Genome-Wide Identification and Functional Analysis of Nitrate Transporter Genes (NPF, NRT2 and NRT3) in Maize

Abstract

Nitrate is the primary form of nitrogen uptake in plants, mainly transported by nitrate transporters (NRTs), including NPF (NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY), NRT2 and NRT3. In this study, we identified a total of 78 <i>NPF</i>, seven <i>NRT2</i>, and two <i>NRT3</i> genes in maize. Phylogenetic analysis divided the <i>NPF</i> family into eight subgroups (<i>NPF1</i>-<i>NPF8</i>), consistent with the results in <i>Arabidopsis thaliana</i> and rice. The <i>NRT2</i> family appears to have evolved more conservatively than the <i>NPF</i> family, as <i>NRT2</i> genes contain fewer introns. The promoters of all <i>NRTs</i> are rich in <i>cis</i>-acting elements responding to biotic and abiotic stresses. The expression of <i>NRTs</i> varies in different tissues and developmental stages, with some <i>NRTs</i> only expressed in specific tissues or developmental stages. RNA-seq analysis using Xu178 revealed differential expression of <i>NRTs</i> in response to nitrogen starvation and nitrate resupply. Moreover, the expression patterns of six key <i>NRTs</i> genes (<i>NPF6.6</i>, <i>NPF6.8</i>, <i>NRT2.1</i>, <i>NRT2.5</i> and <i>NRT3.1A/B</i>) varied in response to alterations in nitrogen levels across distinct maize inbred lines with different nitrogen uptake rates. This work enhances our understanding of the structure and expression of <i>NRTs</i> genes, and their roles in nitrate response, paving the way for improving maize nitrogen efficiency through molecular breeding.