scholarly journals Comparative transcriptomic and physiological analyses of weedy rice and cultivated rice to identify vital differentially expressed genes and pathways regulating the ABA response

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hong Lang ◽  
Yuting He ◽  
Faliang Zeng ◽  
Fan Xu ◽  
Minghui Zhao ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Weedy Rice ◽  
Cultivated Rice ◽  
Biotic Stresses ◽  
Aba Sensitivity ◽  
Aba Catabolism ◽  
Physiological Analysis ◽  
Response To Stress ◽  
Aba Response

AbstractWeedy rice is a valuable germplasm resource characterized by its high tolerance to both abiotic and biotic stresses. Abscisic acid (ABA) serves as a regulatory signal in plant cells as part of their adaptive response to stress. However, a global understanding of the response of weedy rice to ABA remains to be elucidated. In the present study, the sensitivity to ABA of weedy rice (WR04-6) was compared with that of temperate japonica Shennong9816 (SN9816) in terms of seed germination and post-germination growth via the application of exogenous ABA and diniconazole, an inhibitor of ABA catabolism. Physiological analysis and a transcriptomic comparison allowed elucidation of the molecular and physiological mechanisms associated with continuous ABA and diniconazole treatment. WR04-6 was found to display higher ABA sensitivity than SN9816, resulting in the rapid promotion of antioxidant enzyme activity. Comparative transcriptomic analyses indicated that the number of differentially expressed genes (DEGs) in WR04-6 seedlings treated with 2 μM ABA or 10 μM diniconazole was greater than that in SN9816 seedlings. Genes involved in stress defense, hormone signal transduction, and glycolytic and citrate cycle pathways were highly expressed in WR04-6 in response to ABA and diniconazole. These findings provide new insight into key processes mediating the ABA response between weedy and cultivated rice.

scholarly journals Comparative analysis of the transcriptomes of two rice subspecies reveals differentially expressed genes associated with phenotypic differences and reproductive isolation

2019 ◽  
Author(s):  
hongbo pang ◽  
Junrui Wang ◽  
Qiang Chen ◽  
Jiaqi Li ◽  
Yueying Li ◽  
...  
Keyword(s):  
Reproductive Isolation ◽  
Differentially Expressed Genes ◽  
Complex Traits ◽  
Rice Genome ◽  
Active Regions ◽  
Differentially Expressed ◽  
Cultivated Rice ◽  
Phenotypic Differences ◽  
Flanking Regions ◽  
Reproductive Processes

Abstract Background: Rice has been used as a model plant to study adaptation, genome evolution and reproductive isolation among species and the genetics and evolution of complex traits. Two subspecies of cultivated rice, Oryza sativa ssp. indica and O. sativa ssp. japonica, with reproductive isolation and differences in morphology and phenotypic differences, were established during the process of rice domestication. Results: To understand how domestication has changed the transcriptomes of the two rice subspecies and given rise to the phenotypic differences, we obtained approximately 700 Gb RNA-Seq data from 26 indica and 25 japonica plants, and identified 97,005 transcribed fragments and 7702 novel transcriptionally active regions. We also identified 1857 (4.58% in all genes) differentially expressed genes (DEGs) between indica and japonica rice. According to previous population genetic analyses, these DEGs may associate with the phenotypic differences between the two subspecies. Functional annotation of these DEGs indicates that they are involved in cell wall biosynthesis and reproductive processes. Furthermore, compared with the non-DEGs, the DEGs from both subspecies had more 5′ flanking regions with low polymorphism to divergence ratios, indicating a stronger positive selection pressure on the regulation of the DEGs.Conclusion: This study improves our understanding of the rice genome by comparatively analyzing the transcriptomes of indica and japonica rice and identifies DEGs that may be responsible for the reproductive isolation and phenotypic differences between the two rice subspecies.

cDNA-AFLP Analysis of Differentially Expressed Genes in Tobacco Infected by TMV

2013 ◽  
Vol 38 (1) ◽  
pp. 62-70 ◽  
Author(s):  
Rong-Ping CHEN ◽  
Lie LIU ◽  
Xiu-Qing WAN ◽  
En-Jian QIU ◽  
Chun-Jun WANG ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Aflp Analysis

Identification of Differentially Expressed Genes Associated with Papillary Thyroid Carcinoma

2020 ◽  
Vol 23 (6) ◽  
pp. 546-553
Author(s):  
Hongyuan Cui ◽  
Mingwei Zhu ◽  
Junhua Zhang ◽  
Wenqin Li ◽  
Lihui Zou ◽  
...  
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Cellular Proliferation ◽  
Mrna Level ◽  
Thyroid Tissue ◽  
Differentially Expressed ◽  
Thyroid Tumors ◽  
Papillary Thyroid

Objective: Next-generation sequencing (NGS) was performed to identify genes that were differentially expressed between normal thyroid tissue and papillary thyroid carcinoma (PTC). Materials & Methods: Six candidate genes were selected and further confirmed with quantitative real-time polymerase chain reaction (qRT-PCR), and immunohistochemistry in samples from 24 fresh thyroid tumors and adjacent normal tissues. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was used to investigate signal transduction pathways of the differentially expressed genes. Results: In total, 1690 genes were differentially expressed between samples from patients with PTC and the adjacent normal tissue. Among these, SFRP4, ZNF90, and DCN were the top three upregulated genes, whereas KIRREL3, TRIM36, and GABBR2 were downregulated with the smallest p values. Several pathways were associated with the differentially expressed genes and involved in cellular proliferation, cell migration, and endocrine system tumor progression, which may contribute to the pathogenesis of PTC. Upregulation of SFRP4, ZNF90, and DCN at the mRNA level was further validated with RT-PCR, and DCN expression was further confirmed with immunostaining of PTC samples. Conclusion: These results provide new insights into the molecular mechanisms of PTC. Identification of differentially expressed genes should not only improve the tumor signature for thyroid tumors as a diagnostic biomarker but also reveal potential targets for thyroid tumor treatment.

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