Genome-wide identification and expression analysis of NIN-like Protein (NLP) genes reveals their potential roles in the response to nitrate signaling in watermelon

To balance the relationship between high yield and low nitrogen supply, the nitrogen utilization efficiency of watermelon needs to be improved urgently. Nodule inception-like Protein (NLP) transcription factors play a key node role in nitrate response and growth and devel-opment of plant, however, comprehensive analysis of the NLP gene family in watermelon is unclear. This study explored the functional classification, evolutionary characteristics, and expression profile of the ClNLP gene family. Three ClNLPs were categorized into three groups according to their gene structure and phylogeny. All of them contained the conserved RWP-RK and PB1 domains. Evolutionary analysis of ClNLPs revealed that ClNLP1 and ClNLP3 underwent strong purified selection. In addition, cis-acting elements related to plant hormones and abiotic stresses were present in the ClNLP promoter. According to tissue-specific analysis ClNLP was widely expressed in roots, stems, leaves, flowers and fruits, and ClNLP1 was significantly induced in the roots of different nitrogen utilization varieties under different nitrate nitrogen supply. The SRTING functional protein association network suggested that ClNLP1 is associated with most genes, such as NRT1.1, NRT2.1, NIA1, and NIR1, and the dual-luciferase reporter assay found that ClNLP1 positively regulates the expression of ClNRT2.1. We speculated that ClNLP1 might play a central role in regulating the response of watermelon to nitrate nitrogen.