Abstract
The NIN-LIKE PROTEIN (NLP) family of transcription factors were identified as nitrate-responsive cis-element (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.
Highlights
Nitrogen (N) is an essential nutrient and major component of proteins, chlorophyll, nucleotides and plant hormones, and has immense role in determining plant growth and economic yield[1,2]
To correlate the role of NODULE INCEPTION (NIN)-LIKE PROTEIN (NLP) in governing N use efficiency (NUE) of rice, we used four rice genotypes identified based on previous lab studies
Varietal means of Nitrogen utilization efficiency (NUtE) (Fig. 1b) were significantly different as indicated by Sidak’s multiple comparisons test: with respect to N + treatment N- treatment means decreased by 46% and 5.6% in APO and PB1 whereas increased by 36% and 34% in IR-3-1-1 and NL-42 respectively
Summary
Nitrogen (N) is an essential nutrient and major component of proteins, chlorophyll, nucleotides and plant hormones, and has immense role in determining plant growth and economic yield[1,2]. There is an impending requirement to improve the NUE of rice to maintain the steadiness of high crop yields vis-a vis low N fertilizer inputs[7]. Several studies enhanced the comprehensive understanding on nitrate signalling and its role in the regulation of N uptake and assimilation[16,17]. 50 transcription factor encoding genes including NLP7 were targeted by nitrate-CPK module[21]. These findings clearly points out that manoeuvring Ca2+- CPK–NLP signalling cascade is an efficient strategy for improving the NUE22. Aerobic rice soils have a ratio of 6.5:1 of nitrate and ammonical N25, indicating a significant role of understanding nitrate signaling for improving rice NUE in drought prone agriculture situations. We hypothesize that differential expression of NLPs may have regulatory role in NUE of contrasting rice genotypes
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