Submitted to: Genetics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 11/7/2005
Publication Date: 2/1/2006
Citation: Cho, S., Garvin, D.F., Muehlbauer, G.J. 2006. Transcriptome analysis and physical mapping of barley genes in wheat-barley chromosome addition lines. Genetics. 172:1277-1285. Interpretive Summary: Molecular maps have played a major role in revolutionizing diverse aspects of plant biology, including crop improvement. However, available techniques for molecular marker development are time-consuming and expensive. We sought to determine whether a new tool in genomics, gene chips, could be used to facilitate the development of large numbers of new molecular markers for cool season grass crops, including wheat, barley, and rye, in a more efficient fashion. We used a barley gene chip to detect expressed barley genes in seedlings of a wheat variety that contained a single chromosome (6H) from barley. Nearly 500 barley genes were identified in this fashion, and by inference these genes were hypothesized to reside on barley chromosome 6H. Further experiments validated this result and also permitted us to determine on which of the arms of chromosome 6H each of the genes is located. The physical mapping of nearly 500 molecular markers to a single barley chromosome represents a major technological advance in the development of saturated molecular maps for barley and related species such as wheat. With these detailed molecular maps it will be possible to more readily identify markers linked to genes of agricultural interest and to isolate such genes from these species for use in crop improvement.
Technical Abstract: The wheat-barley chromosome addition lines are ideal for examining alien gene expression in a wheat genetic background and to physically map barley genes. We examined RNA profiles of Chinese Spring wheat-Betzes barley chromosome 6(6H) addition lines using the Barley1 Affymetrix GeneChip to determine the extent and modification of barley gene transcript accumulation in a wheat background and to physically map barley genes to chromosome 6H. We detected 7,794, 1,391, 1,795, 1,623, and 1,549 gene transcripts in seedling tissues of Betzes, Chinese Spring, the Chinese Spring-Betzes chromosome 6H disomic addition line, and ditelosomic addition lines with either chromosome arm 6HL or 6HS, respectively. Four hundred and seventy-two barley gene transcripts were detected in the wheat genetic background in association with the presence of barley chromosome 6H, demonstrating large-scale barley gene transcription in the wheat-barley addition lines. Interestingly, 328 of the 472 barley chromosome 6H genes exhibited less transcript accumulation in the addition lines than expected values, indicating a down regulation of barley genes in the addition lines. In addition, our results show that activation and inactivation of transcripts are common phenomenon in the wheat-barley chromosome addition lines. Based on transcript accumulation patterns in the addition lines, 268 and 204 genes were physically mapped to chromosome arms 6HL and 6HS, respectively. The physical map locations of these genes were consistent with genomic PCR of selected barley genes and in silico comparative mapping against the wheat genetic map and rice genome. Our study shows that the use of GeneChip technology in combination with interspecific chromosome addition lines is an efficient method to explore alien gene expression and to physically map genes to the introgressed chromosome.