Plant and Soil

, Volume 427, Issue 1–2, pp 245–268 | Cite as

Integrated genomic and transcriptomic insights into the two-component high-affinity nitrate transporters in allotetraploid rapeseed

  • Ying-peng Hua
  • Ting Zhou
  • Hai-xing Song
  • Chun-yun Guan
  • Zhen-hua Zhang
Regular Article


Background and aims

The two-component high-affinity nitrate (NO3-) transport system (THATS) proteins (NRT2/NAR2) play key roles in the efficient nitrogen (N) uptake and transport under N limitations. We aimed at uncovering the core THATS gene(s) regulating N use efficiency (NUE) in allotetraploid rapeseed (Brassica napus L.).


Genomic information, high-throughput transcriptome sequencing and gene co-expression network were integrated to identify and characterize the core THATS genes.


We identified 17 BnaNRT2 and eight BnaNAR2.1 homologs spanning across the rapeseed genome. Copy number and gene presence/absence variations of BnaNRT2s/BnaNAR2.1 s, undergoing strong purifying selection, occurred. The over-representation of Dof, MYB and WRKY cis-regulatory elements and the enrichment of CpG islands, and protein phosphorylation sites indicated the importance of transcriptional and epigenetic regulation in the BnaNRT2 activities, respectively. qRT-PCR assays and high-throughput RNA-seq revealed that both BnaNRT2s and BnaNAR2.1 s were expressed preferentially in the roots; and they showed significantly differential expression under different N forms or different levels of NO3- supply. A gene co-expression network identified BnaC8.NRT2.1a and BnaC2.NAR2.1 as the core THATS genes.


The core THATS members can serve as elite gene resources for crop NUE improvement. The transcriptomics-assisted gene co-expression network analysis provides novel insights regarding the rapid identification of central members within large gene families of plant species with complex genomes.


Allotetraploid High-affinity Nitrate Rapeseed Two-component Transporter 



Copy number variation


cis-acting regulatory elements


High-affinity transport system


Major facilitator superfamily


Million years ago




Nitrate-assimilation related


Nitrate/nitrite porter


Nitrate transporter




Nitrogen use efficiency


Presence/absence variation


Quantitative reverse-transcription polymerase chain reaction


Transcription factor


Two-component high-affinity NO3- transport system



We thank both Dr. Jianhua Zhang and Dr. Moxian Chen (The Chinese University of Hong Kong) for the manuscript polish. This study was financially supported in part, by the National Key R&D Program of China (2017YFD0200100, 2017YFD0200103); National Natural Science Foundation of China (Grant No.31101596, 31372130); Hunan Provincial Recruitment Program of Foreign Experts; and the National Oilseed Rape Production Technology System of China; “2011 Plan” supported by The Ministry of Education of China.

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Ying-peng Hua
    • 1
  • Ting Zhou
    • 1
  • Hai-xing Song
    • 1
  • Chun-yun Guan
    • 2
  • Zhen-hua Zhang
    • 1
  1. 1.Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental SciencesHunan Agricultural UniversityChangshaChina
  2. 2.National Center of Oilseed Crops Improvement, Hunan BranchChangshaChina

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