College of Agronomy, Hunan Agricultural University, Changsha 420128, China.
Int J Mol Sci. 2023 Jul 16;24(14):11527. doi: 10.3390/ijms241411527.
In this study, a transcriptomic analysis of the dehydration rate of mature rice seeds was conducted to explore candidate genes related to the dehydration rate and provide a theoretical basis for breeding and utilization. We selected two rice cultivars for testing (Baghlani Nangarhar, an extremely rapid dehydration genotype, and Saturn, a slow dehydration genotype) based on the results determined by previous studies conducted on the screening of 165 germplasm materials for dehydration rate phenotypes. A rapid dehydration experiment performed on these two types of seeds was conducted. Four comparative groups were set up under control and dehydration conditions. The differentially expressed genes (DEGs) were quantified via transcriptome sequencing and real-time quantitative PCR (RT-qPCR). GO (Gene ontology) and KEGG(Kyoto Encyclopedia of Genes and Genomes) analyses were also conducted. In Baghlani Nangarhar, 53 DEGs were screened, of which 33 were up-regulated and 20 were down-regulated. In Saturn, 25 DEGs were screened, of which 19 were up-regulated and 6 were down-regulated. The results of the GO analysis show that the sites of action of the differentially expressed genes enriched in the rapid dehydration modes are concentrated in the cytoplasm, internal components of the membrane, and nucleosomes. They play regulatory roles in the processes of catalysis, binding, translocation, transcription, protein folding, degradation, and replication. They are also involved in adaptive responses to adverse external environments, such as reactive oxygen species and high temperature. The KEGG analysis showed that protein processing in the endoplasmic reticulum, amino acid biosynthesis, and oxidative phosphorylation were the main metabolic pathways that were enriched. The key differentially expressed genes and the most important metabolic pathways identified in the rapidly and slowly dehydrated genotypes were protein processing in the endoplasmic reticulum and oxidative phosphorylation metabolism. They were presumed to have important regulatory roles in the mechanisms of stress/defense, energy metabolism, protein synthesis/folding, and signal transduction during the dehydration and drying of mature seeds. The results of this study can potentially provide valuable information for further research on the genes and metabolic pathways related to the dehydration rate of mature rice seeds, and provide theoretical guidance for the selection and breeding of new rice germplasm that can be rapidly dehydrated at the mature stage.
本研究对成熟水稻种子脱水速率进行了转录组分析，旨在探索与脱水速率相关的候选基因，为水稻的选育和利用提供理论依据。我们根据先前对 165 份种质材料脱水率表型筛选的研究结果，选择了两个水稻品种进行测试（快速脱水基因型 Baghlani Nangarhar 和慢速脱水基因型 Saturn）。对这两种类型的种子进行了快速脱水实验。在对照和脱水条件下设置了四个比较组。通过转录组测序和实时定量 PCR（RT-qPCR）定量差异表达基因（DEGs）。还进行了 GO（基因本体论）和 KEGG（京都基因与基因组百科全书）分析。在 Baghlani Nangarhar 中筛选出 53 个差异表达基因，其中 33 个上调，20 个下调。在 Saturn 中筛选出 25 个差异表达基因，其中 19 个上调，6 个下调。GO 分析结果表明，快速脱水模式下富集的差异表达基因的作用部位集中在细胞质、膜内成分和核小体。它们在催化、结合、易位、转录、蛋白质折叠、降解和复制等过程中发挥调节作用。它们还参与了对活性氧和高温等不利外部环境的适应性反应。KEGG 分析表明，内质网蛋白加工、氨基酸生物合成和氧化磷酸化是主要的代谢途径。快速和慢速脱水基因型中富集的关键差异表达基因和最重要的代谢途径是内质网蛋白加工和氧化磷酸化代谢。它们可能在成熟种子脱水和干燥过程中的应激/防御、能量代谢、蛋白质合成/折叠和信号转导机制中具有重要的调节作用。本研究结果可为进一步研究与成熟水稻种子脱水速率相关的基因和代谢途径提供有价值的信息，为选择和培育新的快速脱水成熟水稻种质提供理论指导。
