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High throughput RNA sequencing of a hybrid maize and its parents shows different mechanisms responsive to nitrogen limitation

Yong-Mei Bi1, Ann Meyer2, Gregory S Downs2, Xuejiang Shi3, Ashraf El-kereamy14, Lewis Lukens2 and Steven J Rothstein1*

Author Affiliations

1 Department of Molecular and Cellular Biology, University of Guelph, N1G 2 W1 Guelph, ON, Canada

2 Department of Plant Agriculture, University of Guelph, N1G 2 W1 Guelph, ON, Canada

3 Clinical Genomics Centre, The UHN/MSH Gene Profiling Facility, M5G 1X5 Toronto, ON, Canada

4 Current address: Horticulture Department, Faculty of Agriculture, Ain Shams University, 11241 Cairo, Egypt

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BMC Genomics 2014, 15:77  doi:10.1186/1471-2164-15-77

Published: 28 January 2014



Development of crop varieties with high nitrogen use efficiency (NUE) is crucial for minimizing N loss, reducing environmental pollution and decreasing input cost. Maize is one of the most important crops cultivated worldwide and its productivity is closely linked to the amount of fertilizer used. A survey of the transcriptomes of shoot and root tissues of a maize hybrid line and its two parental inbred lines grown under sufficient and limiting N conditions by mRNA-Seq has been conducted to have a better understanding of how different maize genotypes respond to N limitation.


A different set of genes were found to be N-responsive in the three genotypes. Many biological processes important for N metabolism such as the cellular nitrogen compound metabolic process and the cellular amino acid metabolic process were enriched in the N-responsive gene list from the hybrid shoots but not from the parental lines’ shoots. Coupled to this, sugar, carbohydrate, monosaccharide, glucose, and sorbitol transport pathways were all up-regulated in the hybrid, but not in the parents under N limitation. Expression patterns also differed between shoots and roots, such as the up-regulation of the cytokinin degradation pathway in the shoots of the hybrid and down-regulation of that pathway in the roots. The change of gene expression under N limitation in the hybrid resembled the parent with the higher NUE trait. The transcript abundances of alleles derived from each parent were estimated using polymorphic sites in mapped reads in the hybrid. While there were allele abundance differences, there was no correlation between these and the expression differences seen between the hybrid and the two parents.


Gene expression in two parental inbreds and the corresponding hybrid line in response to N limitation was surveyed using the mRNA-Seq technology. The data showed that the three genotypes respond very differently to N-limiting conditions, and the hybrid clearly has a unique expression pattern compared to its parents. Our results expand our current understanding of N responses and will help move us forward towards effective strategies to improve NUE and enhance crop production.

Maize; mRNA-Seq; Nitrogen limitation; Nitrogen use efficiency; Hybrid; Inbred; Allelic expression