Genome-Wide Identification and Expression Analysis of the NLP Family in Sweet Potato and Its Two Diploid Relatives

NIN-like proteins (NLPs) are conserved, plant-specific transcription factors that play crucial roles in the nitrate signaling response, plant growth and development, and abiotic stress responses. However, their functions have not been explored in sweet potato. In this study, we identified 7 <i>NLPs</i> in cultivated hexaploid sweet potato (<i>Ipomoea batatas</i>, 2n = 6x = 90), 9 <i>NLPs</i> in the diploid relative <i>Ipomoea trifida</i> (2n = 2x = 30), and 12 <i>NLPs</i> in <i>Ipomoea triloba</i> (2n = 2x = 30) via genome structure analysis and phylogenetic characterization, respectively. The protein physiological properties, chromosome localization, phylogenetic relationships, syntenic analysis maps, gene structure, promoter <i>cis</i>-acting regulatory elements, and protein interaction networks were systematically investigated to explore the possible roles of homologous <i>NLPs</i> in the nitrate signaling response, growth and development, and abiotic stress responses in sweet potato. The expression profiles of the identified <i>NLPs</i> in different tissues and treatments revealed tissue specificity and various expression patterns in sweet potato and its two diploid relatives, supporting differences in the evolutionary trajectories of the hexaploid sweet potato. These results are a critical first step in understanding the functions of sweet potato <i>NLPs</i> and offer more candidate genes for improving nitrogen use efficiency and increasing yield in cultivated sweet potato.