the DArT data set was comparable to that of the combined SSR/RFLP/AFLP data set of the FW map.
KeywordsRestriction Fragment Length Polymorphism Amplify Fragment Length Polymorphism Wheat Cultivar Doubled Haploid Call Rate
We thank the Australian Grains Research and Development Cooperation (GRDC; www.grdc.com.au) for financial support. Triticarte P/L (www.triticarte.com) is a joint venture of Diversity Arrays Technology P/L (DArT P/L; www.DiversityArrays.com) and the Value Added Wheat Cooperative Research Centre (VAWCRC; www.wheat-research.com.au). The Triticarte/DArT team thank their colleagues at CAMBIA (www.cambia.org) for their friendship and collaborative spirit as well as many interesting discussions during the period when CAMBIA was sharing laboratory facilities with Triticarte/DArT. We also thank two anonymous reviewers for their detailed comments, which have helped to improve the manuscript.
- Anderson MJ (2003) PCO: a FORTRAN computer program for principal component analysis. Department of Statistics, University of Auckland, Auckland, New ZealandGoogle Scholar
- Chalmers KJ, Campbell AW, Kretschmer J, Karakousis A, Henschke PH, Pierens S, Harker N, Pallotta M, Cornish GB, Shariflou MR, Rampling LR, McLauchlan A, Daggard G, Sharp PJ, Holton TA, Sutherland MW, Appels R, Langridge P (2001) Construction of three linkage maps in bread wheat. Triticum aestivum. Aust J Agric Res 52:1089–1119CrossRefGoogle Scholar
- Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:1–15Google Scholar
- Kilian A, Huttner E, Wenzl P, Jaccoud D, Carling J, Caig V, Evers M, Heller-Uszynska, Cayla C, Patarapuwadol S, Xia L, Yang S, Thomson B (2005) The fast and the cheap: SNP and DArT-based whole genome profiling for crop improvement. In: Tuberosa R, Phillips RL, Gale M (eds) Proceedings of the international congress “In the wake of the double helix: from the green revolution to the gene revolution”, 27–31 May, 2003, Avenue Media, Bologna, Italy, pp 443–461Google Scholar
- Lehmensiek A, Eckermann PJ, Verbyla AP, Appels R, Sutherland MW, Daggard GE (2005) Curation of wheat maps to improve map accuracy and QTL detection. Aust J Agric Res 56:1347–1354Google Scholar
- Liu BH, Knapp SJ (1990) GMENDEL: a program for Mendelian segregation and linkage analysis of individual or multiple progeny populations using log-likelihood ratios. J Hered 81:407–418Google Scholar
- McIntosh RA, Wellings CR, Park RF (1995) Wheat rusts: an atlas of resistance genes. CSIRO, Melbourne, Vic., AustraliaGoogle Scholar
- van Ooijen JW, Voorrips RE (2001) Joinmap 3.0, software for the calculation of genetic linkage maps. Plant Research International, Wageningen, The NetherlandsGoogle Scholar