IC4R020-RNA-Seq-2016-26752408 - Revision history

Guangyi at 14:48, 13 July 2016

2016-07-13T14:48:56Z

2016-07-11T10:50:31Z

‎Project Title

2016-07-11T10:47:20Z

‎Research Findings

2016-07-11T10:36:49Z

‎Labs working on this Project

2016-07-11T10:35:46Z

2016-07-11T10:33:16Z

2016-07-11T10:27:36Z

2016-07-11T09:06:55Z

‎Research Findings

2016-07-11T08:59:19Z

2016-07-11T08:37:54Z

‎The Background of This Project

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 ==Plant Culture & Treatment==
 *Seeds of Dongxiang wild rice (Oryza rufipogon Griff.; Dongxiang County, Jiangxi Province) and rice Xieqingzao B (O. sativa L. ssp. indica) were immersed in distilled water in the dark,and the uniformly germinated seeds were sown in 96-well plates supported by a plastic container. Seeds were grown in a growth chamber, as previously described [12]. The growth culture solution was renewed every 3 days. After the seedlings had been grown for 14 days, they were transferred on their 96-well plates into containers filled with 200 mM NaCl solution, or with control solution for 12 days. The seedlings were then recovered under normal solution for 3 days, and survival rates were calculated. The experiment was a randomized complete block design with three replications. For RNA-Seq analysis, 14-day-old seedlings of Dongxiang wild rice were grown with or without 200 mM NaCl treatment for 3 days and then the leaves (penultimate leaves) and total roots (separated from the culture solution and washed carefully) of these seedlings were collected and immediately frozen in liquid nitrogen, respectively. For RNA extraction from each treatment group, 10 plants were collected and mixed, to minimize the effect of transcriptome unevenness among plants.
 <br>
 ==Research Findings==

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 ==Project Title==
-*Transcriptome Analysis of Salt Stress Responsiveness in the Seedlings of Dongxiang Wild Rice (Oryza rufipogon Griff.)
+*'''Transcriptome Analysis of Salt Stress Responsiveness in the Seedlings of Dongxiang Wild Rice (Oryza rufipogon Griff.)'''
 <br>
 ==The Background of This Project==
 *Rice (Oryza sativa L.) is one of the most important food crops in the world and also a model for genomic research in monocots. However, salinity is one of the most devastating abiotic stresses in rice, and the salt-affected soils currently account for about 20% of the total paddy rice planting area.More seriously, the area of salt-affected irrigated land is expanding and spreading in China.

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 [[File:IC4R020-RNA-Seq-2016-26752408-f3a.png |center |thumb |10000px |]]
-[[File:IC4R020-RNA-Seq-2016-26752408.png |center |thumb |10000px |''''''Fig 3. Gene ontology (GO) classification of the unigenes from the LS-vs-LCK (A) and RS-vs-RCK (B).'''''']]
+[[File:IC4R020-RNA-Seq-2016-26752408-f3b.png |center |thumb |10000px |''''''Fig 3. Gene ontology (GO) classification of the unigenes from the LS-vs-LCK (A) and RS-vs-RCK (B).'''''']]
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 *The researcher further identified over-represented KEGG Orthology (KO) terms (Q-value < 0.05), and classified them into 10 categories, respectively (Fig 4). As shown in Fig 4, these transcripts belonged mainly to the following KEGG pathways both in the LS vs. LCK and RS vs. RCK: Biosynthesis of other secondary metabolites, carbohydrate metabolism, global map, metabolism of terpenoids and polyketides, translation, and transport and catabolism.
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 [[File:IC4R020-RNA-Seq-2016-26752408-f4b.png |center |thumb |10000px |''''''KEGG pathway assignments in the LS vs. LCK (A) and RS vs. RCK (B). The represented categories (Q-value� 0.05) and the number of transcripts predicted to belong to each category are shown.'''''']]
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 ==Labs working on this Project==
 *College of Life Sciences, Jiangxi Normal University, Nanchang, China

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 *Institute for Advanced Study,Jiangxi Normal University, Nanchang, China
 <br>
 ==Corresponding Author==
 *'''Yi Zhou:'''zhouyi25@mail2.sysu.edu.cn; & '''Jiankun Xie:''' xiejiankun@yahoo.com
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 *The researcher further identified over-represented KEGG Orthology (KO) terms (Q-value < 0.05), and classified them into 10 categories, respectively (Fig 4). As shown in Fig 4, these transcripts belonged mainly to the following KEGG pathways both in the LS vs. LCK and RS vs. RCK: Biosynthesis of other secondary metabolites, carbohydrate metabolism, global map, metabolism of terpenoids and polyketides, translation, and transport and catabolism.
 <br>
+[[File:IC4R020-RNA-Seq-2016-26752408-f4a.png |center |thumb |10000px |]]
 ==Labs working on this Project==
 *College of Life Sciences, Jiangxi Normal University, Nanchang, China

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 ==Research Findings==
 *To investigate the character of salt stress resistance in the DXWR seedlings, two-week-old seedlings of DXWR and Xieqingzao B (O. sativa L. ssp. indica, hereafter referred as XB), which is a representative maintainer line in hybrid rice breeding system in China [12] were exposed to the hydroponic solution with 200 mM NaCl for 12 days. When grown under normal, the DXWR and XB seedlings were all green and alive. After exposure to the salt stress, most DXWR seedlings remained green and showed continuous growth, whereas XB seedlings were all dead (Fig 1).
 [[File:IC4R020-RNA-Seq-2016-26752408-f1.png |center |thumb |10000px |''''''Fig 1. The seedlings of DXWR showed stronger salt resistance than the seedlings of XB.'''''']]
+*A total of 15,636 and 17,937 transcripts were assigned GO terms for the DEGs in the LS vs. LCK and RS vs. RCK, respectively. Among the 15,636 transcripts from the LS vs. LCK (Fig 3A), there were 5,633 transcripts at the cellular level, 5,068 transcripts at the molecular level and 4,935 transcripts at the biological level. Among the 17,937 transcripts from the RS vs. RCK (Fig 3B), there were 6,302 transcripts at the cellular level, 5,907 transcripts at the molecular level and 5,728 transcripts at the biological level.
 ==Labs working on this Project==
 *College of Life Sciences, Jiangxi Normal University, Nanchang, China

← Older revision		Revision as of 09:06, 11 July 2016
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	==Research Findings==		==Research Findings==
		+	*To investigate the character of salt stress resistance in the DXWR seedlings, two-week-old seedlings of DXWR and Xieqingzao B (O. sativa L. ssp. indica, hereafter referred as XB), which is a representative maintainer line in hybrid rice breeding system in China [12] were exposed to the hydroponic solution with 200 mM NaCl for 12 days. When grown under normal, the DXWR and XB seedlings were all green and alive. After exposure to the salt stress, most DXWR seedlings remained green and showed continuous growth, whereas XB seedlings were all dead (Fig 1).
		+	[[File:IC4R020-RNA-Seq-2016-26752408-f1.png \|center \|thumb \|10000px \|''''''Fig 1. The seedlings of DXWR showed stronger salt resistance than the seedlings of XB.'''''']]

	==Labs working on this Project==		==Labs working on this Project==