Array-based genotyping and expression analysis of barley cv. Maythorpe and Golden Promise

The level of polymorphism between the two genotypes was explored 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. The Barley1 GeneChip was used to examine transcript abundance in different tissues and stages during development. Several genes within the polymorphic haplotype blocks were differentially regulated. Additionally, a more global difference in the jasmonic acid pathway regulation was detected 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 polymorphic 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.Barley (Hordeum vulgare L.) is rated as a salt-tolerant member of the tribe Triticeae on the basis of grain yield in saline environments [1]. Salt tolerance in Triticeae is generally associated with Na+ ion exclusion during growth under saline conditions [2,3]. Considerable genetic variation exists in salt tolerance with respect to Na+ ion exclusion in barley as well as in Triticeae in general. Barley cultivar, Golden Promise was reported to be a gamma-ray induced mutant of cultivar Maythorpe [4]. Golden Promise was selected for its desirable agronomic traits such as short stature and earliness, and became a popular malting variety. It was later discovered that Golden Promise also has a more effective Na+ exclusion than Maythorpe in a salt tolerance screening experiment conducted at the Scottish Crop Research Institute [5]. Golden Promise accumulates lower Na+ in shoot tissue compared to Maythorpe under high salt cond