title: Generation of different sizes and classes of small RNAs in barley is locus, chromosome and/or cultivar-dependent.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
authors.affiliation: Computational Genomics and Bioinformatics Group, Genetics Department, University of Granada, 18071, Granada, Spain.
authors.forename: Michael
authors.initials: M
authors.lastname: Hackenberg
authors.affiliation: Genomics and Bioinformatics Platform of Andalusia (GBPA), Edificio INSUR, Calle Albert Einstein, 41092, Seville, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Rueda
authors.affiliation: USDA-ARS, 206 Curtis Hall, University of Missouri, Columbia, MO, 65211-7020, USA.
authors.forename: Perry
authors.initials: P
authors.lastname: Gustafson
authors.affiliation: Australian Centre for Plant Functional Genomics, The University of Adelaide, Adelaide, South Australia 5005, Australia.
authors.forename: Peter
authors.initials: P
authors.lastname: Langridge
authors.affiliation: Australian Centre for Plant Functional Genomics, The University of Adelaide, Adelaide, South Australia 5005, Australia. bujun.shi@adelaide.edu.au.
authors.forename: Bu-Jun
authors.initials: BJ
authors.lastname: Shi
mesh_terms: D032461:Chromosomes, Plant; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D056426:Genetic Loci; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D001467:Hordeum / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics*; D058727:RNA, Small Untranslated / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant; D058727:RNA, Small Untranslated
keywords: Barley cultivar; Chromosome location; Conservation; Origin; Small RNA expression