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Background  Tomato ( Solanum lycopersicum ) is one of the most important horticultural crops, with a marked preference for nitrate as an inorganic nitrogen source. The molecular mechanisms of nitrate uptake and assimilation are poorly understood in tomato. NIN-like proteins (NLPs) are conserved, plant-specific transcription factors that play crucial roles in nitrate signaling.    Results  In this study, genome-wide analysis identified six  NLP  members in tomato genome. These members were clustered into three clades in a phylogenetic tree. Comparative genomic analysis showed that  SlNLP  genes exhibited collinear relationships to  NLP s in Arabidopsis, canola, maize and rice, and that the expansion of the  SlNLP  family mainly resulted from segmental duplications in the tomato genome. Tissue-specific expression analysis showed that one of the close homologs of  AtNLP6/7 ,  SlNLP3 , was strongly expressed in roots during both the seedling and flowering stages, that  SlNLP4  and  SlNLP6  exhibited preferential expression in stems and leaves and that  SlNLP6  was expressed at high levels in fruits. Furthermore, the nitrate uptake in tomato roots and the expression patterns of  SlNLP  genes were measured under nitrogen deficiency and nitrate resupply conditions. Four  SlNLPs ,  SlNLP1 ,  SlNLP2 ,  SlNLP4  and  SlNLP6 , were upregulated after nitrogen starvation. And  SlNLP1  and  SlNLP5  were induced rapidly and temporally by nitrate.    Conclusions  These results provide significant insights into the potential diverse functions of  SlNLPs  to regulate nitrate uptake.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-03116-0.

Genome-wide survey and expression analysis of NIN-like Protein (NLP) genes reveals its potential roles in the response to nitrate signaling in tomato