Candidate genes for salinity tolerance in barley revealed by RNA-seq analysis of near-isogenic lines

Salinity stress is one of the major abiotic stresses which affects grain yield and quality in barley. A major QTL QSl.TxNn.2H has been identified from a Chinese Landrace variety TX9425 on chromosome 2H. To assist in the identification of candidate genes, the roots of a pair of near-isogenic lines (NILs) containing the major salinity tolerance QTL (QSl.TxNn.2H) were analysed by RNA-seq after exposing the plants to 300 mM NaCl for 48 h. In total, 1256 and 809 differentially expressed genes were identified in the salt-tolerant and sensitive lines, T46 and N33, respectively. Of these genes, 572 were specifically up-regulated and 326 down-regulated in the salt-tolerant line T46, while 170 genes were specifically up-regulated and 281 down-regulated in the sensitive line N33. There are 146 genes in the QSl.TxNn.2H mapping region. Among them the transcript expression levels of 11 genes were changed in either N33 or T46 under salinity stress. A gene encoding a heat shock protein 90 (HSP90) was up-regulated more in the tolerant line T46 compared to the sensitive line N33 while a gene encoding a protein kinase WAK was up-regulated only in T46. Both may confer barley salinity tolerance by participating in Ca2+ signaling and hormone metabolism, maintaining the integrity of cell wall, regulating ion homeostasis, participating in lipid metabolism and regulating nitrogen and sugar transportation.