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Plant Molecular Biology

, Volume 86, Issue 4–5, pp 543–554 | Cite as

Genome-wide identification of housekeeping genes in maize

  • Feng Lin
  • Lu Jiang
  • Yuhe Liu
  • Yuanda Lv
  • Huixue Dai
  • Han Zhao
Article

Abstract

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.

Keywords

Maize Housekeeping gene Reference gene Nitrogen qPCR 

Notes

Acknowledgments

This work was supported by Grant from the Natural Science Foundation of China (No. 31271728) and Jiangsu Agriculture Science and Technology Innovation Fund [cx(12)2032].

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11103_2014_246_MOESM1_ESM.xlsx (19 kb)
Supplementary material 1 (XLSX 19 kb)
11103_2014_246_MOESM2_ESM.xlsx (36 kb)
Supplementary material 2 (XLSX 35 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Feng Lin
    • 1
  • Lu Jiang
    • 1
  • Yuhe Liu
    • 2
  • Yuanda Lv
    • 1
  • Huixue Dai
    • 3
  • Han Zhao
    • 1
  1. 1.Institute of Biotechnology, Provincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjingChina
  2. 2.Department of Crop SciencesUniversity of Illinois at Urbana-ChampaignUrbanaUSA
  3. 3.Nanjing Institute of Vegetable SciencesNanjingChina

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