The RNA-Seq-based high resolution gene expression atlas of chickpea (Cicer arietinum L.) reveals dynamic spatio-temporal changes associated with growth and development
The RNA-Seq-based high resolution gene expression atlas of chickpea (Cicer arietinum L.) reveals dynamic spatio-temporal changes associated with growth and development
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DOI：
10.1111/pce.13210
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发表时间：
2018-09-01
影响因子：
7.3
通讯作者：
Varshney, Rajeev K.
中科院分区：
文献类型：
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作者：
Kudapa, Himabindu;Garg, Vanika;Varshney, Rajeev K.
鹰嘴豆是世界上最大的种植豆类之一，是人类饮食中优质蛋白质的极好来源。植物的生长和发育是由一系列基因在给定的时间、阶段和组织中的程序化表达来控制的。了解基因组序列如何在关键发育阶段转化为特定的植物表型，关于基因表达模式的信息是至关重要的。在这里，我们提出了一个涵盖鹰嘴豆整个生活史的不同植物发育阶段和器官的全面的鸡冠花基因表达图谱(CaGEA)。ICC4958是一个广泛应用的耐旱品种，已被用来从植物5个主要发育阶段的27个样本中产生RNA-Seq数据。总共产生了8.16亿个原始读数，其中7.94亿个经过过滤的读数在质量控制(QC)之后接受了下游分析。在不同的成对组织组合中，总共鉴定了15,947个独特的差异表达基因。在这项研究中推测，在开花、结瘤、种子和根发育过程中起作用的基因表达模式存在显著差异。此外，还验证了与鹰嘴豆干旱胁迫反应相关的QTL热点区域差异表达的候选基因。建立了覆盖鹰嘴豆整个生活史的植物主要发育阶段和器官的综合基因表达图谱(CaGEA)。产生的CaGEA和确定的候选基因将作为有用的资源，加速鹰嘴豆的遗传研究和育种应用。
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.A comprehensive Cicer arietinum Gene Expression Atlas (CaGEA) across major plant developmental stages and organs covering the entire life cycle of chickpea has been developed. The CaGEA generated and the candidate genes identified will serve as useful resource to accelerate genetic research and breeding applications in chickpea.