Transcriptome analysis of phosphorus stress responsiveness in the seedlings of Dongxiang wild rice (Oryza rufipogon Griff.)

Abstract

BackgroundLow phosphorus availability is a major factor restricting rice growth. Dongxiang wild rice (Oryza rufipogon Griff.) has many useful genes lacking in cultivated rice, including stress resistance to phosphorus deficiency, cold, salt and drought, which is considered to be a precious germplasm resource for rice breeding. However, the molecular mechanism of regulation of phosphorus deficiency tolerance is not clear.ResultsIn this study, cDNA libraries were constructed from the leaf and root tissues of phosphorus stressed and untreated Dongxiang wild rice seedlings, and transcriptome sequencing was performed with the goal of elucidating the molecular mechanisms involved in phosphorus stress response. The results indicated that 1184 transcripts were differentially expressed in the leaves (323 up-regulated and 861 down-regulated) and 986 transcripts were differentially expressed in the roots (756 up-regulated and 230 down-regulated). 43 genes were up-regulated both in leaves and roots, 38 genes were up-regulated in roots but down-regulated in leaves, and only 2 genes were down-regulated in roots but up-regulated in leaves. Among these differentially expressed genes, the detection of many transcription factors and functional genes demonstrated that multiple regulatory pathways were involved in phosphorus deficiency tolerance. Meanwhile, the differentially expressed genes were also annotated with gene ontology terms and key pathways via functional classification and Kyoto Encyclopedia of Gene and Genomes pathway mapping, respectively. A set of the most important candidate genes was then identified by combining the differentially expressed genes found in the present study with previously identified phosphorus deficiency tolerance quantitative trait loci.ConclusionThe present work provides abundant genomic information for functional dissection of the phosphorus deficiency resistance of Dongxiang wild rice, which will be help to understand the biological regulatory mechanisms of phosphorus deficiency tolerance in Dongxiang wild rice.Electronic supplementary materialThe online version of this article (10.1186/s40659-018-0155-x) contains supplementary material, which is available to authorized users.

Identification of phosphorus stress related proteins in the seedlings of Dongxiang wild rice (Oryza rufipogon Griff.) using label-free quantitative proteomic analysis

“…The surface sterilized seeds were rst soaked in petri dishes containing 20 mL deionized water at room temperature for 3 days. Then the seeds were selected with same growth and planted in the plastic pot in a climate control chamber at day/night 14 h/10 h (30℃/26℃) [18]. Germinated seeds with coleoptiles 10 mm approximately in length, adding Yoshida culture medium (pH5.8) [46].…”

“…found in the northernmost distribution latitude to date, which is a unique wild plant resource in Jiangxi Province. Because DXWR grows in the wild for a long time and suffers from various adverse environmental choices, it has more abundant genetic diversity than cultivated rice, and contains a large number of excellent genes that are not or have been lost in cultivated rice, including low-P resistance [15,16,17,18].…”

“…In order to understand the molecular mechanism related to low-P resistance of DXWR, transcriptome analysis of low-P stress responsiveness in the seedlings of DXWR have been completed [18]. In this study, a proteomic approach involving liquid chromatography and tandem mass spectrometry was conducted to root samples to identify potential unique low-P response genes in DXWR during seedlings.…”

Transcriptome Analysis for Abiotic Stresses in Rice (Oryza sativa L.)

“…Phosphorus (P) is an essential trace element required for proper plant growth and development where it plays an important role in energy transfer, signal transduction, photosynthesis, and respiration [77]. A comparative transcriptome study has been carried out in leaf and root tissues during phosphorus stress to elucidate their molecular mechanisms [78]. The transcriptome analysis suggested that many differentially expressed TFs and functional genes were uniquely involved in multiple regulatory pathways (including RNA transport and mRNA monitoring path) during phosphorus deficiency tolerance [78].…”

“…A comparative transcriptome study has been carried out in leaf and root tissues during phosphorus stress to elucidate their molecular mechanisms [78]. The transcriptome analysis suggested that many differentially expressed TFs and functional genes were uniquely involved in multiple regulatory pathways (including RNA transport and mRNA monitoring path) during phosphorus deficiency tolerance [78].…”