Combined analysis of mRNA and miRNA identifies dehydration and salinity responsive key molecular players in citrus roots

Xie, Rui; Zhang, Jin; Ma, Yue; Pan, Xiaoting; Dong, Cuicui; Pang, Shijin; He, Shuang-Hui; Deng, Lie; Yi, Shilai; Zheng, Yongqiang; Lv, Qiang

doi:10.1038/srep42094

Cited by 50 publications

(43 citation statements)

References 93 publications

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“…with salt tolerance, abiotic stresses in rice, and other crops. Manu Kumar et al elaborated on the relationship of OsSta2 with salt tolerance and abiotic stress in rice [52][53][54][55][56][57][58]. Salt tolerant varieties can be produced using marker-assisted selection or genetic engineering by introducing salt-tolerance genes [43].…”

Section: Discussionmentioning

confidence: 99%

Screening and Evaluation of Saline–Alkaline Tolerant Germplasm of Rice (Oryza sativa L.) in Soda Saline–Alkali Soil

2018

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The improvement and development of saline–alkali land is of great significance for promoting food production and sustainable development. It is necessary to study the mechanism of saline–alkaline tolerance and breed saline–alkaline tolerant crops to improve the utilization of saline–alkali land. For this study, we conducted a three-year pot experiment to screen the saline–alkaline tolerant germplasm of 72 rice genotypes from hundreds of elite cultivars during the whole growth period using a certain proportion of soda saline–alkali soil. The selected salt-tolerant variety was combined with a salt-sensitive variety to analyze the saline–alkaline tolerance mechanism by using the saline–alkaline soil leachate. We eliminated 36 genotypes with low seedling survival rates under salt–alkali stress, and the salt-tolerant Jiudao-66 (D68) variety had a higher survival rate than most varieties. The membership degree of Jiudao-66, according to the salt tolerance index of multiple agronomic traits, is higher than that of 34 varieties, with a higher survival rate except when compared to D36. The survival rate and these salt tolerance indexes of Jiudao-66 were significantly higher than those of Kitaake (salt-sensitive). Under the stress of leachate, the content of proline and soluble sugars in the shoots of Jiudao-66 were higher than that of Kitaake, and the total antioxidant capacity was stronger than that of Kitaake. However, the content of malondialdehyde was lower than that of Kitaake. Additionally, the Na+/K+ ratios in shoots and roots were not significantly differently between Kitaake and Jiudao-66. The results showed that Jiudao-66, as a salt-tolerant variety, is more tolerant to salt and alkali in a near-natural state due to its stronger tolerance of osmotic stress, and it can accumulate more proline and soluble sugars under stress. At the same time, Jiudao-66 also has a stronger antioxidant capacity. Its ion regulation ability has no obvious advantage.

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Section: Discussionmentioning

confidence: 99%

Screening and Evaluation of Saline–Alkaline Tolerant Germplasm of Rice (Oryza sativa L.) in Soda Saline–Alkali Soil

2018

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“…The results showed that the morphological changes were consistent with previous observations, and a large number of DEGs and DE miRNAs were identified. Some reports have demonstrated that the miRNA-mRNA regulatory network responds to abiotic stress (Xie et al, 2017). In this work, we attempted to construct a low-Pi-induced miRNA-mRNA regulatory network according to the DEG and DE miRNA datasets.…”

Section: Discussion 10mentioning

confidence: 99%

Integrated mRNA and miRNA expression profiling analyses of Pinus massoniana roots and shoots in response to phosphate deficiency

