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

BACKGROUND: 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 8...

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Autores principales: Chen, Risheng, Cheng, Yunfeng, Han, Suying, Van Handel, Ben, Dong, Ling, Li, Xinmin, Xie, Xiaoqing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5569538/
https://www.ncbi.nlm.nih.gov/pubmed/28835208
http://dx.doi.org/10.1186/s12864-017-4037-3
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author Chen, Risheng
Cheng, Yunfeng
Han, Suying
Van Handel, Ben
Dong, Ling
Li, Xinmin
Xie, Xiaoqing
author_facet Chen, Risheng
Cheng, Yunfeng
Han, Suying
Van Handel, Ben
Dong, Ling
Li, Xinmin
Xie, Xiaoqing
author_sort Chen, Risheng
collection PubMed
description BACKGROUND: 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). RESULTS: 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. CONCLUSIONS: 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-4037-3) contains supplementary material, which is available to authorized users.
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spelling pubmed-55695382017-08-29 Whole genome sequencing and comparative transcriptome analysis of a novel seawater adapted, salt-resistant rice cultivar – sea rice 86 Chen, Risheng Cheng, Yunfeng Han, Suying Van Handel, Ben Dong, Ling Li, Xinmin Xie, Xiaoqing BMC Genomics Research Article BACKGROUND: 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). RESULTS: 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. CONCLUSIONS: 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-4037-3) contains supplementary material, which is available to authorized users. BioMed Central 2017-08-23 /pmc/articles/PMC5569538/ /pubmed/28835208 http://dx.doi.org/10.1186/s12864-017-4037-3 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Chen, Risheng
Cheng, Yunfeng
Han, Suying
Van Handel, Ben
Dong, Ling
Li, Xinmin
Xie, Xiaoqing
Whole genome sequencing and comparative transcriptome analysis of a novel seawater adapted, salt-resistant rice cultivar – sea rice 86
title Whole genome sequencing and comparative transcriptome analysis of a novel seawater adapted, salt-resistant rice cultivar – sea rice 86
title_full Whole genome sequencing and comparative transcriptome analysis of a novel seawater adapted, salt-resistant rice cultivar – sea rice 86
title_fullStr Whole genome sequencing and comparative transcriptome analysis of a novel seawater adapted, salt-resistant rice cultivar – sea rice 86
title_full_unstemmed Whole genome sequencing and comparative transcriptome analysis of a novel seawater adapted, salt-resistant rice cultivar – sea rice 86
title_short Whole genome sequencing and comparative transcriptome analysis of a novel seawater adapted, salt-resistant rice cultivar – sea rice 86
title_sort whole genome sequencing and comparative transcriptome analysis of a novel seawater adapted, salt-resistant rice cultivar – sea rice 86
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5569538/
https://www.ncbi.nlm.nih.gov/pubmed/28835208
http://dx.doi.org/10.1186/s12864-017-4037-3
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