The differentially expressed genes identification in dwarf mutant of Gossypium hirsutum by RNA-Seq approach

Q1 Agricultural and Biological Sciences

Agri Gene Pub Date : 2017-09-01 DOI:10.1016/j.aggene.2017.08.001

Zhao Liang , Di Jiachun , Guo Qi , Zhao Jun , Zhou Xiangyang , Chen Xusheng

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引用次数: 2

Abstract

Demands for dwarf plants are increasing, because dwarfism is one of the most important traits in modern crop breeding. Gibberellin (GA) is an essential hormone that is involved in many aspects of plant growth and development. A cotton mutant shows that ultra-dwarf (average plant height is 10 cM), blade twisting and cannot grow normally, but the mutant could change to normal plant with GA treatment in the process of growth. To comprehensively survey the patterns of gene expression, RNA-Seq was used in this paper. Approximately 93.5% of all tags could be mapped reference sequences. 77,686 genes could detect expression level by the map. A total of 11,403 DEGs between the samples were detected. Quantitative real-time PCR was used to evaluate the results of RNA-Seq for gene expression profiles. Based on KEGG analysis, a total of 425 genes involved in plant hormone biosynthesis and signal transduction. Among those genes, 27 DEGs involved in GA biosynthesis and 20 in signal transduction. Gh_A06G1386 and Gh_D06G1730, a pair of homoeologous genes, may be candidate genes based on results of fine mapping and RNA-Seq analysis.

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用RNA-Seq方法鉴定棉矮化突变体差异表达基因

矮化是现代作物育种中最重要的性状之一，对矮化植物的需求日益增加。赤霉素(giberellin, GA)是一种重要的激素，参与植物生长发育的许多方面。一个棉花突变体表现为超矮(株高平均为10 cM)，叶片扭曲，不能正常生长，但在生长过程中经GA处理后可转为正常植株。为了全面调查基因表达模式，本文采用RNA-Seq技术。大约93.5%的标签可以被映射为参考序列。该图谱可检测77,686个基因的表达水平。样品间共检测到11,403个deg。采用实时荧光定量PCR对基因表达谱的RNA-Seq结果进行评价。基于KEGG分析，共有425个基因参与了植物激素的生物合成和信号转导。其中27个基因参与GA生物合成，20个基因参与信号转导。Gh_A06G1386和Gh_D06G1730是一对同源基因，根据精细定位和RNA-Seq分析结果，可能是候选基因。

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Agri Gene Agricultural and Biological Sciences-Agricultural and Biological Sciences (miscellaneous)

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期刊介绍： Agri Gene publishes papers that focus on the regulation, expression, function and evolution of genes in crop plants, farm animals, and agriculturally important insects and microorganisms. Agri Gene strives to be a diverse journal and topics in multiple fields will be considered for publication so long as their main focus is on agriculturally important organisms (plants, animals, insects, or microorganisms). Although not limited to the following, some examples of potential topics include: Gene discovery and characterization. Genetic markers to guide traditional breeding. Genetic effects of transposable elements. Evolutionary genetics, molecular evolution, population genetics, and phylogenetics. Profiling of gene expression and genetic variation. Biotechnology and crop or livestock improvement. Genetic improvement of biological control microorganisms. Genetic control of secondary metabolic pathways and metabolic enzymes of crop pathogens. Transcription analysis of beneficial or pest insect developmental stages Agri Gene encourages submission of novel manuscripts that present a reasonable level of analysis, functional relevance and/or mechanistic insight. Agri Gene also welcomes papers that have predominantly a descriptive component but improve the essential basis of knowledge for subsequent functional studies, or which provide important confirmation of recently published discoveries provided that the information is new.