Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India.
Plant Cell Environ. 2018 Sep;41(9):2209-2225. doi: 10.1111/pce.13210. Epub 2018 May 16.
Chickpea is one of the world's largest cultivated food legumes and is an excellent source of high-quality protein to the human diet. Plant growth and development are controlled by programmed expression of a suite of genes at the given time, stage, and tissue. Understanding how the underlying genome sequence translates into specific plant phenotypes at key developmental stages, information on gene expression patterns is crucial. Here, we present a comprehensive Cicer arietinum Gene Expression Atlas (CaGEA) across different plant developmental stages and organs covering the entire life cycle of chickpea. One of the widely used drought tolerant cultivars, ICC 4958 has been used to generate RNA-Seq data from 27 samples at 5 major developmental stages of the plant. A total of 816 million raw reads were generated and of these, 794 million filtered reads after quality control (QC) were subjected to downstream analysis. A total of 15,947 unique number of differentially expressed genes across different pairwise tissue combinations were identified. Significant differences in gene expression patterns contributing in the process of flowering, nodulation, and seed and root development were inferred in this study. Furthermore, differentially expressed candidate genes from "QTL-hotspot" region associated with drought stress response in chickpea were validated.
鹰嘴豆是世界上最大的栽培食用豆类之一，是人类饮食中高质量蛋白质的极好来源。植物的生长和发育受特定时间、阶段和组织中一组基因的程序性表达所控制。了解潜在的基因组序列如何在关键发育阶段转化为特定的植物表型，了解基因表达模式的信息至关重要。在这里，我们展示了鹰嘴豆不同发育阶段和器官的综合基因表达图谱（CaGEA），涵盖了鹰嘴豆的整个生命周期。我们使用了广泛使用的耐旱品种 ICC 4958，从植物的 5 个主要发育阶段的 27 个样本中生成了 RNA-Seq 数据。总共生成了 8.16 亿个原始读数，经过质量控制（QC）后，其中 7.94 亿个过滤读数被用于下游分析。在不同的成对组织组合中，总共鉴定到 15947 个差异表达基因。在这项研究中，推断出了在开花、结瘤和种子及根发育过程中基因表达模式的显著差异。此外，还验证了与鹰嘴豆干旱胁迫反应相关的“QTL 热点”区域的差异表达候选基因。
