Plant Molecular Biology Reporter

, Volume 31, Issue 1, pp 160–173 | Cite as

Comparative Analysis of Differentially Expressed Genes in Rice Under Nitrogen and Phosphorus Starvation Stress Conditions

  • Hongmei Cai
  • Weibo Xie
  • Xingming Lian
Original Paper


Nitrogen (N) and phosphorus (P) are two major mineral nutrients required for plant growth and development. Deficiencies in N or P results in both morphological and molecular changes such that plants develop adaptive responses to low N or P availability. In this study, we applied the Affymetrix Rice Genome array to analyze the overlap between the differentially expressed gene response to N and P starvation conditions. The results showed that a large number of genes were expressed differentially both under N starvation conditions and under P starvation conditions, including genes encoding a sulfate transporter, Fd-glutamate synthase, peroxidases, transcription factors, kinases and cytochrome P450s. In roots, 61, 42 and 159 genes were significantly up-regulated after 1 h, 24 h and 7 days, respectively, under both N and P starvation conditions, whereas 104, 50 and 166 genes, respectively, were significantly down-regulated. In shoots, 56, 104 and 101 genes were significantly up-regulated after 1 h, 24 h and 7 days, respectively, under both N and P starvation conditions, whereas 15, 80 and 59 genes, respectively, were significantly down-regulated. Generally, these differentially expressed genes belonged primarily to six biological process categories: molecular transport, molecular metabolism, regulation and modification, organism development, stress stimuli and electron transport. Our results may indicate some common physiological and genetic mechanisms in plant responses to environmental variations.


Nitrogen Phosphorus Transcription Comparative analysis Rice 



This research was supported in part by grants from the National Natural Science Foundation of China (31000932); the Special Fund for Agro-scientific Research in the Public Interest (201003016); the Specialized Research Found for the Doctoral Program of Higher Education, the Ministry of Education of China (20100146120017).

Supplementary material

11105_2012_485_Fig4_ESM.jpg (384 kb)
Supplementary Fig. S1a,b

Clustering analysis of rice genes that exhibited differential expression in response to N or P starvation at three time points examined in either roots or shoots. a Comparative analysis of differentially expressed genes in roots at 1 h (NR1-CR1), 24 h (NR2-CR2) and 7 days (NR3-CR3) after N starvation and at 1 h (PR1-CR1), 24 h (PR2-CR2) and 7 days (PR3-CR3) after P starvation; b Comparative analysis of differentially expressed genes in shoots at 1 h (NS1-CS1), 24 h (NS2-CS2) and 7 days (NS3-CS3) after N starvation and at 1 h (PS1-CS1), 24 h (PS2-CS2) and 7 days (PS3-CS3) after P starvation. (JPEG 384 kb)

11105_2012_485_MOESM16_ESM.tif (549 kb)
High resolution image (TIFF 548 kb)
11105_2012_485_Fig5_ESM.jpg (776 kb)
Supplementary Fig. S2

Heatmap of gene ontology (GO) enrichment analyses at 1 h, 24 h and 7 days in roots (NR) and shoots (NS) under N starvation and in roots (PR) and shoots (PS) under P starvation. Significant GO categories were identified using the weight FET method (P-value < 0.05) in the topGO package and categories higher than level six (based on the GO tree structure) were selected. Then, the P-values of the GO categories were transformed to base 10 logarithms. The logarithm was reversed to minus if the GO category was significantly down-regulated. The up-regulated GO category is denoted in magenta, while down-regulated is denoted in blue. GO categories significant in both the up-regulated and down-regulated direction are not displayed in this figure. (JPEG 775 kb)

11105_2012_485_MOESM17_ESM.tiff (1.3 mb)
High resolution image (TIFF 1351 kb)
11105_2012_485_MOESM1_ESM.doc (175 kb)
Supplementary Table S1 GO enrichments both for N (-N) and P (-P) starvation after 1 h treatment. (DOC 175 kb)
11105_2012_485_MOESM2_ESM.doc (74 kb)
Supplementary Table S2 GO enrichments both for N (-N) and P (-P) starvation after 24 h treatment. (DOC 73 kb)
11105_2012_485_MOESM3_ESM.doc (173 kb)
Supplementary Table S3 GO enrichments both for N (−N) and P (−P) starvation after 7 days treatment. (DOC 173 kb)
11105_2012_485_MOESM4_ESM.doc (268 kb)
Supplementary Table S4 GO enrichments for N starvation only after 1 h treatment. (DOC 268 kb)
11105_2012_485_MOESM5_ESM.doc (212 kb)
Supplementary Table S5 GO enrichments for N starvation only after 24 h treatment. (DOC 212 kb)
11105_2012_485_MOESM6_ESM.doc (250 kb)
Supplementary Table S6 GO enrichments for N starvation only after 7 days treatment. (DOC 250 kb)
11105_2012_485_MOESM7_ESM.doc (126 kb)
Supplementary Table S7 GO enrichments for P starvation only after 1 h treatment. (DOC 126 kb)
11105_2012_485_MOESM8_ESM.doc (146 kb)
Supplementary Table S8 GO enrichments for P starvation only after 24 h treatment. (DOC 146 kb)
11105_2012_485_MOESM9_ESM.doc (167 kb)
Supplementary Table S9 GO enrichments for P starvation only after 7 day treatment. (DOC 167 kb)
11105_2012_485_MOESM10_ESM.doc (218 kb)
Supplementary Table S10 Significantly changed genes related to molecular transport under N starvation (−N) and P starvation (−P) conditions. (DOC 218 kb)
11105_2012_485_MOESM11_ESM.doc (548 kb)
Supplementary Table S11 Significantly changed genes involved in molecular metabolism under N starvation (−N) and P starvation (−P) conditions. (DOC 547 kb)
11105_2012_485_MOESM12_ESM.doc (856 kb)
Supplementary Table S12 Significantly changed genes involved in regulation and modification under N starvation (−N) and P starvation (−P) conditions. (DOC 856 kb)
11105_2012_485_MOESM13_ESM.doc (244 kb)
Supplementary Table S13 Significantly changed genes related to organism development under N starvation (−N) and P starvation (−P) conditions. (DOC 243 kb)
11105_2012_485_MOESM14_ESM.doc (363 kb)
Supplementary Table S14 Significantly changed genes response to stress stimuli under N starvation (−N) and P starvation (−P) conditions. (DOC 363 kb)
11105_2012_485_MOESM15_ESM.doc (304 kb)
Supplementary Table S15 Significantly changed genes related to electron transport under N starvation (−N) and P starvation (−P) conditions. (DOC 304 kb)


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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  1. 1.Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtse River), Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
  2. 2.National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina

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