Genome wide analysis of NLP transcription factors reveals their role in nitrogen stress tolerance of rice

Abstract

The NIN-LIKE PROTEIN (NLP) family of transcription factors were identified as nitrate-responsive ciselement (NRE)-binding proteins, which function as transcriptional activators in the nitrate-regulated expression of downstream genes. this study was aimed at genome-wide analysis of NLP gene family in rice and the expression profiling of NLPs in response to nitrogen (N) supply and deficiency in rice genotypes with contrasting N use efficiency (NUE). Based on in silico analysis, 6 NLP genes (including alternative splice forms 11 NLPs) were identified from rice. Expression of NLPs was promoted by nitrate supply as well as N deficiency (NLP1, NLP3, NLP4 and NLP5). Four rice genotypes APO (high NUE under sufficient N), IR83929-B-B-291-3-1-1 (IR-3-1-1), Nerica-L-42 (NL-42) (High NUE at low N), and Pusa Basmati 1 (PB1, low NUE) to correlate traits governing NUE and expression of NLPs. Analysis of rate of nitrate uptake and expression of N assimilatory and uptake genes established that IR-3-1-1 has high uptake and assimilation efficiency, translating into high NUE, whereas PB1 is efficient in uptake only when N availability is high. Along with the transcriptional upregulation of NLPs, genotype IR-3-1-1, displayed highest expression of OsNRT1.1B gene, the closest rice homologue of nitrate transceptor AtNRT1.1 and plays major role in nitrate uptake, translocation and signaling in rice. The results showed that high NUE rice genotypes has both high Nitrogen uptake efficiency (NUpE) and Nitrogen utilization efficiency (NUtE), resulting from the effective and coordinated signal transduction network involving the rice homologue of nitrate transceptor OsNRT1.1B, the probable primary nitrate response (PNR) regulator OsNLP1 and the master response regulator OsNLP3, a homologue of AtNLP6/7. Nitrogen (N) is an essential nutrient and major component of proteins, chlorophyll, nucleotides and plant hormones, and therefore has immense role in determining plant growth and economic yield 1,2. In order to meet the food demand of ever-growing human population, enormous amounts of N fertilizers are applied inorder to tap the maximum crop yield potential worldwide 3. The global demand for N fertilizers in 2014 was 1.13 M tonnes and is projected to grow at approximately 1.4% per year, reaching 1.22 M tonnes by 2020 4. On the other hand, around 50% of the applied N fertilizer is lost to the environment depending on the cropping conditions and plant species. The loss of fertilizer N results in contamination of soil water and water bodies and production of nitrogenous greenhouse gases like nitrous oxide (N 2 O) which has high global warming potential 5. Nitrogen use efficiency (NUE) of rice is particularly low (around 40%), though genetic variation for the trait has been reported 6. Consequently, there is an impending requirement to improve the NUE of rice to maintain the steadiness of high crop yields visa vis low N fertilizer inputs 7. Transgenic manipulation is one of the potent way to achieve the current demand for high NUE, which necessitates...

Rice NIN‐LIKE PROTEIN 4 plays a pivotal role in nitrogen use efficiency

“…According to the publicly available transcriptome data (Hruz et al ., 2008; Jagadhesan et al ., 2020), rice NLPs are expressed in almost all organs, with OsNLP1 and OsNLP3 preferentially expressed in source organs, and OsNLP6 expressed at very low level. Different from the other 5 OsNLPs , expression of OsNLP4 is repressed by many abiotic stresses and induced by low phosphate availability (Chardin et al ., 2014).…”

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

“…In Arabidopsis, nlp7 mutants show features of a nitrogen-starved plant (Castaings et al, 2009); AtNLP7 overexpression increases plant biomass under both nitrogen-poor and -rich conditions (Yu et al, 2016). Expression of rice NLPs (OsNLP1, OsNLP4 and OsNLP5) was promoted by nitrogen de ciency as well as nitrate supply (Jagadhesan et al, 2020). Overexpression of OsNLP1 could enhance rice nitrogen use e ciency (Alfatih et al, 2020).…”

Genetic analysis of rice seedling traits related to machine transplanting under different seeding densities

“…This region was found to contain ve putative genes, two of them were involved in auxin (LOC_Os01g13520) [63,64] and ABA (LOC_Os01g13530) [65] signals. NLP3 (LOC_Os01g13540) played a major role in nitrate uptake, translocation and signaling in rice root [66]. Both LOC_Os01g13570 [67] and LOC_Os01g13740 [68] participated in abiotic stress response.…”