Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India.
Institute of Molecular Plant Biology, ETH Zurich, Zurich, Switzerland.
Plant Mol Biol. 2024 Nov 13;114(6):124. doi: 10.1007/s11103-024-01517-x.
Existence of potent in vitro regeneration system is a prerequisite for efficient genetic transformation and functional genomics of crop plants. In this study, two contrasting cultivars differencing in their in vitro regeneration efficiency were identified. Tissue culture friendly cultivar Golden Promise (GP) and tissue culture resistant DWRB91(D91) were selected as contrasting cultivars to investigate the molecular basis of regeneration efficiency through multiomics analysis. Transcriptomics analysis revealed 1487 differentially expressed genes (DEGs), in which 795 DEGs were upregulated and 692 DEGs were downregulated in the GP-D91 transcriptome. Genes encoding proteins localized in chloroplast and involved in ROS generation were upregulated in the embryogenic calli of GP. Moreover, proteome analysis by LC-MS/MS revealed 3062 protein groups and 16,989 peptide groups, out of these 1586 protein groups were differentially expressed proteins (DEPs). Eventually, GC-MS based metabolomics analysis revealed the higher activity of plastids and alterations in key metabolic processes such as sugar metabolism, fatty acid biosynthesis, and secondary metabolism. TEM analysis also revealed differential plastid development. Higher accumulation of sugars, amino acids and metabolites corresponding to lignin biosynthesis were observed in GP as compared to D91. A comprehensive examination of gene expression, protein profiling and metabolite patterns unveiled a significant increase in the genes encompassing various functions, such as ion homeostasis, chlorophyll metabolic process, ROS regulation, and the secondary metabolic pathway.
存在有效的体外再生系统是作物遗传转化和功能基因组学高效进行的前提。在这项研究中，我们鉴定了两个在体外再生效率上存在差异的对照品种。选择组织培养友好型品种 Golden Promise（GP）和组织培养抗性品种 DWRB91（D91）作为对照品种，通过多组学分析研究再生效率的分子基础。转录组学分析显示，有 1487 个差异表达基因（DEGs），其中 GP-D91 转录组中有 795 个上调基因和 692 个下调基因。在 GP 的胚性愈伤组织中，编码定位于叶绿体并参与 ROS 生成的蛋白质的基因上调。此外，通过 LC-MS/MS 进行的蛋白质组学分析揭示了 3062 个蛋白质组和 16989 个肽组，其中 1586 个蛋白质组是差异表达蛋白（DEPs）。最终，基于 GC-MS 的代谢组学分析显示，质体的活性更高，并且关键代谢过程（如糖代谢、脂肪酸生物合成和次生代谢）发生改变。TEM 分析还揭示了质体发育的差异。与 D91 相比，GP 中观察到糖、氨基酸和与木质素生物合成相对应的代谢物的积累更高。对基因表达、蛋白质谱和代谢物模式的综合检查揭示了涉及各种功能的基因的显著增加，例如离子稳态、叶绿素代谢过程、ROS 调节和次生代谢途径。
