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Background  PhasiRNAs (phased secondary siRNAs) play important regulatory roles in the development processes and biotic or abiotic stresses in plants. Some of phasiRNAs involve in the reproductive development in grasses, which include two categories, 21-nt (nucleotide) and 24-nt phasiRNAs. They are triggered by miR2118 and miR2275 respectively, in premeiotic and meiotic anthers of rice, maize and other grass species. Wheat ( Triticum aestivum ) with three closely related subgenomes (subA, subB and subD), is a model of allopolyploid in plants. Knowledge about the role of phasiRNAs in the inflorescence development of wheat is absent until now, and the evolution of  PHAS  loci in polyploid plants is also unavailable.    Results  Using 261 small RNA expression datasets from various tissues, a batch of  PHAS  (phasiRNA precursors) loci were identified in the young spike of wheat, most of which were regulated by miR2118 and miR2275 in their target site regions. Dissection of  PHAS  and their trigger miRNAs among the diploid (AA and DD), tetraploid (AABB) and hexaploid (AABBDD) genomes of  Triticum  indicated that distribution of  PHAS  loci were dominant randomly in local chromosomes, while miR2118 was dominant only in the subB genome. The diversity of  PHAS  loci in the three subgenomes of wheat and their progenitor genomes (AA, DD and AABB) suggested that they originated or diverged at least before the occurrence of the tetraploid AABB genome. The positive correlation between the  PHAS  loci or the trigger miRNAs and the ploidy of genome indicated the expansion of genome was the major drive force for the increase of  PHAS  loci and their trigger miRNAs in  Triticum . In addition, the expression profiles of the  PHAS  transcripts suggested they responded to abiotic stresses such as cold stress in wheat.    Conclusions  Altogether, non-coding phasiRNAs are conserved transcriptional regulators that display quick plasticity in  Triticum  genome. They may be involved in reproductive development and abiotic stress in wheat. It could be referred to molecular research on male reproductive development in  Triticum .

Evolution of PHAS loci in the young spike of Allohexaploid wheat