Genome-wide identification of sucrose nonfermenting-1-related protein kinase (SnRK) genes in barley and RNA-seq analyses of their expression in response to ABA treatment

Abstract Background: Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play important roles in regulating metabolism and stress responses in plants, providing a conduit for crosstalk between metabolic and stress signalling, in some cases involving the stress hormone, abscisic acid (ABA). The burgeoning and divergence of the plant gene family has led to the evolution of three subfamilies, SnRK1 , SnRK2 and SnRK3 , of which SnRK2 and SnRK3 are unique to plants. Therefore, the study of SnRKs in crops may lead to the development of strategies for breeding crop varieties that are more resilient under stress conditions. In the present study we describe the SnRK gene family of barley ( Hordeum vulgare ), the widespread cultivation of which can be attributed to its good adaptation to different environments Results: The barley HvSnRK gene family was elucidated in its entirety from publicly-available genome data and found to comprise 50 genes. Phylogenetic analyses assigned six of the genes to the HvSnRK1 subfamily, 10 to HvSnRK2 and 34 to HvSnRK3 . The search was validated by applying it to Arabidopsis ( Arabidopsis thaliana ) and rice ( Oryza sativa ) genome data, identifying 50 SnRK genes in rice (four OsSnRK1 , 11 OsSnRK2 and 35 OsSnRK3 ) and 39 in Arabidopsis (three AtSnRK1 , 10 AtSnRK2 and 26 AtSnRK3 ). Specific motifs were identified in the encoded barley proteins, and multiple putative regulatory elements were found in the gene promoters, with light-regulated elements (LRE), ABA response elements (ABRE) and methyl jasmonate response elements (MeJa) the most common. RNA-seq analysis of the roots of seedlings grown with and without ABA treatment showed that many of the genes responded to ABA, some positively, some negatively and some with complex time-dependent responses. Conclusions: The barley HvSnRK gene family is large, comprising 50 members, subdivided into HvSnRK1 (6 members), HvSnRK2 (10 members) and SnRK3 (34 members), showing differential positive and negative responses to ABA.