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RNA-Seq and validation analysis on the important genes involved in early responses to salinity stress of Malaysian rice seedlings (Oryza sativa ssp. Indica)

Salinization of rice cultivation land has progressively enlarged, thus negatively impaired the world's rice bowl. Due to the polygenic nature and complexity of salinity tolerance mechanisms in plants, the development of new rice varieties with better adaptation to salinity has become a great ch...

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Main Authors: Juri, Nor Mustaiqazah, Abu Bakar, Norliza, Zainal Abidin, Rabiatul Adawiah, Mahmood, Maziah, Saidi, Noor Baity, Awang, Yahya, Shaharuddin, Noor Azmi
Format: Article
Language:English
Published: Smith and Franklin Academic Publishing 2019
Online Access:http://psasir.upm.edu.my/id/eprint/82035/1/RNA-Seq%20and%20validation%20analysis%20on%20the%20important%20genes%20involved%20in%20early%20responses%20to%20salinity%20stress%20of%20Malaysian%20rice%20seedlings%20%28Oryza%20sativa%20ssp.%20Indica%29.pdf
http://psasir.upm.edu.my/id/eprint/82035/
https://www.cabdirect.org/cabdirect/abstract/20203271303
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spelling my.upm.eprints.820352021-09-08T00:57:41Z http://psasir.upm.edu.my/id/eprint/82035/ RNA-Seq and validation analysis on the important genes involved in early responses to salinity stress of Malaysian rice seedlings (Oryza sativa ssp. Indica) Juri, Nor Mustaiqazah Abu Bakar, Norliza Zainal Abidin, Rabiatul Adawiah Mahmood, Maziah Saidi, Noor Baity Awang, Yahya Shaharuddin, Noor Azmi Salinization of rice cultivation land has progressively enlarged, thus negatively impaired the world's rice bowl. Due to the polygenic nature and complexity of salinity tolerance mechanisms in plants, the development of new rice varieties with better adaptation to salinity has become a great challenge. Regarding this, transcriptomic profiling has been seen as a promising approach for a holistic understanding of salinity tolerance mechanisms in rice. Using Illumina RNA-Seq method, transcriptomes of two contrasting Malaysian rice varieties named as salt-tolerant MR211 and salt-sensitive MR220 were analysed within a short-term exposure (9 h) to salt-shock treatment (12 dS m-1) at early seedling stage. Transcriptomic analysis using Tuxedo package enabled the identification of 252 differentially expressed genes (DEGs). Interestingly, 93.3% of the DEGs (n=235) were identified as higher and specifically expressed in salt-tolerant MR211 compared to the sensitive variety (MR220's FPKM ≤ 0). This group of DEGs was assigned in 33 KEGG pathways, with the highest number of transcripts accounted in purine and thiamine metabolism pathways. Meanwhile, functional annotation analyses revealed the presence of regulatory genes, annotated functional and unknown genes involved in various salt adaptation mechanisms in the salt-tolerant variety MR211. The expression accuracy and reproducibility of the 252 DEGs identified from the RNA-Seq experiment were further verified through semi-quantitative RT-PCR followed by real time PCR analysis. Smith and Franklin Academic Publishing 2019 Article PeerReviewed text en http://psasir.upm.edu.my/id/eprint/82035/1/RNA-Seq%20and%20validation%20analysis%20on%20the%20important%20genes%20involved%20in%20early%20responses%20to%20salinity%20stress%20of%20Malaysian%20rice%20seedlings%20%28Oryza%20sativa%20ssp.%20Indica%29.pdf Juri, Nor Mustaiqazah and Abu Bakar, Norliza and Zainal Abidin, Rabiatul Adawiah and Mahmood, Maziah and Saidi, Noor Baity and Awang, Yahya and Shaharuddin, Noor Azmi (2019) RNA-Seq and validation analysis on the important genes involved in early responses to salinity stress of Malaysian rice seedlings (Oryza sativa ssp. Indica). International Journal of Agriculture and Biology, 22 (6). pp. 1681-1696. ISSN 1560–8530; ISSN: 1814–9596 https://www.cabdirect.org/cabdirect/abstract/20203271303 10.17957/IJAB/15.1250
