Differential transcriptome profiling of chilling stress response between shoots and rhizomes of Oryza longistaminata using RNA sequencing

Zhang, Ting; Huang, Liying; Wang, Yinxiao; Wang, Wensheng; Zhao, Xiuqin; Zhang, Shilai; Zhang, Jing; Hu, Fengyi; Fu, Binying; Li, Zhikang

doi:10.1371/journal.pone.0188625

Cited by 35 publications

(24 citation statements)

References 92 publications

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“…The number of DEGs in C3 and C4 were more than C1 and C2, and the number of down-regulated DEGs was less than the number of up-regulated DEGs in every library, particularly in C1 and C2. This is consistent with a result from previous reports in other plants under cold stress, such as rice ( Oryza longistaminata ) [ 39 ], patience dock [ 28 ], and crowtoe [ 25 ]. Furthermore, there were 433, 266, 791, and 1644 DEGs specifically modulated in C1, C2, C3, and C4, respectively.…”

Section: Resultssupporting

confidence: 93%

Multiple Regulatory Networks Are Activated during Cold Stress in Medicago sativa L.

Zhou

Luo²,

Chai³

et al. 2018

IJMS

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Cultivated alfalfa (Medicago sativa L.) is one of the most important perennial legume forages in the world, and it has considerable potential as a valuable forage crop for livestock. However, the molecular mechanisms underlying alfalfa responses to cold stress are largely unknown. In this study, the transcriptome changes in alfalfa under cold stress at 4 °C for 2, 6, 24, and 48 h (three replicates for each time point) were analyzed using the high-throughput sequencing platform, BGISEQ-500, resulting in the identification of 50,809 annotated unigenes and 5283 differentially expressed genes (DEGs). Metabolic pathway enrichment analysis demonstrated that the DEGs were involved in carbohydrate metabolism, photosynthesis, plant hormone signal transduction, and the biosynthesis of amino acids. Moreover, the physiological changes of glutathione and proline content, catalase, and peroxidase activity were in accordance with dynamic transcript profiles of the relevant genes. Additionally, some transcription factors might play important roles in the alfalfa response to cold stress, as determined by the expression pattern of the related genes during 48 h of cold stress treatment. These findings provide valuable information for identifying and characterizing important components in the cold signaling network in alfalfa and enhancing the understanding of the molecular mechanisms underlying alfalfa responses to cold stress.

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Section: Resultssupporting

confidence: 93%

Multiple Regulatory Networks Are Activated during Cold Stress in Medicago sativa L.

Zhou

Luo²,

Chai³

et al. 2018

IJMS

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“…The analysis suggested that some typical cold stress-related genes were of basic helix-loop-helix (bHLH) gene and leucine-rich repeat (LRR) domain genes, and several genes associated with phytohormones like abscisic acid (ABA), gibberellic acid (GA), auxin, and ethylene [70]. Similarly, the wild rice, O. longistaminata, tolerates nonfreezing cold temperatures, is used for the identification of molecular mechanisms in response to low temperature in its shoots and rhizomes at seedling and reproductive stages using transcriptome analysis [71]. They found photosynthesis pathway-related genes were prevalent in shoots, whereas metabolic pathways and the programmed cell death process-related genes were expressed only in rhizomes.…”

Section: Transcriptome Data For Cold Stressmentioning

confidence: 99%

“…The cis-regulatory element analysis suggested the enrichment of ICE1binding site, GATA element, and W-box in both tissues. And the highly expressed genes in shoots were associated with photosynthesis, whereas signal transductionrelated genes were highly expressed in rhizomes [71].…”

Section: Transcriptome Data For Cold Stressmentioning

confidence: 99%

Transcriptome Analysis for Abiotic Stresses in Rice (Oryza sativa L.)

Kumar¹,

Dash²

2019

Transcriptome Analysis

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Rice, a model monocot system, belongs to the family Poaceae and genus Oryza. Rice is the second largest produced cereal and staple food crop fulfilling the demand of half the world's population. Though rice demand is growing exponentially, its production is severely affected by variable environmental changes. The various abiotic factors drastically reduce the rice plant growth and yield by affecting its different growth stages. To fulfill the growing demand of rice, it is imperative to understand its molecular responses during stresses and to develop new varieties to overcome the stresses. Earlier, the microarray experiments have been used for the identification of coexpressive gene networks during various conditions in crop plants. Though the microarray experiments provided very useful information, the unviability of genomewide information did not provide complete information about the regulatory gene networks involved in the stress response. The advancement of molecular techniques provided breakthrough to understanding the complex regulatory gene networks and their signaling pathways during stresses. The high-throughput RNA sequencing data have opened the floodgate of transcriptome data in rice. Here we have summarized some of the transcriptome data for abiotic molecular responses in rice, which further help to understand their complex regulatory mechanism.

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“…Rice ( Oryza sativa L.) is one of the most important cereal crops, providing food for more than half of the world’s population (Zhang et al 2017). Rice production can be seriously affected by environmental stresses, including low temperature, since it is normally grown in tropical and temperate climate zones, and therefore is sensitive to chilling (Mukhopadhyay et al 2004; Byun et al 2017).…”

Section: Introductionmentioning

confidence: 99%