The TIR1/AFB Family in <i>Solanum melongena</i>: Genome-Wide Identification and Expression Profiling under Stresses and Picloram Treatment

TIR1/AFB proteins are a class of auxin receptors with key roles in plant development and biotic and abiotic stress responses; several have been identified as targets of the auxin-mimicking herbicide picloram. In this study, we identified five putative <i>TIR1/AFB</i> gene family members in the important vegetable crop <i>Solanum melongena</i> (eggplant) and characterized them using bioinformatics tools and gene expression analyses. Phylogenetic analysis of the TIR1/AFBs classified them into three subgroups based on their <i>Arabidopsis</i> and <i>Solanum lycopersicum</i> homologs. AFB6 homologs were present only in <i>S. melongena</i> and <i>S. lycopersicum</i>, whereas AFB2/3 homologs were found only in <i>Arabidopsis</i>. One pair of <i>S. melongena TIR1</i> homologs were located in syntenic regions in the genome and appeared to have arisen by segmental duplication. Promoter analysis revealed 898 <i>cis</i>-elements in the TIR1/AFB promoters, 125 of which were related to hormones, stress, light, or growth responses, but only <i>SmAFB5</i> had a <i>cis</i>-acting regulatory element involved in auxin responsiveness (AuxRR-core). RNA sequencing and expression profiling showed that the TIR1/AFB genes were differentially expressed at different growth stages and in response to light, temperature, and drought. Only <i>SmTIR1A</i> expression was significantly induced by picloram treatment and different growth stages. <i>TIR1/AFB</i> expression is regulated by microRNAs (miRNAs) in other plant species, and we identified 6 or 29 miRNAs that potentially targeted the five <i>TIR1/AFB</i> genes on the basis of comparisons with <i>S. lycopersicum</i> and <i>S. tuberosum</i> miRNAs, respectively. Three-dimensional protein structure predictions revealed that all the TIR1/AFB proteins were very similar in structure, differing only in the numbers of alpha helices and in one angle linking an α helix and a β sheet. For measuring the function of TIR1/AFB genes in response to drought, SmAFB5 was selected, and knockdown by virus-induced gene silence (VIGS) <i>35S::SmAFB5</i> lines showed resistance to drought compared to controls. These analyses provide insight into the potential functions of TIR1/AFBs during growth and in response to stress; they highlight differences among the SmTIR1/AFBs that may be useful for eggplant breeding.