Fan¹,

Shang²,

Ding³

et al. 2020

Preprint

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Background Masson pine ( Pinus massoniana ) is primarily present in subtropical and tropical areas of China, which are severely deficient in inorganic phosphate (Pi). Although some studies identified transcriptomic and proteomic responses to Pi deficiency in Masson pine seedlings, different tissues, especially the roots, that exhibit primary responses to low-Pi stress, have not been well studied. To shed further light on the complex responses of Masson pine to Pi deficiency, a spatiotemporal experiment was performed to identify differentially expressed mRNAs and miRNAs under Pi-deficient conditions. Results Spatiotemporal analyses of 72 RNA sequencing libraries provided a comprehensive overview of the dynamic responses of Masson pine to low-Pi stress. Differentially expressed gene analysis revealed several high-affinity phosphate transporters and nitrate transporters, reflecting the crosstalk between nitrate and Pi homeostasis in plants. The MYB family was the most abundant transcription factor family identified. miRNA differential expression analysis identified several families that were associated with Pi deficiency, such as miR399. In addition, some other families, including novel miRNA families in Masson pine, were dramatically changed in response to Pi starvation. GO and KEGG analyses of these mRNAs and targets of miRNAs indicated that metabolic processes were most enriched under Pi deficiency. Conclusions This study provided abundant spatiotemporal transcriptomic information to functionally dissect the response of Masson pine seedlings to Pi deficiency, which will aid in further elucidation of the biological regulatory mechanisms of pines in response to low-Pi stress.

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“…A large body of evidence has shown that miRNA-mediated posttranscriptional regulation plays a fundamental role in plant responses to stressful factors, including pathogen infection, salt, drought, heat, cold, nutrient deficiency and metal toxicity [81][82][83][84][85][86]. A great deal of effort has been focused on the identification and functional analysis of plant miRNAs in response to the infection of pathogens, such as viruses [87][88][89], bacteria [16,[90][91][92] and fungi [13,93,94], which have provided valuable information as to the role miRNAs play in plant-pathogen interactions [95,96].…”

Section: Discussionmentioning

confidence: 99%

Identification of Appropriate Reference Genes for Normalizing miRNA Expression in Citrus Infected by Xanthomonas citri subsp. citri

Lyu

et al. 2019

Genes

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MicroRNAs (miRNAs) are short noncoding RNA molecules that regulate gene expression at the posttranscriptional level. Reverse transcription-quantitative PCR (RT-qPCR) is one of the most common methods used for quantification of miRNA expression, and the levels of expression are normalized by comparing with reference genes. Thus, the selection of reference genes is critically important for accurate quantification. The present study was intended to identify appropriate miRNA reference genes for normalizing the level of miRNA expression in Citrus sinensis L. Osbeck and Citrus reticulata Blanco infected by Xanthomonas citri subsp. citri, which caused citrus canker disease. Five algorithms (Delta Ct, geNorm, NormFinder, BestKeeper and RefFinder) were used for screening reference genes, and two quantification approaches, poly(A) extension RT-qPCR and stem-loop RT-qPCR, were used to determine the most appropriate method for detecting expression patterns of miRNA. An overall comprehensive ranking output derived from the multi-algorithms showed that poly(A)-tailed miR162-3p/miR472 were the best reference gene combination for miRNA RT-qPCR normalization in citrus canker research. Candidate reference gene expression profiles determined by poly(A) RT-qPCR were more consistent in the two citrus species. To the best of our knowledge, this is the first systematic comparison of two miRNA quantification methods for evaluating reference genes. These results highlight the importance of rigorously assessing candidate reference genes and clarify some contradictory results in miRNA research on citrus.

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Combined analysis of mRNA and miRNA identifies dehydration and salinity responsive key molecular players in citrus roots

Cited by 50 publications

References 93 publications

Screening and Evaluation of Saline–Alkaline Tolerant Germplasm of Rice (Oryza sativa L.) in Soda Saline–Alkali Soil

Screening and Evaluation of Saline–Alkaline Tolerant Germplasm of Rice (Oryza sativa L.) in Soda Saline–Alkali Soil

Integrated mRNA and miRNA expression profiling analyses of Pinus massoniana roots and shoots in response to phosphate deficiency

Identification of Appropriate Reference Genes for Normalizing miRNA Expression in Citrus Infected by Xanthomonas citri subsp. citri

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