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Root transcriptomes of two acidic soil adapted Indica rice genotypes suggest diverse and complex mechanism of low phosphorus tolerance

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Abstract

Low phosphorus (P) tolerance in rice is a biologically and agronomically important character. Low P tolerant Indica-type rice genotypes, Sahbhagi Dhan (SD) and Chakhao Poreiton (CP), are adapted to acidic soils and show variable response to low P levels. Using RNAseq approach, transcriptome data was generated from roots of SD and CP after 15 days of low P treatment to understand differences and similarities at molecular level. In response to low P, number of genes up-regulated (1318) was more when compared with down-regulated genes (761). Eight hundred twenty-one genes found to be significantly regulated between SD and CP in response to low P. De novo assembly using plant database led to further identification of 1535 novel transcripts. Functional annotation of significantly expressed genes suggests two distinct methods of low P tolerance. While root system architecture in SD works through serine-threonine kinase PSTOL1, suberin-mediated cell wall modification seems to be key in CP. The transcription data indicated that CP relies more on releasing its internally bound Pi and coping with low P levels by transcriptional and translational modifications and using dehydration response-based signals. Role of P transporters seems to be vital in response to low P in CP while sugar- and auxin-mediated pathway seems to be preferred in SD. At least six small RNA clusters overlap with transcripts highly expressed under low P, suggesting role of RNA super clusters in nutrient response in plants. These results help us to understand and thereby devise better strategy to enhance low P tolerance in Indica-type rice.

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Acknowledgments

This work was supported by grant from Indian Council of Agricultural Research, National Agricultural Innovative Project [C30033/415101-036 to W.T.]. We are grateful to Drs. T. Mohapatra and A.K. Singh, NAIP, for helpful suggestions during initial design of the experiment and for sharing of seeds of SD, respectively. We are also grateful to Dr. P. Dasaradhi for fruitful discussions. Julia S. Yumnam and Aibanshan K. Dohling are acknowledged for technical assistance.

Note: The RNAseq data reported are available in NCBI sequence read archive under the accession number SRP058964 (PRJNA285664).

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Authors and Affiliations

  1. School of Crop Improvement, College of Post-Graduate Studies, Central Agricultural University (Imphal), Umroi Road, Umiam, Meghalaya, 793103, India

    Wricha Tyagi & Mayank Rai

Authors
  1. Wricha Tyagi
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  2. Mayank Rai
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Correspondence to Wricha Tyagi.

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Handling Editor: Bhumi Nath Tripathi

Supplementary materials

Below is the link to the electronic supplementary material.

Figure S1

Experimental design and bioinformatics flow. (PPT 168 kb)

Figure S2

cDNA library bioanalyzer profile on high sensitivity chip of the four samples. (PPT 422 kb)

Figure S3

Venn diagram showing the number of genes expressed under different conditions in SD (a) and CP (b). Venn diagrams display the overlap between expressed genes in roots following treatment with low P (green circles, right) compared with control (peach circles, left). The total gene count for each category is shown within each circle. (PPT 186 kb)

Figure S4

Volcano plot showing significantly different genes between the two genotypes, SD and CP. (PPT 126 kb)

Figure S5

K-means clustering of differentially expressed genes under low P conditions into five distinct clusters. (PPT 142 kb)

Figure S6

Global overview and hierarchical clustering of Sahbhagi Dhan (SD) and Chakhao Poreiton (CP) transcriptional changes. Mean expression versus log fold change plots (MA-plots) were computed for significantly expressed transcripts in SD and CP; normalized expression mean values are plotted versus log2 fold changes and called DEGs (FDR<0.05) are plotted in red. Bar at the top represents log2 transformed values, thereby values 0, 40 and 200 represent low, intermediate and high expression, respectively (PPT 388 kb)

Figure S7

Selected genomic origins showing target for small RNAs. The potential target transcript is written at the right side of each snapshot with locus ID (LOC_). The number of individual clusters within a region is indicated on top of the line. (PPT 244 kb)

Table S1

List of transcripts differentially regulated in SD and CP under low P conditions. (XLS 640 kb)

Table S2

List of GOSlim term assignment to SD and CP transcripts in different categories of biological process under control (C; normal P levels) and treatment conditions (T; low P levels). (XLS 204 kb)

Table S3

The mapping statistics of SD and CP treated samples on Kasalath BAC clones. (DOC 26 kb)

Table S4

Denovo assembly of unused reads for genotype, SD. (XLS 2104 kb)

Table S5

Denovo assembly of unused reads for genotype, CP. (XLS 7542 kb)

Table S6

List of functionally annotated transcripts based on denovo assembly. (XLS 240 kb)

Table S7

List and functional annotation of highly upregulated transcripts under low P conditions in genotypes, SD and CP. (XLS 33 kb)

Table S8

Log2 fold expression of putative copper oxidase transcripts under low P conditions in genotypes, SD and CP. (XLS 185 kb)

Table S9

List of cis-acting elements. (TXT 1 kb)

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Tyagi, W., Rai, M. Root transcriptomes of two acidic soil adapted Indica rice genotypes suggest diverse and complex mechanism of low phosphorus tolerance. Protoplasma 254, 725–736 (2017). https://doi.org/10.1007/s00709-016-0986-7

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