Guangxi TCM Resources General Survey and Data Collection Key Laboratory, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.
Guangxi Medicinal Resources Conservation and Genetic Improvement Key Laboratory, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.
BMC Genomics. 2023 Mar 2;24(1):99. doi: 10.1186/s12864-023-09202-x.
In Amomum tsaoko breeding, the low germination rate is the major limitation for their large-scale reproduction. We found that warm stratification was an effective treatment to break the seed dormancy of A. tsaoko prior to sowing and could be an important component of improving breeding programs. The mechanism of seed dormancy release during warm stratification remains unclear. Therefore, we studied the differences between transcripts and proteomes at 0, 30, 60, and 90 days of warm stratification, to identify some regulatory genes and functional proteins that may cause seed dormancy release in A. tsaoko and reveal their regulatory mechanism.
RNA-seq was performed for the seed dormancy release process, and the number of differentially expressed genes (DEGs) was 3196 in three dormancy release periods. Using TMT-labelling quantitative proteome analysis, a total of 1414 proteins were defined as differentially expressed proteins (DEPs). Functional enrichment analyses revealed that the DEGs and DEPs were mainly involved in signal transduction pathways (MAPK signaling, hormone) and metabolism processes (cell wall, storage and energy reserves), suggesting that these differentially expressed genes and proteins are somehow involved in response to seed dormancy release process, including MAPK, PYR/PYL, PP2C, GID1, GH3, ARF, AUX/IAA, TPS, SPS, and SS. In addition, transcription factors ARF, bHLH, bZIP, MYB, SBP, and WRKY showed differential expression during the warm stratification stage, which may relate to dormancy release. Noteworthy, XTH, EXP, HSP and ASPG proteins may be involved in a complex network to regulate cell division and differentiation, chilling response and the seed germination status in A. tsaoko seed during warm stratification.
Our transcriptomic and proteomic analysis highlighted specific genes and proteins that warrant further study in fully grasping the precise molecular mechanisms that control the seed dormancy and germination of A. tsaoko. A hypothetical model of the genetic regulatory network provides a theoretical basis for overcoming the physiological dormancy in A. tsaoko in the future.
在砂仁的繁殖中，发芽率低是其大规模繁殖的主要限制因素。我们发现，温层积是一种有效的处理方法，可以打破砂仁种子的休眠，这可能是提高繁殖计划的一个重要组成部分。在温层积过程中种子休眠解除的机制尚不清楚。因此，我们研究了温层积 0、30、60 和 90 天的转录组和蛋白质组之间的差异，以鉴定一些可能导致砂仁种子休眠解除的调节基因和功能蛋白，并揭示其调节机制。
进行了种子休眠解除过程的 RNA-seq，在三个休眠解除期有 3196 个差异表达基因（DEGs）。使用 TMT-标记定量蛋白质组分析，共定义了 1414 个差异表达蛋白（DEPs）。功能富集分析表明，DEGs 和 DEPs 主要参与信号转导途径（MAPK 信号、激素）和代谢过程（细胞壁、储存和能量储备），表明这些差异表达基因和蛋白在某种程度上参与了种子休眠解除过程，包括 MAPK、PYR/PYL、PP2C、GID1、GH3、ARF、AUX/IAA、TPS、SPS 和 SS。此外，在温层积阶段，转录因子 ARF、bHLH、bZIP、MYB、SBP 和 WRKY 表现出差异表达，这可能与休眠解除有关。值得注意的是，XTH、EXP、HSP 和 ASPG 蛋白可能参与了一个复杂的网络，以调节细胞分裂和分化、冷胁迫响应和 A. tsaoko 种子在温层积过程中的发芽状态。
我们的转录组和蛋白质组分析突出了特定的基因和蛋白质，这值得进一步研究，以充分掌握控制 A. tsaoko 种子休眠和发芽的确切分子机制。遗传调控网络的假设模型为未来克服 A. tsaoko 的生理休眠提供了理论基础。
