Identification of Salt Tolerance-related microRNAs and Their Targets in Maize (Zea mays L.) Using High-throughput Sequencing and Degradome Analysis

Fu, Rong; Zhang, Mi; Zhao, Yongming; He, Xuechuan; Ding, Chenyun; Wang, Shuangkuai; Yan, Feng; Song, Xianliang; Li, Ping; Wang, Baohua

doi:10.3389/fpls.2017.00864

Cited by 82 publications

(53 citation statements)

References 60 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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“…Recent advances in plant miRNA research have been possible due to advancements in high-throughput sequencing. Plant miRNAs play crucial roles in biotic and abiotic stress responses, including in drought [38] and salt stress [39]. In the present study, 385 known miRNAs from 59 miRNA families and 94 novel miRNAs were identified from GLY and CK samples, and most of them were 21 nt in length, followed by 22 nt and 24 nt.…”

Section: Discussionmentioning

confidence: 61%

Identification and integrated analysis of glyphosate stress-responsive microRNAs, lncRNAs, and mRNAs in rice using genome-wide high-throughput sequencing

Zhai

Zhu

et al. 2020

BMC Genomics

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Background: Glyphosate has become the most widely used herbicide in the world. Therefore, the development of new varieties of glyphosate-tolerant crops is a research focus of seed companies and researchers. The glyphosate stress-responsive genes were used for the development of genetically modified crops, while only the EPSPS gene has been used currently in the study on glyphosate-tolerance in rice. Therefore, it is essential and crucial to intensify the exploration of glyphosate stress-responsive genes, to not only acquire other glyphosate stress-responsive genes with clean intellectual property rights but also obtain non-transgenic glyphosate-tolerant rice varieties. This study is expected to elucidate the responses of miRNAs, lncRNAs, and mRNAs to glyphosate applications and the potential regulatory mechanisms in response to glyphosate stress in rice. Results: Leaves of the non-transgenic glyphosate-tolerant germplasm CA21 sprayed with 2 mg·ml − 1 glyphosate (GLY) and CA21 plants with no spray (CK) were collected for high-throughput sequencing analysis. A total of 1197 DEGs, 131 DELs, and 52 DEMs were identified in the GLY samples in relation to CK samples. Genes were significantly enriched for various biological processes involved in detoxification of plant response to stress. A total of 385 known miRNAs from 59 miRNA families and 94 novel miRNAs were identified. Degradome analysis led to the identification of 32 target genes, of which, the squamosa promoter-binding-like protein 12 (SPL12) was identified as a target of osa-miR156a_L + 1. The lncRNA-miRNA-mRNA regulatory network consisted of osa-miR156a_L + 1, two transcripts of SPL12 (LOC_Os06g49010.3 and LOC_Os06g49010.5), and 13 lncRNAs (e.g., MSTRG.244.1 and MSTRG.16577.1). Conclusion: Large-scale expression changes in coding and noncoding RNA were observed in rice mainly due to its response to glyphosate. SPL12, osa-miR156, and lncRNAs (e.g., MSTRG.244.1 and MSTRG.16577.1) could be a novel ceRNA mechanism in response to glyphosate in rice by regulating transcription and metal ions binding. These findings provide a theoretical basis for breeding glyphosate-tolerant rice varieties and for further research on the biogenesis of glyphosate-tolerance in rice.

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“…Since the first discovery of miRNAs, the basic understanding of how gene expression is controlled deeply changed. In the last ten years, studies demonstrated that miRNAs play crucial roles in modulating stress response, including salinity [78], drought [79], waterlogging [80], UV-B radiation and cold stress [81,82], and in several cases their biological role has been clarified. For instance, miR394 and miR397 have been reported to positively regulate cold tolerance via the CBF-dependent pathway [83,84], whereas miR319 activates the CBF regulon and triggers reactive oxygen species (ROS) elimination from the cells [85].…”

Section: Genomics and Machine Learning: A Case Study To Predict Diffementioning

confidence: 99%

Applications and Trends of Machine Learning in Genomics and Phenomics for Next-Generation Breeding

Esposito¹,

Carputo

Cardi³

et al. 2019

Plants

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Crops are the major source of food supply and raw materials for the processing industry. A balance between crop production and food consumption is continually threatened by plant diseases and adverse environmental conditions. This leads to serious losses every year and results in food shortages, particularly in developing countries. Presently, cutting-edge technologies for genome sequencing and phenotyping of crops combined with progress in computational sciences are leading a revolution in plant breeding, boosting the identification of the genetic basis of traits at a precision never reached before. In this frame, machine learning (ML) plays a pivotal role in data-mining and analysis, providing relevant information for decision-making towards achieving breeding targets. To this end, we summarize the recent progress in next-generation sequencing and the role of phenotyping technologies in genomics-assisted breeding toward the exploitation of the natural variation and the identification of target genes. We also explore the application of ML in managing big data and predictive models, reporting a case study using microRNAs (miRNAs) to identify genes related to stress conditions.

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Identification of Salt Tolerance-related microRNAs and Their Targets in Maize (Zea mays L.) Using High-throughput Sequencing and Degradome Analysis

Cited by 82 publications

References 60 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

Identification and integrated analysis of glyphosate stress-responsive microRNAs, lncRNAs, and mRNAs in rice using genome-wide high-throughput sequencing

Applications and Trends of Machine Learning in Genomics and Phenomics for Next-Generation Breeding

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