Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome

Abstract

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 x 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.

Mapping of the leaf rust resistance gene Lr38 on wheat chromosome arm 6DL using SSR markers

“…developed wheat diversity array technology (DArT) markers (Semagn et al 2006;Akbari et al 2006) appear very attractive due to the large number of parallel studies which are possible with these techniques.…”

The first genetic map of pigeon pea based on diversity arrays technology (DArT) markers

“…DArT generates genetic fingerprints by scoring the presence versus absence of DNA fragments in genomic representations generated from samples of genomic DNA. Hence, DArT was rapidly applied to a number of other plants and animals such as: apple, Arabidopsis thaliana, banana, barley, cassava, chickpea, coconut, eucalyptus, several fungal pathogens, lupin, pigeon pea, potato, quinoa, rice, ryegrass, sorghum, tomato, mouse, sheep and cattle (Jaccoud et al 2001;Lezar et al 2004;Wenzl et al 2004;Kilian et al 2005;Wittenberg et al 2005;Xia et al 2005;Yang et al 2006;Akbari et al 2006;www.diversityarrays.com). The other advantage of DArT is the speed of development in a new species.…”

“…DArT marker system has been developed as a technology for whole-genome profiling in barley (Wenzl et al 2004), cassava (Xia et al 2005), Arabidopsis thaliana (Wittenberg et al 2005), bread wheat (Akbari et al 2006), etc. As very few (∼10%) polymorphisms have been identified in cultivated pigeon pea lines using a limited number of SSR and DArT markers (Burns et al 2001;Yang et al 2006), an interspecific mapping population was developed by using pigeon pea (C. cajan) accession ICP 28 and ICPW 94 from a wild relative species of pigeon pea (C. scarabaeoides) to avail maximum polymorphism and to generate the first generation linkage map.…”

Characterisation of genetic variation for aluminium resistance and polyphenol oxidase activity in genebank accessions of spelt wheat

“…More recently, DArT markers have been developed and utilised in common wheat for this purpose (Akbari et al 2006, Stodart et al 2007. The comparative usefulness of DArT, AFLP and SSR-based markers was evaluated previously for assessing genetic diversity in wheat (Stodart et al 2005(Stodart et al , 2007.…”