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Int. J. Mol. Sci. 2014, 15(4), 6137-6160; doi:10.3390/ijms15046137

RNA Sequencing Analysis Reveals Transcriptomic Variations in Tobacco (Nicotiana tabacum) Leaves Affected by Climate, Soil, and Tillage Factors

1
Key Laboratory of Molecular Genetics, China National Tobacco Corporation, Guizhou Academy of Tobacco Science, Longbatan Road 29, Guanshanhu District, Guiyang 550081, China
2
Engineering Research Center of South Upland Agriculture, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400715, China
These authors contributed equally to this work.
*
Authors to whom correspondence should be addressed.
Received: 24 January 2014 / Revised: 18 March 2014 / Accepted: 1 April 2014 / Published: 11 April 2014
(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)
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Abstract

The growth and development of plants are sensitive to their surroundings. Although numerous studies have analyzed plant transcriptomic variation, few have quantified the effect of combinations of factors or identified factor-specific effects. In this study, we performed RNA sequencing (RNA-seq) analysis on tobacco leaves derived from 10 treatment combinations of three groups of ecological factors, i.e., climate factors (CFs), soil factors (SFs), and tillage factors (TFs). We detected 4980, 2916, and 1605 differentially expressed genes (DEGs) that were affected by CFs, SFs, and TFs, which included 2703, 768, and 507 specific and 703 common DEGs (simultaneously regulated by CFs, SFs, and TFs), respectively. GO and KEGG enrichment analyses showed that genes involved in abiotic stress responses and secondary metabolic pathways were overrepresented in the common and CF-specific DEGs. In addition, we noted enrichment in CF-specific DEGs related to the circadian rhythm, SF-specific DEGs involved in mineral nutrient absorption and transport, and SF- and TF-specific DEGs associated with photosynthesis. Based on these results, we propose a model that explains how plants adapt to various ecological factors at the transcriptomic level. Additionally, the identified DEGs lay the foundation for future investigations of stress resistance, circadian rhythm and photosynthesis in tobacco. View Full-Text
Keywords: climate factors; soil factors; tillage factors; tobacco leaves; transcriptome; RNA-seq climate factors; soil factors; tillage factors; tobacco leaves; transcriptome; RNA-seq
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This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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Lei, B.; Lu, K.; Ding, F.; Zhang, K.; Chen, Y.; Zhao, H.; Zhang, L.; Ren, Z.; Qu, C.; Guo, W.; Wang, J.; Pan, W. RNA Sequencing Analysis Reveals Transcriptomic Variations in Tobacco (Nicotiana tabacum) Leaves Affected by Climate, Soil, and Tillage Factors. Int. J. Mol. Sci. 2014, 15, 6137-6160.

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