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Subgenomic analysis of microRNAs in polyploid wheat

Subgenomic analysis of microRNAs in polyploid wheat

Melda Kantar & Bala Anı Akpınar & Miroslav Valárik &
Stuart J. Lucas & Jaroslav Doležel & Pilar Hernández &
Hikmet Budak &


Abstract
In this study, a survey of miRNAs using the nextgeneration sequencing data was performed at subgenomic level. After analyzing shotgun sequences from chromosome 4A of bread wheat (Triticum aestivum L.), a total of 68 different miRNAs were predicted in silico, of which 37 were identified in wheat for the first time. The long arm of the
chromosome was found to harbor a higher variety (51) and representation (3,928) of miRNAs compared with the short arm (49; 2,226). Out of the 68 miRNAs, 32 were detected to be common to both arms, revealing the presence of separate miRNA clusters in the two chromosome arms. The differences in degree of representation of the different miRNAs were found to be highly variable, ranging 592-fold, which may have an effect on target regulation. Targets were retrieved for 62 (out of 68) of wheat-specific, newly identified miRNAs indicated that fundamental aspects of plant morphology such as height and flowering were predicted to be affected. In silico expression blast analysis indicated 24 (out of 68) were found to give hits to expressed sequences. This is the first report of species- and chromosome-specific miRNAs. 

Conclusions
In this study, we have computationally identified miRNAs on wheat chromosome 4A and performed a series of analysis on their representation on 4AS ad 4AL and their homology to known homologous miRNAs in other plants. We have identified a total of 68 miRNAs; 51 and 49 located on the small and long arms of 4A, respectively. Targets were also predicted for 62 identified T. aestivum miRNAs. The identified mature miRNAs, and miRNA targets were found to be consistent with previous reports. To our knowledge, we have for the first time presented a systematic identification of conserved miRNAs at the subgenomic, chromosome arm level, and the predicted miRNAs described here on chromosome 4A provide insights into genomic distribution and evolution of wheat miRNAs. The study confirmed the utility of chromosome genomics to study the structure and function of the as yet unsequenced genome of bread wheat. In addition to reducing DNA sample complexity, the chromosome arm- entered approach should allow for dissecting miRNAs from homeologous chromosomes to establish their contribution to gene regulation in polyploid wheat during development and responses to environment.