Generation of different sizes and classes of small RNAs in barley is locus, chromosome and/or cultivar-dependent Hackenberg , Michael Rueda, Antonio Gustafson, Perry Langridge, Peter Shi, Bu-Jun Small RNA expression Origin Chromosome location Conservation Barley cultivar 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. 2018-03-07T10:15:43Z 2018-03-07T10:15:43Z 2016 info:eu-repo/semantics/article Hackenberg, M.; et al. Generation of different sizes and classes of small RNAs in barley is locus, chromosome and/or cultivar-dependent. BMC Genomics, 17: 735 (2016). [http://hdl.handle.net/10481/49876] 1471-2164 http://hdl.handle.net/10481/49876 10.1186/s12864-016-3023-5 eng http://creativecommons.org/licenses/by-nc-nd/3.0/ info:eu-repo/semantics/openAccess Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License Biomed Central