institution Universiti Putra Malaysia
building UPM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Putra Malaysia
content_source UPM Institutional Repository
url_provider http://psasir.upm.edu.my/
language English
description Salinization of rice cultivation land has progressively enlarged, thus negatively impaired the world's rice bowl. Due to the polygenic nature and complexity of salinity tolerance mechanisms in plants, the development of new rice varieties with better adaptation to salinity has become a great challenge. Regarding this, transcriptomic profiling has been seen as a promising approach for a holistic understanding of salinity tolerance mechanisms in rice. Using Illumina RNA-Seq method, transcriptomes of two contrasting Malaysian rice varieties named as salt-tolerant MR211 and salt-sensitive MR220 were analysed within a short-term exposure (9 h) to salt-shock treatment (12 dS m-1) at early seedling stage. Transcriptomic analysis using Tuxedo package enabled the identification of 252 differentially expressed genes (DEGs). Interestingly, 93.3% of the DEGs (n=235) were identified as higher and specifically expressed in salt-tolerant MR211 compared to the sensitive variety (MR220's FPKM ≤ 0). This group of DEGs was assigned in 33 KEGG pathways, with the highest number of transcripts accounted in purine and thiamine metabolism pathways. Meanwhile, functional annotation analyses revealed the presence of regulatory genes, annotated functional and unknown genes involved in various salt adaptation mechanisms in the salt-tolerant variety MR211. The expression accuracy and reproducibility of the 252 DEGs identified from the RNA-Seq experiment were further verified through semi-quantitative RT-PCR followed by real time PCR analysis.
format Article
author Juri, Nor Mustaiqazah
Abu Bakar, Norliza
Zainal Abidin, Rabiatul Adawiah
Mahmood, Maziah
Saidi, Noor Baity
Awang, Yahya
Shaharuddin, Noor Azmi
spellingShingle Juri, Nor Mustaiqazah
Abu Bakar, Norliza
Zainal Abidin, Rabiatul Adawiah
Mahmood, Maziah
Saidi, Noor Baity
Awang, Yahya
Shaharuddin, Noor Azmi
RNA-Seq and validation analysis on the important genes involved in early responses to salinity stress of Malaysian rice seedlings (Oryza sativa ssp. Indica)
author_facet Juri, Nor Mustaiqazah
Abu Bakar, Norliza
Zainal Abidin, Rabiatul Adawiah
Mahmood, Maziah
Saidi, Noor Baity
Awang, Yahya
Shaharuddin, Noor Azmi
author_sort Juri, Nor Mustaiqazah
title RNA-Seq and validation analysis on the important genes involved in early responses to salinity stress of Malaysian rice seedlings (Oryza sativa ssp. Indica)
title_short RNA-Seq and validation analysis on the important genes involved in early responses to salinity stress of Malaysian rice seedlings (Oryza sativa ssp. Indica)
title_full RNA-Seq and validation analysis on the important genes involved in early responses to salinity stress of Malaysian rice seedlings (Oryza sativa ssp. Indica)
title_fullStr RNA-Seq and validation analysis on the important genes involved in early responses to salinity stress of Malaysian rice seedlings (Oryza sativa ssp. Indica)
title_full_unstemmed RNA-Seq and validation analysis on the important genes involved in early responses to salinity stress of Malaysian rice seedlings (Oryza sativa ssp. Indica)
title_sort rna-seq and validation analysis on the important genes involved in early responses to salinity stress of malaysian rice seedlings (oryza sativa ssp. indica)
publisher Smith and Franklin Academic Publishing
publishDate 2019
url http://psasir.upm.edu.my/id/eprint/82035/1/RNA-Seq%20and%20validation%20analysis%20on%20the%20important%20genes%20involved%20in%20early%20responses%20to%20salinity%20stress%20of%20Malaysian%20rice%20seedlings%20%28Oryza%20sativa%20ssp.%20Indica%29.pdf
http://psasir.upm.edu.my/id/eprint/82035/
https://www.cabdirect.org/cabdirect/abstract/20203271303
_version_ 1710677153208598528
score 13.211869

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