Title: Genome-Wide Survey and Expression Analysis of NIN-Like Protein (NLP) Genes Reveals Its Potential Roles in the Response to Nutrition Deficiency in Tomato

Background: Tomato ( Solanum lycopersicum ) is one of the most important horticultural crops, with a marked preference of nitrate as 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 revealed six NLP members in tomato genome. They were clustered into three clades in a phylogenic tree. Comparative genomic analysis showed that SlNLP genes had 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 tomato genome. Tissue-specific expression analysis showed that the close homologues of AtNLP6/7 , SlNLP3 , was strongly expressed in roots during both seedling and flowering stages; SlNLP4 and SlNLP6 exhibited preferential expression in stems and leaves; and SlNLP6 were expressed in high levels in fruits. Further, the nitrate uptake in tomato roots and expression patterns of SlNLP genes were measured under nitrogen/phosphate/potassium deficiency and nitrate resupply conditions. The transcript abundance of SlNLP3 decreased to 70% under phosphate/potassium deficiency. Most of SlNLPs were up-regulated after nitrogen starvation. SlNLP1 and SlNLP5 were induced rapidly and temporally by nitrate. Conclusions: These results provided significant insights into the potential diverse functions of SlNLPs to regulate nitrate uptake.