Please use this identifier to cite or link to this item:
https://hdl.handle.net/2440/113273
Citations | ||
Scopus | Web of Science® | Altmetric |
---|---|---|
?
|
?
|
Type: | Journal article |
Title: | Generation of different sizes and classes of small RNAs in barley is locus, chromosome and/or cultivar-dependent |
Author: | Hackenberg, M. Rueda, A. Gustafson, P. Langridge, P. Shi, B. |
Citation: | BMC Genomics, 2016; 17(1):735-1-735-11 |
Publisher: | BioMed Central |
Issue Date: | 2016 |
ISSN: | 1471-2164 1471-2164 |
Statement of Responsibility: | Michael Hackenberg, Antonio Rueda, Perry Gustafson, Peter Langridge and Bu-Jun Shi |
Abstract: | Background: Various small RNA (sRNA) sizes and varieties have been identified, but their relationship as well as relationship with their origins and allocations have not been well understood or investigated. Results: By comparing sRNAs generated from two barley cultivars, Golden Promise (GP) and Pallas, we identified that the generation of different sizes and types of sRNAs in barley was locus-, chromosome- and/or cultivar-dependent. 20-nt sRNAs mainly comprising miRNAs and chloroplast-derived sRNAs were significantly over-expressed in Pallas vs. GP on chromosomes 3H and 6H. MiRNAs-enriched 21-nt sRNAs were significantly over-expressed in Pallas vs. GP only on chromosome 4H. On chromosome 5H this size of sRNAs was significantly under-expressed in Pallas, so were 22-nt sRNAs mainly comprising miRNAs and repeat-derived sRNAs. 24-nt sRNAs mostly derived from repeats were evenly distributed in all chromosomes and expressed similarly between GP and Pallas. Unlike other sizes of sRNAs, 24-nt sRNAs were little conserved in other plant species. Abundant sRNAs were mostly generated from 3' terminal regions of chromosome 1H and 5' terminal regions of chromosome 5H. Over-expressed miRNAs in GP vs. Pallas primarily function in stress responses and iron-binding. Conclusions: Our study indicates that 23-24-nt sRNAs may be linked to repressive chromatin modifications and function in genome stability while 20-21-nt sRNAs may be important for the cultivar specificity. This study provides a novel insight into the mechanism of sRNA expression and function in barley. |
Keywords: | Small RNA expression; origin; chromosome location; conservation; barley cultivar |
Rights: | © 2016 The Author(s). Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
DOI: | 10.1186/s12864-016-3023-5 |
Grant ID: | ARC |
Published version: | http://dx.doi.org/10.1186/s12864-016-3023-5 |
Appears in Collections: | Agriculture, Food and Wine publications Aurora harvest 8 |
Files in This Item:
File | Description | Size | Format | |
---|---|---|---|---|
hdl_113273.pdf | Published Version | 1.63 MB | Adobe PDF | View/Open |
Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.