Evolution of PHAS Loci in the Young Spike of Allohexaploid Wheat

Abstract Background PhasiRNAs (phased secondary siRNAs) play important regulatory roles in the development processes and biotic and abiotic stresses in plants. A class of phasiRNAs involve in the reproductive development in grasses. Reproductive-associated phasiRNAs include two categories, 21-nt (nucleotide) and 24-nt phasiRNAs, which are triggered by miR2118 and miR2275 in premeiotic and meiotic anthers, respectively, which had been reported in rice, maize and other grass species. However, there were still absence in Triticum The allohexaploid wheat ( Triticum aestivum ) genome consists of three closely related subgenomes (subA, subB and subD), which is a model of allopolyploid in plants. And the evolution of PHAS loci in polyploid plants is still unavailable.Results Here, 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 triggered 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 their trigger 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 before the occurrence of AABB. The positive relationship 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 PHAS transcripts responded to abiotic stresses such as cold stress in wheat.Conclusions Altogether, non-coding phasiRNAs are conserved transcriptional regulators that display quick plasticity in genome dominance and sequence diversity and are involved in reproductive development and abiotic stress in wheat. It could be referred to molecular research on male reproductive development in Triticum .