TY - JOUR
T1 - Mapping barley genes to chromosome arms by transcript profiling of wheat-barley ditelosomic chromosome addition lines
AU - Bilgic, Hatice
AU - Cho, Seungho
AU - Garvin, David F.
AU - Muehlbauer, Gary J.
PY - 2007/10
Y1 - 2007/10
N2 - Wheat-barley disomic and ditelosomic chromosome addition lines have been used as genetic tools for a range of applications since their development in the 1980s. In the present study, we used the Affymetrix Barley1 GeneChip for comparative transcript analysis of the barley cultivar Betzes, the wheat cultivar Chinese Spring, and Chinese Spring - Betzes ditelosomic chromosome addition lines to physically map barley genes to their respective chromosome arm locations. We mapped 1257 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 with our previous chromosome-based physical mapping, comparative in silico mapping with rice and wheat, and single feature polymorphism (SFP) analysis. We found our physical mapping of barley genes to chromosome arms to be consistent with our previous physical mapping to whole 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 63.2% and 65.5%, respectively. In the 1257 mapped genes, we identified SFPs in 924 genes between the appropriate ditelosomic line and Chinese Spring that supported physical map placements. We also identified a single small rearrangement event between rice chromosome 9 and barley chromosome 4H that accounts for the loss of synteny for several genes.
AB - Wheat-barley disomic and ditelosomic chromosome addition lines have been used as genetic tools for a range of applications since their development in the 1980s. In the present study, we used the Affymetrix Barley1 GeneChip for comparative transcript analysis of the barley cultivar Betzes, the wheat cultivar Chinese Spring, and Chinese Spring - Betzes ditelosomic chromosome addition lines to physically map barley genes to their respective chromosome arm locations. We mapped 1257 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 with our previous chromosome-based physical mapping, comparative in silico mapping with rice and wheat, and single feature polymorphism (SFP) analysis. We found our physical mapping of barley genes to chromosome arms to be consistent with our previous physical mapping to whole 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 63.2% and 65.5%, respectively. In the 1257 mapped genes, we identified SFPs in 924 genes between the appropriate ditelosomic line and Chinese Spring that supported physical map placements. We also identified a single small rearrangement event between rice chromosome 9 and barley chromosome 4H that accounts for the loss of synteny for several genes.
KW - Barley1 GeneChip
KW - Chromosomal rearrangement
KW - Physical mapping
KW - Single feature polymorphism
KW - Synteny
KW - Transcriptome
KW - Wheat-barley ditelosomic addition line
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U2 - 10.1139/G07-059
DO - 10.1139/G07-059
M3 - Article
C2 - 18059553
AN - SCOPUS:36349012436
SN - 0831-2796
VL - 50
SP - 898
EP - 906
JO - Genome
JF - Genome
IS - 10
ER -