Genome-wide identification, characterization and evolutionary analysis of SNF1-related kinase (SnRK) and late embryogenesis abundant (LEA) protein-encoding genes in Hordeum vulgare under drought stress

SnRK and LEA proteins play an important role in abiotic stress tolerance in plants. This is the first study to identify LEA protein-encoding genes in barley via genome-wide analysis. SNF1-related kinase ( SnRK) and Late embryogenesis abundant ( LEA) proteins were identified, characterized and analyzed in Hordeum vulgare . The qRT‒PCR results indicated that HvSnRK and HvLEA were upregulated, with fold changes of 6.12 and 7.58, respectively, under drought stress. Genome-wide analysis revealed 81 Hv SnRK and 93 Hv LEA genes in H. vulgare. Domain analysis confirmed the presence of the ten domains and of six domain on the HvSnRK and HvLEA proteins, respectively. Motif and gene structure analyses indicated that genes with closer phylogenetic relationships exhibited more similar genetic structures. Most HvSnRK proteins were located in the cytoplasm and chloroplasts, whereas most HvLEA proteins were located in the located in the nucleus and cytoplasm. A total of 107 microRNAs were predicted to target HvSnRK genes, whereas 51 microRNA was predicted to target HvLEA genes. SnRK and LEA genes were detected on all chromosomes. The Ka / Ks ratio indicated that the SnRK and three LEA genes were influenced primarily by purifying selection, whereas the Ka / Ks ratios of other two LEA paralogous gene pairs were > 1 suggested positive selection, which tends to reduce diversity at linked neutral loci. Synteny analysis revealed collinear orthologous relationships in Solanum lycopersicum , Zea mays and Arabidopsis thaliana . Collinearity analysis revealed that 110 orthologous SnRK genes and 61 orthologous LEA genes were paired with those in Z. mays . In addition, collinearity analysis revealed that 9 orthologous SnRK genes and 20 orthologous LEA genes were paired with those in S. lycopersicum . Additionally, collinearity analysis revealed that 11 orthologous SnRK genes and 6 orthologous LEA genes were paired with those in A. thaliana. Gene Ontology enrichment analysis confirmed the functional role of SnRK and LEA proteins in the stress response. The results of the present study will improve the understanding of the functions of the HvSnRK and HvLEA genes in response to drought stress.