Although this technique is still limited to only a few laboratories at this stage, barley consensus maps [ 35] have been constructed to link DArT markers with many SSR and RFLP markers which have been previously developed and applied widely in barley mapping studies and to provide plant breeders with practically useful molecular markers for improving barley waterlogging tolerance.
The data are a valuable genomic resource for an improved genome annotation, transcriptome studies of drought adaptation and a source of new genetic markers for future barley improvement.
We have shown that ESTs are a good source of SSRs that can be exploited to develop microsatellite markers for wheat, barley and rice.
Allele-specific markers for the barley VIP4-like genes, which were absent from the exome-enrichment assay, were designed based on the Sanger sequencing data of PCR fragments (see primers in Table S4).
Oligonucleotide sequences for amplification of the markers from barley genomic DNA were reported in [ 11].
Our assembly that unifies the mapped EST markers currently available for barley and wheat has already been used to map more than 2700 cDNAs to homoeologous chromosomes of barley and wheat.
The results have also shown that microRNA target sites can be an interesting source for the identification of functional genetic variability, representing an interesting source of candidate molecular markers for application in barley breeding.
Due to the effect of gene-target association to identify SNP markers for use in barley [ 35], the association between two candidate genes, HvNAM1 and HvNAM2, and GPC was analyzed, in order to examine the genetic architecture of GPC and to identify GPC loci in barley.
Szűcs et al. [ 10] included 1472 of the SNPs developed in the present work in addition to SSRs, AFLPs and DArT markers, making the resulting OWB map an excellent new point of cross-reference for barley markers.
This bridge marker frequency is comparable to other recent consensus map studies, including [ 34] who used 10% of all markers as bridge markers to construct a consensus map for barley from 3 doubled haploid populations.
