scholarly journals Global Transcriptome and Co-Expression Network Analysis Reveal Contrasting Response of Japonica and Indica Rice Cultivar to γ Radiation

2019 ◽  
Vol 20 (18) ◽  
pp. 4358 ◽  
Author(s):  
Xiaoxiang Zhang ◽  
Niansheng Huang ◽  
Lanjing Mo ◽  
Minjia Lv ◽  
Yingbo Gao ◽  
...  

Japonica and indica are two important subspecies in cultivated Asian rice. Irradiation is a classical approach to induce mutations and create novel germplasm. However, little is known about the differential response between japonica and indica rice after γ radiation. Here, we utilized the RNA sequencing and Weighted Gene Co-expression Network Analysis (WGCNA) to compare the transcriptome differences between japonica Nipponbare (NPB) and indica Yangdao6 (YD6) in response to irradiation. Japonica subspecies are more sensitive to irradiation than the indica subspecies. Indica showed a higher seedling survival rate than japonica. Irradiation caused more extensive DNA damage in shoots than in roots, and the severity was higher in NPB than in YD6. GO and KEGG pathway analyses indicate that the core genes related to DNA repair and replication and cell proliferation are similarly regulated between the varieties, however the universal stress responsive genes show contrasting differential response patterns in japonica and indica. WGCNA identifies 37 co-expressing gene modules and ten candidate hub genes for each module. This provides novel evidence indicating that certain peripheral pathways may dominate the molecular networks in irradiation survival and suggests more potential target genes in breeding for universal stress tolerance in rice.

Biology ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 417
Author(s):  
Ha Thi Nguyen ◽  
Salah Eddine Oussama Kacimi ◽  
Truc Ly Nguyen ◽  
Kamrul Hassan Suman ◽  
Roselyn Lemus-Martin ◽  
...  

MicroRNAs (miRNAs) are small non-coding RNAs. They can regulate the expression of their target genes, and thus, their dysregulation significantly contributes to the development of cancer. Growing evidence suggests that miRNAs could be used as cancer biomarkers. As an oncogenic miRNA, the roles of miR-21 as a diagnostic and prognostic biomarker, and its therapeutic applications have been extensively studied. In this review, the roles of miR-21 are first demonstrated via its different molecular networks. Then, a comprehensive review on the potential targets and the current applications as a diagnostic and prognostic cancer biomarker and the therapeutic roles of miR-21 in six different cancers in the digestive system is provided. Lastly, a brief discussion on the challenges for the use of miR-21 as a therapeutic tool for these cancers is added.


2000 ◽  
Vol 3 (3) ◽  
pp. 254-256 ◽  
Author(s):  
Prapa Sripichitt ◽  
Takashi Ozawa ◽  
Motoyasu Otani ◽  
Takiko Shimada

Author(s):  
Man Wang ◽  
Jiehu Chen ◽  
Feng Zhou ◽  
Jianming Yuan ◽  
Libin Chen ◽  
...  

Cryobiology ◽  
2018 ◽  
Vol 85 ◽  
pp. 122-123
Author(s):  
Maryam Hezavehi ◽  
Ghasem Hosseini Salekdeh ◽  
Mohsen Sharafi ◽  
Poopack Eftekhari Yazdi ◽  
Rouhollah Fathi ◽  
...  

2011 ◽  
Vol 123 (2) ◽  
pp. 130-138 ◽  
Author(s):  
Yoichiro Kato ◽  
Amelia Henry ◽  
Daisuke Fujita ◽  
Keisuke Katsura ◽  
Nobuya Kobayashi ◽  
...  

2007 ◽  
Vol 2 (2) ◽  
pp. 144-150
Author(s):  
Houcong Wang ◽  
Huakang Huang ◽  
Simi Qiu ◽  
Shi Zhang ◽  
Yashun Fang ◽  
...  

2021 ◽  
Author(s):  
Wenpeng Zhu ◽  
Manyu Zhang ◽  
Jianyi Li ◽  
Hewen Zhao ◽  
Kezhong Zhang ◽  
...  

Abstract BackgroundAcer rubrum L. is a colorful ornamental tree with great economic value. Because this tree is difficult to root under natural conditions and the seedling survival rate is low, vegetative propagation methods are often used. Because the formation of adventitious roots (ARs) is essential for the survival of asexual propagation of A. rubrum, it is necessary to investigate the molecular regulatory mechanisms in the formation of ARs of A. ruburm. To address this knowledge gap, we sequenced the transcriptome and sRNA of the A. rubrum variety ‘Autumn Fantasy’ using high-throughput sequencing and explored changes in gene and microRNA (miRNA) expression in response to exogenous auxin treatment. ResultsWe identified 82,468 differentially expressed genes between the treated and untreated ARs, as well as 48 known and 95 novel miRNAs. We also identified 172 target genes of the known miRNAs using degradome sequencing. Two regulatory pathways (ubiquitin mediated proteolysis and plant hormone signal transduction), Ar-miR160a and the target gene ArARF10 were shown to be involved in the auxin response. We further investigated the expression patterns and regulatory roles of ArARF10 through subcellular localization, transcriptional activation, plant transformation, qRT-PCR analysis, and GUS staining. ConclusionsDifferential expression patterns indicated the Ar-miR160a-ArARF10 interaction might play a significant role in the regulation of AR formation in A. rubrum. Our study provided new insights into mechanisms underlying the regulation of AR formation in A. rubrum.


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