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

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Abstract

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.).

Methods

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

Results

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.

Conclusions

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.

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Abbreviations

CNV:

Copy number variation

CRE:

cis-acting regulatory elements

HATS:

High-affinity transport system

MFS:

Major facilitator superfamily

MYA:

Million years ago

N:

Nitrogen

NAR:

Nitrate-assimilation related

NNP:

Nitrate/nitrite porter

NRT:

Nitrate transporter

NO3 - :

Nitrate

NUE:

Nitrogen use efficiency

PAV:

Presence/absence variation

qRT-PCR:

Quantitative reverse-transcription polymerase chain reaction

TF:

Transcription factor

THATS:

Two-component high-affinity NO3- transport system

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Acknowledgments

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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Authors and Affiliations

  1. Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China

    Ying-peng Hua, Ting Zhou, Hai-xing Song & Zhen-hua Zhang

  2. National Center of Oilseed Crops Improvement, Hunan Branch, Changsha, China

    Chun-yun Guan

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  1. Ying-peng Hua
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  2. Ting Zhou
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  3. Hai-xing Song
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  4. Chun-yun Guan
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  5. Zhen-hua Zhang
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Correspondence to Zhen-hua Zhang.

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We identified the core members of the two-component high-affinity nitrate transport system in allotetraploid rapeseed, which can serve as elite gene resources for nitrogen use efficiency enhancement in crops, and the transcriptomics-assisted gene co-expression network analysis provide reference regarding the rapid identification of central members within the large gene families in plant species with complex genomes.

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Hua, Yp., Zhou, T., Song, Hx. et al. Integrated genomic and transcriptomic insights into the two-component high-affinity nitrate transporters in allotetraploid rapeseed. Plant Soil 427, 245–268 (2018). https://doi.org/10.1007/s11104-018-3652-3

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  • DOI: https://doi.org/10.1007/s11104-018-3652-3

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