Characterization of GmNPF genes prioritizes candidate genes for soybean yield and protein improvement

Abstract

Nitrate uptake and translocation are crucial for plant growth and development, with Nitrate Transporter 1/Peptide Transporter family (NRTs) being critical in mediating nitrogen supply. Soybean (Glycine max) has been a major source of plant-based protein globally, and it requires high amounts of nitrogen to support the plant’s development and protein accumulation in seeds. However, genes accounting for nitrogen uptake and usage have yet to be systematically identified. This study focuses on the characterization of Nitrate Transporter 1/Peptide Transporter family (NPF) genes belonging to the NRTs in soybean. In total, 126 GmNPF genes were identified in the soybean genome, and they exhibit evolutionary conservation and functional diversity based on the analysis of protein physicochemical properties, chromosomal localization, phylogenetic relationship, synteny correlation, conserved domain, motif, gene structure and cis-acting element prediction. Additionally, spatiotemporal expression specificity analyses revealed that several GmNPFs are potentially important in root, stem, leaf and seed. In addition, we also identified a set of GmNPF genes inducible by low nitrogen stress or being regulated by POWR1 and SWEET10a/b (SWEET39), two major high protein QTL genes in soybean, suggesting their participation in nitrogen absorption and seed protein deposition in soybean. Importantly, we also identified six GmNPFs showing contrasting allelic frequencies between cultivated and wild soybean, and the allelic variation was tightly associated with the variation in protein levels in cultivated soybean. The study uncovers a set of candidate genes with great potential in improving soybean protein and yield via enhanced nitrogen uptake and utilization.