Genome-wide systematic characterization of the NRT2 gene family and its expression profile in wheat (Triticum aestivum L.) during plant growth and in response to nitrate deficiency

Abstract

Background Wheat (Triticum aestivum L.) is a major cereal crop that is grown worldwide, and it is highly dependent on sufficient N supply. The molecular mechanisms associated with nitrate uptake and assimilation are still poorly understood in wheat. In plants, NRT2 family proteins play a crucial role in NO3– acquisition and translocation under nitrate limited conditions. However, the biological functions of these genes in wheat are still unclear, especially their roles in NO3– uptake and assimilation. Results In this study, a comprehensive analysis of wheat TaNRT2 genes was conducted using bioinformatics and molecular biology methods, and 49 TaNRT2 genes were identified. A phylogenetic analysis clustered the TaNRT2 genes into three clades. The genes that clustered on the same phylogenetic branch had similar gene structures and nitrate assimilation functions. The identified genes were further mapped onto the 13 wheat chromosomes, and the results showed that a large duplication event had occurred on chromosome 6. To explore the TaNRT2 gene expression profiles in wheat, we performed transcriptome sequencing after low nitrate treatment for three days. Transcriptome analysis revealed the expression levels of all TaNRT2 genes in shoots and roots, and based on the expression profiles, three highly expressed genes (TaNRT2-6A.2, TaNRT2-6A.6, and TaNRT2-6B.4) were selected for qPCR analysis in two different wheat cultivars (‘Mianmai367’ and ‘Nanmai660’) under nitrate-limited and normal conditions. All three genes were upregulated under nitrate-limited conditions and highly expressed in the high nitrogen use efficiency (NUE) wheat ‘Mianmai367’ under low nitrate conditions. Conclusion We systematically identified 49 NRT2 genes in wheat and analysed the transcript levels of all TaNRT2s under nitrate deficient conditions and over the whole growth period. The results suggest that these genes play important roles in nitrate absorption, distribution, and accumulation. This study provides valuable information and key candidate genes for further studies on the function of TaNRT2s in wheat.

Functional analyses of the NRT2 family of nitrate transporters in Arabidopsis

“…Furthermore, new information have been obtained about unexpected peculiar roles played by some NRT2 genes. The NRT2 transporter family has at least 4 members in Lotus japonicus ( Criscuolo et al., 2012 ), 5 in Oryza sativa ( Feng et al., 2011b ) and 49 in the Wheat genome ( Deng et al., 2023 ). In Lotus japonicus , high NO 3 - treatment attenuated nodulation, but the effect of nitrate was suppressed by the LjNRT2.1 mutation ( Misawa et al., 2022 ).…”

The Functional Diversity of the High-Affinity Nitrate Transporter Gene Family in Hexaploid Wheat: Insights from Distinct Expression Profiles

“…The diversity of NRT2 genes highlights the complexity of nitrate transport in plants. Recent publications focusing on bread wheat confirmed the presence of multiple genes in the wheat genome [ 26 , 27 , 28 ]. However, these studies have reported different numbers while proposing distinct nomenclatures, thus leading to inconsistencies and potential confusion in the wheat research community.…”

“…This table provides details on the identified wheat NRT2 and NRT3 genes, including their accession numbers, chromosomal locations, and length of encoded proteins. The corresponding gene names from previous studies [26][27][28] were aligned with the suggested nomenclature. A total of 11 NRT3-encoding genes were identified in the hexaploid wheat genome, forming four homoeologous subgroups (Table 1).…”

“…Furthermore, the homoeologous relationships between the genes present in the A, B, and D wheat sub-genomes have been described. A new nomenclature is proposed that accounts for these homoeologous subgroups (Table 1), and a conversion table is presented, thereby aligning the present nomenclature with that of recent publications [26][27][28]. This resource aims to facilitate future research and avoid inconsistencies in gene names.…”

“…Hence, the aim of this study, is to identify and characterize the phylogenetic relations of the hexaploid wheat NRT2 and NRT3 genes compared with their orthologs from Arabidopsis, Brachypodium, rice, and barley ( Hordeum vulgare ). Three recent studies have also focused on the NRT2s in wheat [ 26 , 27 , 28 ]; however, each study suggested different nomenclature for the identified NRT2s . The presence of different names for the same gene accession can cause confusion and is a major problem in the wheat research community.…”