Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/28/2007
Publication Date: 10/1/2007
Citation: Bilgic, H., Cho, S., Garvin, D.F., Muehlbauer, G.J. 2007. Mapping barley genes to chromosome arms by transcript profiling of wheat-barley ditelosomic chromosome addition lines. Genome. 50:898-906. Interpretive Summary: Molecular markers are an important resource with diverse uses in plant biological research and crop improvement. However, molecular marker development can be time-consuming and expensive. We used a new tool in genomics, microarrays, to identify and map a large number of new molecular markers for cool season grass crops, including wheat, barley, and rye, in an efficient fashion. We used a barley microarray to detect barley genes expressed in a panel of wheat lines that each contained a different single chromosome arm from barley. In total, more than 1,000 expressed barley genes were detected. By considering the presence of messenger RNA for a given barley gene in one of these lines as an indicator of that gene's presence, these genes were mapped to individual barley chromosome arm locations. The physical mapping of more than 1,000 molecular markers to their individual barley chromosome arm positions is a major advance in developing saturated molecular maps for barley and related species such as wheat. With these detailed molecular maps, it will be possible to more readily identify molecular markers linked to genes of agricultural interest and to isolate these genes for use in crop improvement.
Technical Abstract: Wheat-barley disomic and ditelosomic chromosome addition lines have been used as genetic tools for a range of applications since their development in the 1980's. In the present study, we utilized the Barley1 Affymetrix GeneChip for comparative transcript analysis of Betzes barley, Chinese Spring wheat, and Chinese SpringBetzes ditelosomic chromosome addition lines to physically map barley genes to their respective chromosome arm locations. We mapped 1,257 barley genes to chromosome arms (1HS, 2HS, 2HL, 3HS, 3HL, 4HS, 4HL, 5HS, 5HL, 7HS, and 7HL) based on their transcript levels in the ditelosomic addition lines. The number of genes assigned to individual chromosome arms ranged from 24 to 197. We validated the physical locations of the genes through comparison to our previous chromosome-based physical mapping, comparative in silico mapping with rice and wheat, and single feature polymorphism (SFP) analysis. We found our chromosome arm physical mapping of barley genes to be consistent with our previous physical mapping to chromosomes. In silico comparative mapping of barley genes assigned to chromosome arms revealed that the average genomic synteny to wheat and rice chromosome arms was 63.0 percent and 65.8 percent, respectively. We identified 924 SFPs between the appropriate ditelosomic line and Chinese Spring in 1,257 mapped barley genes. We also identified a single small rearrangement event between rice chromosome 9 and barley chromosome 4HS that accounts for the loss of synteny for several genes.