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Title: Array-Based Genotyping and Expression Analysis of Barley cv. Maythorpe and Gold Promise

Author
item WALIA, HARKAMAL - UC RIVERSIDE, CA
item Wilson, Clyde
item CONDAMINE, PASCAL - UC RIVERSIDE, CA
item ISMAIL, ABDELBAGI - INT'L RICE RESEARCH INST
item XU, JIN - UC RIVERSIDE, CA
item CUI, XINPING - UC RIVERSIDE, CA
item CLOSE, TIMOTHY - UC RIVERSIDE, CA

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/30/2007
Publication Date: 3/30/2007
Citation: Walia, H., Wilson, C., Condamine, P., Ismail, A.M., Xu, J., Cui, X., Close, T.J. 2007. Array-Based Genotyping and Expression Analysis of Barley cv. Maythorpe and Gold Promise. Biomed Central (BMC) Genomics. Vol 8:87-100

Interpretive Summary: Barley (Hordeum vulgare L.) is considered moderately salt-tolerant compared to other cereals. Maythorpe is an older cultivar which is less salt tolerant than its closer relatives. Golden Promise is a salt-tolerant spring barley cultivar closely related to Maythorpe. Salt tolerance in Golden Promise is currently believed to be due to a single mutation resulting from irradiation of Maythorpe. Golden Promise accumulates lower shoot Na+ compared to Maythorpe when growing under saline conditions. We were interested in elucidating the genetic basis and mechanisms involved in this difference. We explored genetic difference between the two genotypes using the Barley1 GeneChip by looking at genetics features called 1) single feature polymorphisms (SFPs) and 2) an oligonucleotide pool assay for single nucleotide polymorphisms (SNPs). Our analyses revealed several differences. We also used the Barley GeneChip to examine transcript level in different tissues and stages during development. Again, we found several genes that were differentially regulated. We also found a more global difference in that the jasmonic acid pathway is differentially regulated between the two genotypes. Our results confirm that Golden Promise and Maythorpe are genetically very closely related, but, more importantly, establish that they are not isogenic, as previously reported. Futhermore, our transcriptome analysis indicates that the response of the two genotypes to salinity stress is quite different. Additionally, the response to salinity stress in the roots and shoot tissue is strikingly different. This will be the focus of future investigations.

Technical Abstract: Golden Promise is a salt-tolerant spring barley closely related to Maythorpe. Salt tolerance in Golden Promise has been attributed to a single mutation at the Ari-e locus (on 5H) resulting from irradiation of Maythorpe. Golden Promise accumulates lower shoot Na+ compared to Maythorpe when growing under saline conditions. We were interested in elucidating the genetic basis and mechanisms involved in this difference. We explored the level of polymorphism between the two genotypes using the Barley1 GeneChip for single feature polymorphisms (SFPs) and an oligonucleotide pool assay for single nucleotide polymorphisms (SNPs). Polymorphism analyses revealed three haplotype blocks spanning 6.4 cM on chromosome 1H, 23.7 cM on chromosome 4H and 3.0 cM on 5H. We also used the Barley GeneChip to examine transcript abundance in different tissues and stages during development. Several genes within the polymorphic haplotype blocks were differentially regulated, but we also found a more global difference in that the jasmonic acid pathway is differentially regulated between the two genotypes. The results confirm that Golden Promise and Maythorpe are genetically very closely related but establish that they are not isogenic, as previously reported, due to three haplotype blocks. Transcriptome analysis indicates that the response of the two genotypes to salinity stress is quite different. Additionally, the response to salinity stress in the roots and shoot tissue is strikingly different.