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ARS Home » Midwest Area » St. Paul, Minnesota » Plant Science Research » Research » Publications at this Location » Publication #170351
Title: TRANSCRIPTOME ANALYSIS AND PHYSICAL MAPPING OF BARLEY GENES IN WHEAT-BARLEY CHROMOSOME ADDITION LINES

Author
item CHO, SEUNGHO - UNIVERSITY OF MINNESOTA
item Garvin, David
item MUEHLBAUER, GARY - UNIVERSITY OF MINNESOTA

Submitted to: Plant and Animal Genome VX Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 1/14/2005
Publication Date: 1/15/2005
Citation: Cho, S., Garvin, D.F., Muehlbauer, G.J. 2005. Transcriptome analysis and physical mapping of barley genes in wheat-barley chromosome addition lines [abstract]. Plant and Animal Genome XIII Abstracts. Paper No. 308.

Interpretive Summary:

Technical Abstract: We used the Barley1 Affymetrix GeneChip in combination with wheat-barley chromosome addition lines to examine barley transcript accumulation in wheat and physically map barley genes to chromosomes. Using this GeneChip, which represents 22,792 barley genes, we examined transcript abundance in Betzes barley, Chinese Spring wheat, and six different Chinese Spring-Betzes disomic chromosome addition lines harboring chromosomes 2H, 3H, 4H, 5H, 6H, or 7H. In total, 6,471 transcripts were detected in Betzes but not Chinese Spring, and 573, 504, 437, 567, 331, 593 of the Betzes-specific transcripts were specifically detected in the disomic chromosome 2H, 3H, 4H, 5H, 6H, and 7H addition lines, respectively. We also identified 809 barley transcripts detected in more than one chromosome addition line. Approximately 50% of the barley gene transcripts showed at least a 75% reduction in transcript levels in the wheat-barley addition lines compared to those in Betzes. This indicates that alterations of barley gene expression in the wheat genetic background are extensive. In silico comparative mapping of the barley genes detected in the addition lines was conducted against mapped wheat ESTs and the rice genome sequence. Approximately 70% of the barley genes were homologous to wheat ESTs and/or rice sequences located on syntenous wheat and rice chromosomes. In addition, no specific chromosomal distribution patterns were evident for wheat EST homologs of the barley genes detected in more than one addition line. In total, 3,814 barley genes were physically mapped to 6 different barley chromosomes based on barley chromosome-specific transcript patterns. Our study demonstrates the efficiency of using the Barley1 GeneChip in combination with the wheat-barley addition lines to examine barley transcript accumulation in wheat and to physically map barley genes to chromosome arms.