BackgroundMicroRNAs (miRNAs) are small, non-coding RNAs playing essential roles in plant growth, development, and stress responses. Sequencing of small RNAs is a starting point for understanding their number, diversity, expression and possible roles in plants.ResultsIn this study, we conducted a genome-wide survey of wheat miRNAs from 11 tissues, characterizing a total of 323 novel miRNAs belonging to 276 families in wheat. A miRNA conservation analysis identified 191 wheat-specific miRNAs, 2 monocot-specific miRNAs, and 30 wheat-specific variants from 9 highly conserved miRNA families. To understand possible roles of wheat miRNAs, we determined 524 potential targets for 124 miRNA families through degradome sequencing, and cleavage of a subset of them was validated via 5′ RACE. Based on the genome-wide identification and characterization of miRNAs and their associated target genes, we further identified 64 miRNAs preferentially expressing in developing or germinating grains, which could play important roles in grain development.ConclusionWe discovered 323 wheat novel miRNAs and 524 target genes for 124 miRNA families in a genome-wide level, and our data will serve as a foundation for future research into the functional roles of miRNAs in wheat.

In Arabidopsis and rice, miR159-regulated GAMYB-like family transcription factors function in flower development and gibberellin (GA) signaling in cereal aleurone cells. In this study, the involvement of miR159 in the regulation of its putative target TaGAMYB and its relationship to wheat development were investigated. First, we demonstrated that cleavage of TaGAMYB1 and TaGAMYB2 was directed by miR159 using 5′-RACE and a transient expression system. Second, we overexpressed TamiR159, TaGAMYB1 and mTaGAMYB1 (impaired in the miR159 binding site) in transgenic rice, revealing that the accumulation in rice of mature miR159 derived from the precursor of wheat resulted in delayed heading time and male sterility. In addition, the number of tillers and primary branches in rice overexpressing mTaGAMYB1 increased relative to the wild type. Our previous study reported that TamiR159 was downregulated after two hours of heat stress treatment in wheat (Triticum aestivum L.). Most notably, the TamiR159 overexpression rice lines were more sensitive to heat stress relative to the wild type, indicating that the downregulation of TamiR159 in wheat after heat stress might participate in a heat stress-related signaling pathway, in turn contributing to heat stress tolerance.

Seed germination is important for grain yield and quality and rapid, near-simultaneous germination helps in cultivation; however, cultivars that germinate too readily can undergo preharvest sprouting (PHS), which causes substantial losses in areas that tend to get rain around harvest time. Moreover, our knowledge of mechanisms regulating seed germination in wheat () remains limited. In this study, we analyzed function of a wheat-specific microRNA 9678 (miR9678), which is specifically expressed in the scutellum of developing and germinating seeds. Overexpression of miR9678 delayed germination and improved resistance to PHS in wheat through reducing bioactive gibberellin (GA) levels; miR9678 silencing enhanced germination rates. We provide evidence that miR9678 targets a long noncoding RNA () and triggers the generation of phased small interfering RNAs that play a role in the delay of seed germination. Finally, we found that abscisic acid (ABA) signaling proteins bind the promoter of miR9678 precursor and activate its expression, indicating that miR9678 affects germination by modulating the GA/ABA signaling.

COR27 and COR28 encode nighttime repressors integrating Arabidopsis circadian clock and cold response FA Summary It was noted that circadian components function in plant adaptation to diurnal temperature cycles and freezing tolerance. Our genome-wide transcriptome analysis revealed that evening-phased COR27 and COR28 mainly repress the transcription of clockassociated evening genes PRR5, ELF4 and cold-responsive genes. Chromatin immunoprecipitation indicated that CCA1 is recruited to the site containing EE elements of COR27 and COR28 promoters in a temperaturedependent way. Further genetic analysis shows COR28 is essential for the circadian function of PRR9 and PRR7. Together, our results support a role of COR27 and COR28 as nighttime repressors integrating circadian clock and plant cold stress responses.Functional clocks confer plants with fitness advantages in their stationary life, including enhanced photosynthesis and vegetative biomass, growth vigor in hybrids and allopolyploids, timely responses to pathogen, cold stress tolerance, photoperiodic flowering, and hormone signaling responses and other agronomic traits (Greenham and McClung 2015; Seo and Mas 2015). The Arabidopsis circadian clock, like the circadian clock found in many other model organisms, is composed of multiple interlocked transcriptional/translational feedback loops (TTFLs). Circadian-associated genes PSEU-DORESPONSE REGULATOR PRR9, PRR7, PRR5, CIRCADIAN CLOCK ASSOCIATED1 (CCA1), LATE ELONGATED HYPO-COTYL (LHY), LUX ARRHYTHMO (LUX), GIGANTEA (GI) and TIMING OF CAB EXPRESSION1 (TOC1, also called PRR1) play critical roles in plant cold responses (Hsu and Harmer 2014). Transcription of Cold-inducible C-repeat (CRT) /dehydration-responsive binding factors CBF1, CBF2, and CBF3 are upregulated in triple mutant prr9-11 prr7-10 prr5-10 (d975). Overexpression of CCA1a isoform results in higher levels of CBF1-3 and GI transcripts (Seo et al. 2012). Temperature-associated alternative splicing of CCA1, LHY, PRR9, PRR7, PRR5, PRR3, TOC1 mediate responses of circadian clock to diurnal temperature changes; especially CCA1b isoform modulates temperature signaling into clock and CCA1a isoform contributes to plant freezing tolerance (James et al. 2012; Seo et al. 2012). Recent study has established preliminary feedback of cold signaling to circadian clock; CBF1 can directly bind to the promoter of LUX, and coldacclimated lux mutants are sensitive to freezing stress (Chow et al. 2014). Despite the importance of the crosstalk between cold-responsive genes in planta, and that the control of low temperature-stress response is one of great interest for circadian research, a known comprehensive architecture of these interactions is still lacking (Bieniawska et al. 2008; Espinoza et al. 2010; Eriksson and Webb 2011; Keily et al. 2013).To identify new evening components contributing to the Arabidopsis circadian transcriptional network, we examined three online platforms of genome-wide expression profiles, NASCArrays (http://affymetrix. arabidopsis.info, closed),...