Genome-wide identification of the apple NLP (NIN-like proteins) family and their potential role under abiotic stress.

Abstract

NIN-like proteins (NLPs), unique to plants, are conserved transcription factors that significantly influence nitrate levels. However, a comprehensive analysis of the apple NLP gene family remains lacking. In this study, five NLP members were identified from the apple (Malus domestica) genome, and structural analysis revealed that each member contains RWP-RK and PB1 domains, which were classified into three branches by phylogenetic analysis. Additionally, cis-acting elements associated with abiotic stresses-such as phytohormone and low-temperature response elements-as well as nitrogen (N) response elements were present in MdNLP promoters. RNA sequencing data across various tissues revealed extensive MdNLP expression in leaves, flowers, and fruits. The MdNLP expression patterns under different abiotic stresses were also examined. MdNLP expression was up-regulated after indole-3-acetic acid (IAA) and gibberellic acid (GA₃) treatments, with MdNLP2 and MdNLP5 showing the most significant up-regulation post-GA₃ treatment. Most MdNLP genes were up-regulated under low-temperature stress, except for MdNLP3, while most were down-regulated under salt stress. Under low-N stress, MdNLP3 and MdNLP4 were significantly up-regulated, suggesting their potential as candidate genes to improve N utilization in apples. Therefore, these results lay the foundation for a better understanding of the MdNLP family's role in the low-N stress response and in apple growth and development.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04375-6.