Samarina Lidiia, Wang Songbo, Malyukova Lyudmila, Bobrovskikh Alexandr, Doroshkov Alexey, Koninskaya Natalia, Shkhalakhova Ruset, Matskiv Alexandra, Fedorina Jaroslava, Fizikova Anastasia, Manakhova Karina, Loshkaryova Svetlana, Tutberidze Tsiala, Ryndin Alexey, Khlestkina Elena
Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia.
Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia.
Front Plant Sci. 2023 May 10;14:1145793. doi: 10.3389/fpls.2023.1145793. eCollection 2023.
Low temperatures and drought are two main environmental constraints reducing the yield and geographical distribution of horticultural crops worldwide. Understanding the genetic crosstalk between stress responses has potential importance for crop improvement.
In this study, Illumina RNA-seq and Pac-Bio genome resequencing were used to annotate genes and analyze transcriptome dynamics in tea plants under long-term cold, freezing, and drought.
The highest number of differentially expressed genes (DEGs) was identified under long-term cold (7,896) and freezing (7,915), with 3,532 and 3,780 upregulated genes, respectively. The lowest number of DEGs was observed under 3-day drought (47) and 9-day drought (220), with five and 112 genes upregulated, respectively. The recovery after the cold had 6.5 times greater DEG numbers as compared to the drought recovery. Only 17.9% of cold-induced genes were upregulated by drought. In total, 1,492 transcription factor genes related to 57 families were identified. However, only 20 transcription factor genes were commonly upregulated by cold, freezing, and drought. Among the 232 common upregulated DEGs, most were related to signal transduction, cell wall remodeling, and lipid metabolism. Co-expression analysis and network reconstruction showed 19 genes with the highest co-expression connectivity: seven genes are related to cell wall remodeling (, , , , , , and ), four genes are related to calcium-signaling (, , , and ), three genes are related to photo-perception (, , and ), two genes are related to hormone signaling ( and ), two genes are involved in ROS signaling ( and ), and one gene is related to the phenylpropanoid pathway ().
Based on our results, several important overlapping mechanisms of long-term stress responses include cell wall remodeling through lignin biosynthesis, o-acetylation of polysaccharides, pectin biosynthesis and branching, and xyloglucan and arabinogalactan biosynthesis. This study provides new insight into long-term stress responses in woody crops, and a set of new target candidate genes were identified for molecular breeding aimed at tolerance to abiotic stresses.
低温和干旱是降低全球园艺作物产量和地理分布的两个主要环境限制因素。了解胁迫反应之间的遗传相互作用对作物改良具有潜在重要性。
在本研究中，利用Illumina RNA测序和Pac-Bio基因组重测序对茶树在长期低温、冷冻和干旱条件下的基因进行注释并分析转录组动态变化。
在长期低温（7896个）和冷冻（7915个）条件下鉴定出的差异表达基因（DEG）数量最多，上调基因分别为3532个和3780个。在3天干旱（47个）和9天干旱（220个）条件下观察到的DEG数量最少，上调基因分别为5个和112个。低温处理后的恢复阶段的DEG数量是干旱恢复阶段的6.5倍。只有17.9%的冷诱导基因受干旱上调。总共鉴定出1492个与57个家族相关的转录因子基因。然而，只有20个转录因子基因在低温、冷冻和干旱条件下共同上调。在232个共同上调的DEG中，大多数与信号转导、细胞壁重塑和脂质代谢有关。共表达分析和网络重建显示19个基因具有最高的共表达连通性：7个基因与细胞壁重塑有关（、、、、、、和），4个基因与钙信号有关（、、、和），3个基因与光感知有关（、、和），2个基因与激素信号有关（和），2个基因参与活性氧信号（和），1个基因与苯丙烷途径有关（）。
基于我们的结果，长期胁迫反应的几个重要重叠机制包括通过木质素生物合成、多糖的O-乙酰化、果胶生物合成和分支以及木葡聚糖和阿拉伯半乳聚糖生物合成进行细胞壁重塑。本研究为木本作物的长期胁迫反应提供了新的见解，并鉴定出一组新的目标候选基因用于旨在耐受非生物胁迫的分子育种。
