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

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Abstract

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.

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Acknowledgments

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).

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  1. Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtse River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China

    Hongmei Cai

  2. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China

    Weibo Xie & Xingming Lian

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  1. Hongmei Cai
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Correspondence to Hongmei Cai.

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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)

High resolution image (TIFF 548 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)

High resolution image (TIFF 1351 kb)

Supplementary Table S1

GO enrichments both for N (-N) and P (-P) starvation after 1 h treatment. (DOC 175 kb)

Supplementary Table S2

GO enrichments both for N (-N) and P (-P) starvation after 24 h treatment. (DOC 73 kb)

Supplementary Table S3

GO enrichments both for N (−N) and P (−P) starvation after 7 days treatment. (DOC 173 kb)

Supplementary Table S4

GO enrichments for N starvation only after 1 h treatment. (DOC 268 kb)

Supplementary Table S5

GO enrichments for N starvation only after 24 h treatment. (DOC 212 kb)

Supplementary Table S6

GO enrichments for N starvation only after 7 days treatment. (DOC 250 kb)

Supplementary Table S7

GO enrichments for P starvation only after 1 h treatment. (DOC 126 kb)

Supplementary Table S8

GO enrichments for P starvation only after 24 h treatment. (DOC 146 kb)

Supplementary Table S9

GO enrichments for P starvation only after 7 day treatment. (DOC 167 kb)

Supplementary Table S10

Significantly changed genes related to molecular transport under N starvation (−N) and P starvation (−P) conditions. (DOC 218 kb)

Supplementary Table S11

Significantly changed genes involved in molecular metabolism under N starvation (−N) and P starvation (−P) conditions. (DOC 547 kb)

Supplementary Table S12

Significantly changed genes involved in regulation and modification under N starvation (−N) and P starvation (−P) conditions. (DOC 856 kb)

Supplementary Table S13

Significantly changed genes related to organism development under N starvation (−N) and P starvation (−P) conditions. (DOC 243 kb)

Supplementary Table S14

Significantly changed genes response to stress stimuli under N starvation (−N) and P starvation (−P) conditions. (DOC 363 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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Cai, H., Xie, W. & Lian, X. Comparative Analysis of Differentially Expressed Genes in Rice Under Nitrogen and Phosphorus Starvation Stress Conditions. Plant Mol Biol Rep 31, 160–173 (2013). https://doi.org/10.1007/s11105-012-0485-8

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