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 <i>QSl.TxNn.2H</i> 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 (<i>QSl.TxNn.2H</i>) 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 <i>QSl.TxNn.2H</i> 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.