Genome-wide expression analysis of <i>LBD</i> genes in tomato (<i>Solanum lycopersicum</i> L.) under different light conditions

Lateral organ boundaries (LOB) domain (<i>LBD</i>) genes, a gene family that encodes the transcription factors (TFs) of plants, plays crucial functions in the development and growth of plants. Currently, genome-wide studies of the <i>LBD</i> family are still limited to tomato (<i>Solanum lycopersicum</i> L.), which is considered an important economic crop. In this study, we performed a genome-wide analysis of <i>LBD</i> in tomato. In total, 56 <i>LBDs</i> were found in the tomato genome. Protein alignment and phylogenetic classification showed that <i>LBDs</i> were conserved with other species. Since light emitting diodes (LEDs) light have promising applications for tomato growth. To better understand the potential function of <i>LBDs</i> in response to LED light in tomato, we conducted a genome-wide expression analysis of <i>LBD</i> genes under different light conditions. As expected, different LED lights affected the tomato growth (e.g. hypocotyl length). RNA-seq data showed that eight <i>LBDs</i> in tomato seedlings were differentially expressed under different light treatments, including white, blue, red, and far-red light, compared to the dark-grown condition. It indicates that these <i>LBDs</i> might regulate plant development in different LED light conditions. Interestingly, two <i>LBD</i> genes (<i>SlLBD1</i> and <i>SlLBD2</i>) were found to be differentially expressed in four distinct lights, which might be involved in regulating the plant architecture via a complicated TF network, which can be taken into consideration in further investigation.侧生器官边界（Lateral organ boundaries, LOB）结构域基因家族（LBD家族）是一类编码植物转录因子（transcription factors, TFs）的基因家族，在植物生长发育过程中发挥关键调控功能。目前，针对LBD家族的全基因组水平研究仍仅局限于作为重要经济作物的番茄（Solanum lycopersicum L.）。本研究针对番茄开展全基因组水平的LBD家族分析，共在番茄基因组中鉴定得到56个LBD家族基因。蛋白质序列比对与系统发育分类分析结果显示，LBD家族基因在不同物种间具有进化保守性。鉴于发光二极管（light emitting diodes, LEDs）光源在番茄栽培中具有良好的应用前景，为深入解析番茄LBD家族基因响应LED光照的潜在功能，我们针对不同光照条件下的番茄LBD基因开展了全基因组表达谱分析。实验结果显示，不同LED光照处理会显著影响番茄生长（如下胚轴长度）。RNA测序（RNA-seq）数据表明，与暗培养条件相比，番茄幼苗中的8个LBD家族基因在白光、蓝光、红光及远红光等不同光照处理下均呈现差异表达特征，提示这些LBD家族基因可能参与调控不同LED光照条件下的植物生长发育。值得注意的是，2个LBD基因（SlLBD1与SlLBD2）在四种不同光照处理下均呈现差异表达，其可能通过复杂的转录因子网络参与调控植物株型构建，该结果可为后续相关研究提供参考方向。