Comparative RNA-seq analysis of the drought-sensitive lentil (Lens culinaris) root and leaf under short- and long-term water deficits

Drought stress is one of the main environmental factors that affects growth and productivity of crop plants, including lentil. To gain insights into the genome-wide transcriptional regulation in lentil root and leaf under short- and long-term drought conditions, we performed RNA-seq on a drought-sensitive lentil cultivar (Lens culinaris Medik. cv. Sultan). After establishing drought conditions, lentil samples were subjected to de novo RNA-seq-based transcriptome analysis. The 207,076 gene transcripts were successfully constructed by de novo assembly from the sequences obtained from root, leaf, and stems. Differentially expressed gene (DEG) analysis on these transcripts indicated that period of drought stress had a greater impact on the transcriptional regulation in lentil root. The numbers of DEGs were 2915 under short-term drought stress while the numbers of DEGs were increased to 18,327 under long-term drought stress condition in the root. Further, Gene Ontology analysis revealed that the following biological processes were differentially regulated in response to long-term drought stress: protein phosphorylation, embryo development seed dormancy, DNA replication, and maintenance of root meristem identity. Additionally, DEGs, which play a role in circadian rhythm and photoreception, were downregulated suggesting that drought stress has a negative effect on the internal oscillators which may have detrimental consequences on plant growth and survival. Collectively, this study provides a detailed comparative transcriptome response of drought-sensitive lentil strain under short- and long-term drought conditions in root and leaf. Our finding suggests that not only the regulation of genes in leaves is important but also genes regulated in roots are important and need to be considered for improving drought tolerance in lentil. mRNA profiles of Lens culinaris Medik. cv. Sultan cells were obtained under short- (24 hours) and long-term (96 hours) drought conditions with no-stress controls by deep sequencing, in two biological replicates, using Illumina HiSeq platform.

干旱胁迫是影响包括小扁豆在内的农作物生长与产量的主要环境胁迫因子之一。为解析小扁豆根与叶片在短期及长期干旱胁迫下的全基因组转录调控机制，本研究以干旱敏感型小扁豆品种（Lens culinaris Medik. cv. Sultan）开展RNA测序（RNA-seq）。在构建干旱胁迫模型后，对小扁豆样本开展基于从头（de novo）组装的转录组分析。通过对根、叶及茎组织的测序序列进行从头组装，成功获得207076条基因转录本。针对上述转录本开展的差异表达基因（DEG）分析结果显示，干旱胁迫时长对小扁豆根部的转录调控影响更为显著：在根部，短期干旱胁迫下的DEG数量为2915个，长期干旱胁迫下则增至18327个。进一步的基因本体（Gene Ontology, GO）分析显示，长期干旱胁迫下以下生物学过程发生了差异调控：蛋白质磷酸化、胚胎发育与种子休眠、DNA复制以及根分生组织身份维持。此外，参与昼夜节律与光感受过程的DEG呈下调趋势，表明干旱胁迫会对植物内源节律振荡器产生负面影响，这可能对植株生长与存活造成不利影响。综上，本研究详细解析了干旱敏感型小扁豆品系在根、叶组织中针对短期与长期干旱胁迫的比较转录组响应特征。本研究结果表明，在培育耐旱小扁豆品种时，不仅需关注叶片中的基因调控，根部的基因调控同样至关重要，需纳入育种考量范畴。本研究采用Illumina HiSeq测序平台，设置两次生物学重复，在短期（24小时）、长期（96小时）干旱胁迫及无胁迫对照条件下，获取了小扁豆品种（Lens culinaris Medik. cv. Sultan）的mRNA表达谱。