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Comparative Morphophysiological Analyses and Molecular Profiling Reveal ‘Pi-Efficient Strategies’ of a Traditional Rice Genotypefor Low Phosphorus Tolerance in Traditional indica Rice

ABSTRACT: Phosphate (Pi) deficiency severely affects crop yield. Modern high yielding rice genotypes are sensitive to Pi deficiency whereas traditional rice cultivars are naturally compatible to low Pi ecosystems. However, the underlying molecular mechanisms for low Pi tolerance in traditional genotypes remain largely elusive. To delineate the molecular mechanisms for low Pi tolerance, two contrasting rice genotypes - Dular (low Pi tolerant) and PB1 (low Pi sensitive) - have been selected. Comparative morphophysiological, global transcriptome and lipidome analyses of root and shoot tissues of both genotypes raised under Pi deficient and sufficient conditions revealed the potential low Pi tolerance mechanisms of traditional genotype. Most of the genes associated with enhanced internal Pi utilization (phospholipid remobilization) and modulation of root system architecture (RSA) are highly induced in traditional rice genotype, Dular. Higher reserve of phospholipid and greater accumulation of galactolipids under low Pi in Dular indicated its better internal Pi utilization. Furthermore, Dular also maintained better root growth than PB1 under low Pi resulting in larger root surface area due to increased lateral root density and root hair length. Genes involved in enhanced low Pi tolerance of traditional genotype can be exploited to improve the low Pi tolerance of modern high yielding rice cultivars.

ORGANISM(S): Oryza sativa

PROVIDER: GSE74795 | GEO | 2016/01/29

SECONDARY ACCESSION(S): PRJNA301556

REPOSITORIES: GEO

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Project description:Rice has developed several morphological and physiological strategies to adapt to phosphate starvation stress. In order to elucidate the molecular bases of response due to phosphate stress particularly the transcriptional profile of genotypes with variation in tolerance to phosphate starvation, we analyzed the gene expression profiles of 3 japonica rice cultivars and an indica cultivar with different levels of tolerance to phosphate starvation using the RNA-Seq method. We constructed a total of 48 libraries corresponding to root and shoot of the 4 cultivars for control (0 d) and âP treatment (22 d) with three biological replicates for root and shoot samples in each cultivar. Approximately 254 million sequenced tags were mapped onto the reference rice genome sequence (IRGSP1.0) and an average of about 5,000 transcripts in each genotype were found to be responsive to Pi-starvation. Comparative analysis of the responsive transcripts revealed an overall similarity in the transcriptome signatures resulting from phosphate starvation as well as distinct differences that distinguish the degree of tolerance among the 4 cultivars. We elucidated a set of core responsive transcripts commonly expressed in both root and shoot with different levels of expression reflecting variation as well genotype specificity in tolerance to Pi-starvation. De novo assembly of unmapped reads generated a large set of sequence assemblies that represent potential new transcripts that may be involved in tolerance to phosphate deficiency. Characterization of 88 assemblies unaligned in the reference genome revealed several dozen transcripts which correspond to plant ESTs. This study provides an overview of the diversity in response to P-starvation stress that can be used to identify the major genes for improving Pi acquisition and utilization in rice and other cereal crops. Note: Samples in DRA were assigned the same sample accession. This is incorrect as there are different samples, hence âSource Nameâ was replaced with new values. Comment[ENA_SAMPLE] contains the original DRA sample accessions.

Project description:Purpose: Rice (Oryza sativa) ssp. indica is the most cultivated species in the South of Brazil. However, these plants face low temperature stress from September to November, which is the period of early sowing, affecting plant development during the initial stages of growth, and reducing rice productivity. This study aimed to characterize the roots of two rice genotypes (CT, cold-tolerant; and CS, cold-sensitive) in response to low temperature stress during the early vegetative stage. Results: RNAseq analysis revealed that contrasting genotypes present a completely different molecular response to cold stress. The number of over-represented functional categories was lower in CT than CS under cold condition, suggesting that CS genotype is more impacted by low temperature stress than CT. Several genes that might contribute to rice cold tolerance, including the ones related with cell wall remodeling (glycosyl hydrolase, cellulose synthase, glycosyl transferase, wall-associated kinase, glycine-rich cell wall structural protein), cytoskeleton and growth (microtubule-associated protein 70, kinesin motor domain containing protein, growth regulating factor protein, auxin-independent growth promoter protein, RopGEF7), signaling (receptor-like protein kinase, Rapid Alkalinization Factor 21)), antioxidant system (glutathione peroxidase, metallothionein), lipid metabolism (fatty acid desaturase and phosphatidylinositol transfer protein), and stress response (Tetratricopeptide Repeat-Containing Protein). On the other hand, high expression of the genes SRC2 (defense), root architecture associated 1 (growth), ACC oxidase, ethylene-responsive transcription factor, and cytokinin-O-glucosyltransferase 2 (hormone-related) seems to be related with cold sensibility. Even though these two genotypes have a similar genetic background (sister lines), some of these genes can probably be involved with cold tolerance or sensitivity and could be used in future biotechnological approaches aiming to increase rice tolerance to low temperature.

Dataset Information

Comparative Morphophysiological Analyses and Molecular Profiling Reveal ‘Pi-Efficient Strategies’ of a Traditional Rice Genotypefor Low Phosphorus Tolerance in Traditional indica Rice

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