Interspecific and intergeneric hybridization is a useful tool in the breeding of cultivated species of Triticeae tribe. This technique has been widely used to transfer desirable traits from wild to cultivated species
[1–3] and to increase the genetic variation of the species by developing new synthetic hexaploid wheats
[4–6] or using Triticum urartu (donor of the A genome) for durum wheat breeding
. Intergeneric hybrids between Hordeum and Triticum genus were attempted since the beginning of the 20th century. Since the first hybrids reported by
 numerous hybrid combinations between both genera have been produced and reviewed by
. However, only a few fertile hybrids have been obtained by chromosome doubling with colchicine. These were the hybrids between T. timopheevii × H. bogdanii, H. chilense × T. aestivum and H. chilense × T. durum. Among Hordeum species, Hordeum chilense Roem. et Schultz. is a native South American diploid perennial wild barley (2n = 2× = 14), included in the section Anisolepsis
. It belongs to a heterogeneous group of South American Hordeum species and it is one of the species of the genus Hordeum with a high potential for cereal breeding purposes, given its high crossability with other members of the Triticeae tribe and other interesting characteristics
. In recent years, molecular and cytological techniques have been developed in H. chilense for basic cytogenetic research, genetic diversity studies and monitoring H. chilense chromosomes in wheat genetic background. Several types of molecular markers, including Random Amplified Polymorphic DNA (RAPD)
, Sequence Characterized Amplified Regions (SCARs)
, Cleaved Amplified Polymorphisms (CAPs)
 or DArTs
 have been developed de novo for H. chilense. Similarly other markers have been transferred from wheat and barley species including Sequence Tagged Sites (STSs)
, genomic or EST-derived simple sequence repeat (SSRs)
[20, 21], ESTs
[22–24] or Conserved Orthologus Sequences (COS)
In addition to marker-assisted selection, genomic in situ hybridization (GISH) and fluorescence in situ hybridization (FISH) are useful tools which have been used for identifying H. chilense chromosomes (or chromosome translocation) in wheat background
Tritordeums (×Tritordeum Ascherson et Graebner) are the fertile amphiploids obtained after chromosome doubling of hybrids between wheat (Triticum sp.) and H. chilense. They have been synthesised at different ploidy levels and genome constitutions, of which hexaploids tritordeums (2n = 6× = 42, AABBHchHch) have been subject of breeding program
. The favourable agronomic traits shown by tritordeums, such as high biomass yield, number of spikelets/spike, seed size and high protein content, suggested its potential to become a new crop
 which was confirmed nearly two decades later
. The high seed carotenoid content
[31, 32] of this species constitutes also an interesting characteristic in the context of developing functional foods. Accordingly, tritordeum has received attention as a potential crop in the last years and a breeding program has been developed including the development of chromosome substitutions involving D and Hch genomes. While the chromosome substitution program has obtained successful results for free threshing ability
 or improved bread-making quality
, it has also complicated the genetic composition of breeding materials since different chromosome substitutions may be present involving D and Hch genomes. Until now tritordeum lines were inspected for H. chilense/wheat substitutions using physically mapped markers per chromosome
 and using cytogenetics tools like GISH
[22, 24] and FISH
. While cytogenetics is useful for a limited set of lines, it is impractical for large amounts of entries included in a breeding program. Furthermore, the use of a limited number of molecular markers is not adequate for managing a large collection of germplasm since the rate of error in classification may be too high compared to whole genome profiling.
Based on the above considerations we embarked on development of Diversity Arrays Technology (DArT) since this technology can overcome these constraints. In addition DArT technology offers low cost per data, high throughput and sequence-independent genotyping
[36, 37] and allows simultaneously determination of several hundred to several thousands of polymorphic loci spread over the genome
. The high number of DArT markers generated in a single assay not only provides a precise estimate of genetic relationships among genotypes, but also their distribution over the genome offers real advantages for a range of molecular breeding and genomics applications.
DArT markers have been developed in more than 70 species (http://www.diversityarrays.com), including cereals such as cultivated barley (Hordeum vulgare), wheat (Triticum aestivum), durum wheat (Triticum durum), and recently wild barley (H. chilense).
DArT array have also been proved useful for polyploidy species with highly complex genomes
; to provide a fast and accurate means of determining the extent of introgression of the genome of the diverse parent in interespecific hybrids
 or to evaluate progenies derived from interespecific crosses between T. aestivum and T. durum.
This paper evaluates the effectiveness of DArT as a high-throughput genotyping technology in tritordeum. This technology offers tritordeum breeding program an alternative approach to whole-genome profiling providing high quality markers that can be exploited in a range of molecular breeding and genomics applications in tritordeum. Additionally we set out to explore the possibility of using DArT array for genome background screening in tritordeum and to determine terms of discriminative ability using 1RS/1BL translocation lines.