Dataset Information

Whole genome sequencing and comparative transcriptome analysis of a novel seawater adapted, salt-resistant rice cultivar - sea rice 86.

ABSTRACT: Rice (Oryza sativa) is critical for human nutrition worldwide. Due to a growing population, cultivars that produce high yields in high salinity soil are of major importance. Here we describe the discovery and molecular characterization of a novel sea water adapted rice strain, Sea Rice 86 (SR86).SR86 can produce nutritious grains when grown in high salinity soil. Compared to a salt resistant rice cultivar, Yanfen 47 (YF47), SR86 grows in environments with up to 3X the salt content, and produces grains with significantly higher nutrient content in 12 measured components, including 2.9X calcium and 20X dietary fiber. Whole genome sequencing demonstrated that SR86 is a relatively ancient indica subspecies, phylogenetically close to the divergence point of the major rice varietals. SR86 has 12 chromosomes with a total genome size of 373,130,791 bps, slightly smaller than other sequenced rice genomes. Via comparison with 3000 rice genomes, we identified 42,359 putative unique, high impact variants in SR86. Transcriptome analysis of SR86 grown under normal and high saline conditions identified a large number of differentially expressed and salt-induced genes. Many of those genes fall into several gene families that have established or suggested roles in salt tolerance, while others represent potentially novel mediators of salt adaptation.Whole genome sequencing and transcriptome analysis of SR86 has laid a foundation for further molecular characterization of several desirable traits in this novel rice cultivar. A number of candidate genes related to salt adaptation identified in this study will be valuable for further functional investigation.

SUBMITTER: Chen R

PROVIDER: S-EPMC5569538 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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Whole genome sequencing and comparative transcriptome analysis of a novel seawater adapted, salt-resistant rice cultivar - sea rice 86.

Chen Risheng R Cheng Yunfeng Y Han Suying S Van Handel Ben B Dong Ling L Li Xinmin X Xie Xiaoqing X

BMC genomics 20170823 1

<h4>Background</h4>Rice (Oryza sativa) is critical for human nutrition worldwide. Due to a growing population, cultivars that produce high yields in high salinity soil are of major importance. Here we describe the discovery and molecular characterization of a novel sea water adapted rice strain, Sea Rice 86 (SR86).<h4>Results</h4>SR86 can produce nutritious grains when grown in high salinity soil. Compared to a salt resistant rice cultivar, Yanfen 47 (YF47), SR86 grows in environments with up to ...[more]

PMID: 28835208

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Project description:BackgroundSerotonin, originally identified as a neurotransmitter in mammals, functions as an antioxidant to scavenge cellular ROS in plants. In rice, the conversion of tryptamine to serotonin is catalyzed by SL (sekiguchi lesion), a member of cytochrome P450 monooxygenase family. The sl mutant, originated from rice cultivar Sekiguchi-asahi, exhibits spontaneous lesions, whereas its immune responses to pathogens have not been clearly characterized.ResultsHere we identified three allelic mutants of SL in an indica rice restore line Minghui 86 (MH86), named as sl-MH-1, - 2 and - 3, all of which present the typical lesions under normal growth condition. Compared with those in MH86, the serotonin content in sl-MH-1 is dramatically decreased, whereas the levels of tryptamine and L-trytophan are significantly increased. The sl-MH-1 mutant accumulates high H2O2 level at its lesion sites and is more sensitive to exogenous H2O2 treatment than the wild type. When treated with the reductant vitamin C (Vc), the lesion formation on sl-MH-1 leaves could be efficiently suppressed. In addition, sl-MH-1 displayed more resistant to both the blast fungus and blight bacteria, Pyricularia oryzae (P. oryzae, teleomorph: Magnaporthe oryzae) and Xanthomonas oryzae pv. Oryzae (Xoo), respectively. The pathogen-associated molecular patterns (PAMPs)-triggered immunity (PTI) responses, like reactive oxygen species (ROS) burst and callose deposition, were enhanced in sl-MH-1. Moreover, loss function of SL resulted in higher resting levels of the defense hormones, salicylic acid and jasmonic acid. The RNA-seq analysis indicated that after P. oryzae infection, transcription of the genes involved in reduction-oxidation regulation was the most markedly changed in sl-MH-1, compared with MH86.ConclusionsOur results indicate that SL, involving in the final step of serotonin biosynthesis, negatively regulates rice resistance against (hemi)biotrophic pathogens via compromising the PTI responses and defense hormones accumulation.

Project description:Natural water certified reference materials (CRMs) are mostly available in a liquid form, and they are produced starting from suitable environmental samples. Many precautions are usually needed to avoid biological or physical degradation, including filtration, acidification, and sterilization. In this study, the drawbacks associated with liquid-based seawater CRMs were tackled by developing a salt-based seawater proxy for nutrients that could be reconstituted in water solution just before use. Phosphate, silicate, and nitrate were chosen as target analytes. Sea salt mimicking the composition of seawater was spiked with an aqueous solution of the analytes and homogenized using a high-energy planetary ball mill (uhom < 1.2%). The salt powder CRM SALT-1 ( https://doi.org/10.4224/crm.2022.salt-1 ) demonstrated good short- and long-term stability for nutrients. When the SALT-1 was reconstituted in water at the 4.0% w/w level, the resulting solution had similar properties with respect to typical seawater in terms of major constituents (± 20%), trace metals, density (1.023 g/mL), pH (8.8-9.0), and optical properties relevant to the photometric characterization. Phosphate and silicate were quantified by photometry (molybdenum blue method, batch mode), whereas nitrate was quantified by isotope dilution GC-MS (uchar < 1.2%). In the SALT-1 reconstituted seawater solution at the 4.0% w/w salt level, the nutrient amount concentration was w(phosphate, PO43-) = 1.615 ± 0.030 μmol/L, w(silicate as SiO2) = 8.89 ± 0.31 μmol/L, and w(nitrate, NO3-) = 18.98 ± 0.45 μmol/L at the 95% confidence (k = 2). Overall, the SALT-1 CRM exhibits similar nutrient profile and general analytical characteristics as the MOOS-3 CRM. However, the SALT-1 has much reduced preparation, storage, and distribution cost, likely much better long-term stability, and it could enable the production of lower cost and more accessible seawater reference materials.

Dataset Information

Whole genome sequencing and comparative transcriptome analysis of a novel seawater adapted, salt-resistant rice cultivar - sea rice 86.

Publications

Whole genome sequencing and comparative transcriptome analysis of a novel seawater adapted, salt-resistant rice cultivar - sea rice 86.

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