Comparative transcriptome analysis of salt-tolerant wheat germplasm lines using wheat genome arrays

Salt-tolerant wheat lines W4909 and W4910 were derived from a cross between AJDAj5 (a disomic addition line carrying a pair of Eb chromosomes from Thinopyrum junceum) and PhI (a line having the PhI allele from Aegilops speltoides, which promotes homoeologous recombination). Both lines have greater salt tolerance than their parental lines, which are more salt-tolerant than the common wheat background, Chinese Spring (CS). Genomic constitution of W4909 and W4910 wheat has been estimated at 1.9% and 2.4% non-CS, respectively. Affymetrix GeneChip® Wheat Arrays were used to identify differentially expressed genes in roots and leaves of the above-mentioned five lines under salt stress at electrical conductivity (EC) of 30 dS/m. Based on expression polymorphisms in AJDAj5 and PhI, differentially expressed genes in W4909 and W4910 were attributed to one or the other parental lines when possible. The PhI parent contributed nearly twice as many expression polymorphisms as AJDAj5 to both W4909 and W4910. Nine transcripts in W4910 showed transgression gene expression significantly higher or lower than either parent. The majority of expression polymorphisms exhibited very low expression levels compared to the control and mapped to three distinct chromosomal locations, 2S, 4L and 2L. Salt treatment responsive gene expression profiles common to all five tested lines provide a short list of candidate salt-tolerance genes in wheat. A gene for tonoplast aquaporin that was transferred from PhI and a gene for putative potassium channel protein that was attributable to AJDAj5 are identified as candidate genes for the tissue salt tolerance in W4909 and W4910.