Deciphering the biological processes underlying tomato biomass production and composition.

After tomato fruits harvesting huge amounts of biomass residues, including plant and immature fruit, remaining in the field can be utilized to produce bioenergy. Little is known about the molecular aspects underlying tomato plant biomass production and hydrolysis. To identify genes involved in the regulation of plant biomass accumulation and composition, two Solanum pennellii introgression lines (ILs) with contrasting phenotypes for plant architecture and biomass characteristics, were analyzed. A multiple approach aimed to characterize such near-isogenic lines was carried out for studying gene expression dynamics, microscopy cell traits and qualitative and quantitative cell wall chemical compounds variation. Transcriptomic analysis showed that the enhanced biomass production observed in IL2-6 line is due to a more effective coordination of chloroplast and mitochondria energy fluxes (photosynthesis, cell division, cell wall and hormone metabolism activation). In parallel, microscopy analysis revealed a higher number of cells and chloroplasts in leaf epidermis in the high biomass line whilst chemical measurements on the two lines pointed out striking differences in the cell wall composition and organization. Taken together, our findings shed light on the mechanisms underlying the tomato biomass production and open new routes for improving the tomato lignocellulosic processability. Overall design: Transcriptome profiles of two tomato introgression lines, IL2-6 and IL3-2 (in triplicate), and the control M82 (one replicate) were generated by RNA sequencing. Please note that the 'M82 Rep 2' (through the variant calling) was used as control to confirm that IL2-6 and IL3-2 were, at genotype level, as expected. After checked this, the IL2-6 and IL3-2 samples were used for differentially expression analysis that is the central part of the current study.番茄果实采收后，田间残留的大量生物质残渣（包括植株与未成熟果实）可用于制备生物能源。目前对于调控番茄植株生物质生成与水解的分子机制尚不明晰。为鉴定参与调控植株生物质积累与组成的基因，本研究针对两个具有显著株型与生物质性状差异的潘那利番茄（Solanum pennellii）渐渗系（introgression lines, ILs）开展分析。本研究采用多维度方法对这些近等基因系进行表征，以分析基因表达动态、显微镜下的细胞特征，以及细胞壁化学成分的定性与定量变化。转录组分析显示，IL2-6株系的生物质产量提升源于叶绿体与线粒体能量流（光合作用、细胞分裂、细胞壁合成及激素代谢激活）的更高效协同调控。与此同时，显微镜分析发现高生物质产量株系的叶片表皮细胞与叶绿体数量更多；而对两个株系的化学成分检测结果表明，二者的细胞壁组成与结构存在显著差异。综上，本研究结果阐明了番茄生物质生成的潜在机制，并为提升番茄木质纤维素加工性能开辟了新途径。实验整体设计：通过RNA测序获取两个番茄渐渗系IL2-6、IL3-2（各3次生物学重复）及对照M82（1次生物学重复）的转录组图谱。需注意，本研究通过变异检测以‘M82 重复2’作为对照，验证了IL2-6与IL3-2的基因型符合预期。完成该验证后，以IL2-6与IL3-2的样本开展差异表达分析，这也是本研究的核心内容。