A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics

Abstract

An integrated barley transcript map (consensus map) comprising 1,032 expressed sequence tag (EST)-based markers (total 1,055 loci: 607 RFLP, 190 SSR, and 258 SNP), and 200 anchor markers from previously published data, has been generated by mapping in three doubled haploid (DH) populations. Between 107 and 179 EST-based markers were allocated to the seven individual barley linkage groups. The map covers 1118.3 cM with individual linkage groups ranging from 130 cM (chromosome 4H) to 199 cM (chromosome 3H), yielding an average marker interval distance of 0.9 cM. 475 EST-based markers showed a syntenic organisation to known colinear linkage groups of the rice genome, providing an extended insight into the status of barley/rice genome colinearity as well as ancient genome duplications predating the divergence of rice and barley. The presented barley transcript map is a valuable resource for targeted marker saturation and identification of candidate genes at agronomically important loci. It provides new anchor points for detailed studies in comparative grass genomics and will support future attempts towards the integration of genetic and physical mapping information.

A high-density transcript linkage map of barley derived from a single population

“…We also expected that there could be a somewhat higher rate of exon SNPs in EST sequences from wild-type and cultivated barley than in those from only cultivated barley because of mutations associated with domestication. However, our SNP rate was not as high as expected compared with the rates of 17-45% reported for three mapping populations by Stein et al (2007). This difference may be due to the higher detection rate of intron SNPs by Stein et al (2007) and the higher expected similarity in coding sequences between these accessions of wild-type and cultivated barley.…”

“…Mapped ESTs also provide access to other genomes, particularly that of rice (Oryza sativa L.), based on sequence similarity. Stein et al (2007) found significant micro-collinearity between the rice and barley genomes using a consensus barley map with 1032 EST-based loci assayed using a combination of marker assays (including 607 RFLPs). Comparative genomic analysis of barley ESTs and rice genome sequences will enable detection of undiscovered barley genome sequences.…”

Inheritance and identification of molecular markers associated with spot blotch (Cochliobolus sativus L.) resistance through microsatellites analysis in barley

“…In barley, molecular mapping for different traits has been an area of active research, which led to the identification of many markers for several important traits (Steffenson et al, 1996;Tuberosa and Salvi, 2004;Bilgic et al, 2005;Stein et al, 2007). In this study we found that with a large population and precise phenotypic characterization it is possible to detect molecular markers for a trait such as spot blotch resistance that is under polygenic control, even though some loci display large effects.…”

The Genetics and Transcriptional Profiles of the Cellulose Synthase-Like HvCslF Gene Family in Barley

“…The HvCslF3 gene could not be mapped directly, but it must also be at this position, given that it is on the same barley BAC as HvCslF4. Barley and rice genes tentatively identified as orthologs were generally located in syntenous regions of the rice and barley genomes (Stein et al, 2007), although chromosomal translocations coupled with local breakdown of colinearity made it difficult to make unequivocal conclusions in some cases (data not shown).…”