A genome-wide analysis of NPF and NRT2 transporter gene families in bread wheat provides new insights into the distribution, function, regulation and evolution of nitrate transporters

Aims Nitrate transporters (NRT) in plants are mainly encoded by the NPF and NRT2 gene families. We aimed to reveal the chromosome distribution, collinearity, coexpression and evolution of the NPF and NRT2 genes in the genome of wheat (Triticum aestivum). Nitrate transport activity of representative proteins was also verified. Methods Genomic information, collinearity analysis, coexpression network analysis, nitrate transport activity and polymorphism analysis were integrated to identify and characterize the NPF and NRT2 genes. Results We identified 331 NPF and 46 NRT2 genes in the wheat genome. Tandem duplication was the main driver of the expansion of the NRT2 genes. The NPF genes were mainly distributed on the 2-, 3- and 7- chromosome groups and in the R2b region. The NRT2 genes were mainly distributed on the 6-chromosome group and in the R1 region. Multiple transcription factor families were coexpressed with NPF and NRT2 genes in wheat. Two NPFs and one NRT2 could transport NO3- under either 0.5 mM or 10 mM nitrate concentrations. One hundred and eighty-five NPF and 27 NRT2 genes fit the neutral selection model. Natural variations in NPF genes resulted in differences in the nitrogen uptake of wheat. Conclusions Duplication events are ubiquitous in NPF and NRT2 gene families in the wheat genome. GRAS may be a previously unrecognized transcription factor that regulates NPF genes expression. It is unreliable to predict the activity of NPF and NRT2 proteins based only on their phylogenetic relationships. Polymorphisms in NPF and NRT2 genes mainly accumulate by random drift.

Automated summary

Duplication events are common in the NPF and NRT2 gene families in the wheat genome, with NPF genes mainly located on chromosome groups 2, 3, and 7, and NRT2 genes primarily on chromosome group 6. Coexpression analysis revealed multiple transcription factor families associated with NPF and NRT2 genes. Two NPFs and one NRT2 demonstrated nitrate transport activity under different nitrate concentrations.