Small RNA profiling and degradome analysis reveal regulation of microRNA in peanut embryogenesis and early pod development

Submergence and drought stresses are the main constraints to crop production worldwide. MicroRNAs (miRNAs) are known to play a major role in plant response to various stresses. In this study, we analyzed the expression of maize and teosinte miRNAs by high-throughput sequencing of small RNA libraries in maize and its ancestor teosinte (Zea mays ssp. parviglumis), under submergence, drought, and alternated stress. We found that the expression patterns of 67 miRNA sequences representing 23 miRNA families in maize and other plants were regulated by submergence or drought. miR159a, miR166b, miR167c, and miR169c were downregulated by submergence in both plants but more severely in maize. miR156k and miR164e were upregulated by drought in teosinte but downregulated in maize. Small RNA profiling of teosinte subject to alternate treatments with drought and submergence revealed that submergence as the first stress attenuated the response to drought, while drought being the first stress did not alter the response to submergence. The miRNAs identified herein, and their potential targets, indicate that control of development, growth, and response to oxidative stress could be crucial for adaptation and that there exists evolutionary divergence between these two subspecies in miRNA response to abiotic stresses.

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Small RNA Profiling in Two Brassica napus Cultivars Identifies MicroRNAs with Oil Production- and Development-Correlated Expression and New Small RNA Classes

PLANT PHYSIOLOGY ◽

10.1104/pp.111.187666 ◽

2011 ◽

Vol 158 (2) ◽

pp. 813-823 ◽

Cited By ~ 92

Author(s):

Ying-Tao Zhao ◽

Meng Wang ◽

San-Xiong Fu ◽

Wei-Cai Yang ◽

Cun-Kou Qi ◽

...

Keyword(s):

Brassica Napus ◽

Small Rna ◽

Oil Production ◽

Rna Profiling

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Genome-wide Small Rna Profiling Reveals Tiller Development in Tall Fescue (Festuca Arundinacea Schreb.)

10.21203/rs.3.rs-27724/v1 ◽

2020 ◽

Author(s):

Tao Hu ◽

Tao Wang ◽

Huiying Li ◽

Misganaw Wassie ◽

Liang Chen

Keyword(s):

Production Rate ◽

Small Rna ◽

Tall Fescue ◽

Festuca Arundinacea ◽

Target Genes ◽

Cool Season ◽

Rna Profiling ◽

Mirna Genes ◽

Genome Wide ◽

A Genome

Abstract Background: Tall fescue (Festuca arundinacea Schreb.) is a major cool-season forage and turfgrass species. The low tiller density and size dramatically limits its turf performance and forage yield. MicroRNAs (miRNA)-genes modules play critical roles in tiller development in plants. In this study, a genome-wide small RNA profiling was carried out in two tall fescue genotypes contrasting for tillering production (‘Ch-3’, high tiller production rate and ‘Ch-5’, low tiller production rate) andtwo types of tissue samples at different tillering development stage (Pre-tillering, grass before tillering; Tillering, grass after tillering). ‘Ch-3’, ‘Ch-5’, Pre-tillering, and Tillering samples were analyzed using high-throughput RNA sequencing.Results: A total of 222 million high-quality clean reads were generated and 208 miRNAs were discovered, including 148 known miRNAs belonging to 70 families and 60 novel ones. Furthermore, 18 miRNAs were involved in tall fescue tiller development process. Among them, 14 miRNAs displayed increased abundance in both Ch-3 and Tillering plants compared with that in Ch-5 and Pre-tillering plants and were positive with tillering, while another four miRNAs were negative with tiller development. Out ofthe three miRNAs osa-miR156a, zma-miR528a-3p and osa-miR444b.2, the rest of 15 miRNAs were newfound controllers mediating tiller development in plants. Based on our previous full-length transcriptome analysis in tall fescue, 2 8927 potential target genes were discoveredfor all identified miRNAs. Most of the 212 target genes of the 18 miRNAs were dominantly enriched into “ubiquitin-mediated proteolysis”, “phagosome”, “fatty acid biosynthesis”, “oxidative phosphorylation”, and “biosynthesis of unsaturated fatty acids” KEGG pathways.Conclusions: This is the first genome-wide miRNA profiles analysis to identifyregulators involved in tiller development in cool-season turfgrass. Tillering related 18 miRNAs and their 212 target genes provide novel information for the understanding of the molecular mechanisms of miRNA-genes mediated tiller development in cool-season turfgrass.

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Genome-wide small RNA profiling reveals tiller development in tall fescue (Festuca arundinacea Schreb.)

10.21203/rs.3.rs-27724/v2 ◽

2020 ◽

Author(s):

Tao Hu ◽

Tao Wang ◽

Huiying Li ◽

Misganaw Wassie ◽

Huawei Xu ◽

...

Keyword(s):

Production Rate ◽

Small Rna ◽

Tall Fescue ◽

Festuca Arundinacea ◽

Target Genes ◽

Cool Season ◽

Rna Profiling ◽

Mirna Genes ◽

Genome Wide ◽

A Genome

Abstract Background: Tall fescue (Festuca arundinacea Schreb.) is a major cool-season forage and turfgrass species. The low tiller density and size dramatically limits its turf performance and forage yield. MicroRNAs (miRNA)-genes modules play critical roles in tiller development in plants. In this study, a genome-wide small RNA profiling was carried out in two tall fescue genotypes contrasting for tillering production (‘Ch-3’, high tiller production rate and ‘Ch-5’, low tiller production rate) and two types of tissue samples at different tillering development stage (Pre-tillering, grass before tillering; Tillering, grass after tillering). ‘Ch-3’, ‘Ch-5’, Pre-tillering, and Tillering samples were analyzed using high-throughput RNA sequencing. Results: A total of 222 million high-quality clean reads were generated and 208 miRNAs were discovered, including 148 known miRNAs belonging to 70 families and 60 novel ones. Furthermore, 18 miRNAs were involved in tall fescue tiller development process. Among them, 14 miRNAs displayed increased abundance in both Ch-3 and Tillering plants compared with that in Ch-5 and Pre-tillering plants and were positive with tillering, while another four miRNAs were negative with tiller development. Out of the three miRNAs osa-miR156a, zma-miR528a-3p and osa-miR444b.2, the rest of 15 miRNAs were newfound and associated with tiller development in plants. Based on our previous full-length transcriptome analysis in tall fescue, 2 8927 potential target genes were discovered for all identified miRNAs. Most of the 212 target genes of the 18 miRNAs were dominantly enriched into “ubiquitin-mediated proteolysis”, “phagosome”, “fatty acid biosynthesis”, “oxidative phosphorylation”, and “biosynthesis of unsaturated fatty acids” KEGG pathways. In addition, bdi-miR167e-3p targets two kinase proteins EIF2AK4 and IRAK4, and osa-miR397a targets auxin response factor 5, which may be the significant miRNA-genes controllers in tillering development. Conclusions: This is the first genome-wide miRNA profiles analysis to identify regulators involved in tiller development in cool-season turfgrass. Tillering related 18 miRNAs and their 212 target genes provide novel information for the understanding of the molecular mechanisms of miRNA-genes mediated tiller development in cool-season turfgrass.

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