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Genome-wide identification of housekeeping genes in maize

文献类型： 外文期刊

作者： Lin, Feng 1 ; Jiang, Lu 1 ; Liu, Yuhe 2 ; Lv, Yuanda 1 ; Dai, Huixue 3 ; Zhao, Han 1 ;

作者机构： 1.Jiangsu Acad Agr Sci, Inst Biotechnol, Prov Key Lab Agrobiol, Nanjing 210014, Jiangsu, Peoples R China

2.Univ Illinois, Dept Crop Sci, Urbana, IL 61801 USA

3.Nanjing Inst Vegetable Sci, Nanjing 210042, Jiangsu, Peoples R China

关键词： Maize;Housekeeping gene;Reference gene;Nitrogen;qPCR

期刊名称：PLANT MOLECULAR BIOLOGY （ 影响因子：4.076； 五年影响因子：4.89 ）

ISSN： 0167-4412

年卷期： 2014 年 86 卷 4-5 期

页码：

收录情况： SCI

摘要： In the wake of recent progress of high throughput transcriptome profiling technologies, extensive housekeeping gene mining has been conducted in humans. However, very few studies have been reported in maize (Zea mays L.), an important crop plant, and none were conducted on a genome -wide level. In this study, we surveyed housekeeping genes throughout the maize transcriptome using RNA-seq and microarray techniques, and validated the housekeeping profile with quantitative polymerase chain reaction (qPCR) under a series of conditions including different genotypes and nitrogen supplies. Seven microarray datasets and two RNA-seq libraries representing 40 genotypes at more than 20 developmental stages were selected to screen for commonly expressed genes. A total of 1,661 genes showed constitutive expression in both microarray and RNA-seq datasets, serving as our starting housekeeping gene candidates. To determine for stably expressed housekeeping genes, NormFinder was used to select the top 20 % invariable genes to be the more likely candidates, which resulted in 48 and 489 entries from microarray and RNA-seq data, respectively. Among them, nine genes (2OG-Fe, CDK, DPP9, DUF, NAC, RPN, SGT1, UPF1 and a hypothetical protein coding gene) were expressed in all 40 maize diverse genotypes tested covering 16 tissues at more than 20 developmental stages under normal and stress conditions, implying these as being the most reliable reference genes. qPCR analysis confirmed the stable expression of selected reference gene candidates compared to two widely used housekeeping genes. All the reference gene candidates showed higher invariability than ACT and GAPDH. The hypothetical protein coding gene exhibited the most stable expression across 26 maize lines with different nitrogen treatments with qPCR, followed by CDK encoding the cyclin-dependent kinase. As the first study to systematically screen for housekeeping genes in maize, we identified candidates by examining the transcriptome atlas generated from RNA-seq and microarray technologies. The nine top-ranked qPCR-validated novel housekeeping genes provide a valuable resource of reference genes for maize gene expression analysis.

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