Genome-wide identification and expression analysis of the U-box E3 ubiquitin ligase gene family related to salt tolerance in sorghum (Sorghum bicolor L.)

Abstract

Plant U-box (PUB) E3 ubiquitin ligases play essential roles in many biological processes and stress responses, but little is known about their functions in sorghum (<i>Sorghum bicolor</i> L.). In the present study, 59 <i>SbPUB</i> genes were identified in the sorghum genome. Based on the phylogenetic analysis, the 59 <i>SbPUB</i> genes were clustered into five groups, which were also supported by the conserved motifs and structures of these genes. <i>SbPUB</i> genes were found to be unevenly distributed on the 10 chromosomes of sorghum. Most <i>PUB</i> genes (16) were found on chromosome 4, but there were no <i>PUB</i> genes on chromosome 5. Analysis of <i>cis</i>-acting elements showed that <i>SbPUB</i> genes were involved in many important biological processes, particularly in response to salt stress. From proteomic and transcriptomic data, we found that several <i>SbPUB</i> genes had diverse expressions under different salt treatments. To verify the expression of <i>SbPUBs</i>, qRT-PCR analyses also were conducted under salt stress, and the result was consistent with the expression analysis. Furthermore, 12 <i>SbPUB</i> genes were found to contain MYB-related elements, which are important regulators of flavonoid biosynthesis. These results, which were consistent with our previous multi-omics analysis of sorghum salt stress, laid a solid foundation for further mechanistic study of salt tolerance in sorghum. Our study showed that <i>PUB</i> genes play a crucial role in regulating salt stress, and might serve as promising targets for the breeding of salt-tolerant sorghum in the future.