Table_2_Identification of Metabolic Pathways Differentially Regulated in Somatic and Zygotic Embryos of Maritime Pine.docx

Embryogenesis is a complex phase of conifer development involving hundreds of genes, and a proper understanding of this process is critical not only to produce embryos with different applied purposes but also for comparative studies with angiosperms. A global view of transcriptome dynamics during pine somatic and zygotic embryogenesis is currently missing. Here, we present a genome-wide transcriptome analysis of somatic and zygotic embryos at three developmental stages to identify conserved biological processes and gene functions during late embryogenesis. Most of the differences became more significant as the developmental process progressed from early to cotyledonary stages, and a higher number of genes were differentially expressed in somatic than in zygotic embryos. Metabolic pathways substantially affected included those involved in amino acid biosynthesis and utilization, and this difference was already observable at early developmental stages. Overall, this effect was found to be independent of the line (genotype) used to produce the somatic embryos. Additionally, transcription factors differentially expressed in somatic versus zygotic embryos were analyzed. Some potential hub regulatory genes were identified that can provide clues as to what transcription factors are controlling the process and to how the observed differences between somatic and zygotic embryogenesis in conifers could be regulated.

胚胎发生是针叶植物（conifer）发育过程中的复杂阶段，涉及数百个基因的参与。对该过程的充分认知，不仅是培育具备各类应用需求胚胎的核心前提，同时也为开展与被子植物（angiosperms）的比较研究奠定了关键基础。目前学界仍缺乏关于松树体细胞胚胎发生与合子胚胎发生过程中转录组（transcriptome）全局动态变化的系统认知。本研究针对三个发育阶段的松树体细胞与合子胚胎开展全基因组转录组分析，以期鉴定晚期胚胎发生过程中保守的生物学过程与基因功能。随着发育进程从早期阶段向子叶期推进，两类胚胎间的表达差异逐渐加剧，且体细胞胚胎中差异表达的基因数量多于合子胚胎。受显著影响的代谢通路主要涉及氨基酸的生物合成与利用，且该差异在发育早期即可被观测到。整体而言，该差异现象与用于制备体细胞胚胎的遗传株系（基因型）无关。此外，本研究还分析了体细胞与合子胚胎间差异表达的转录因子（transcription factors），并鉴定出若干潜在的核心调控基因，可为解析调控胚胎发生过程的转录因子网络，以及针叶植物体细胞与合子胚胎发生间差异的调控机制提供重要线索。