There is a lack of knowledge on the tissue-specific expression of miRNAs in response to dehydration stress in Brachypodium (Brachypodium distachyon (L.) Beauv), a model for temperate grass species. In this study, miRNA expression patterns of drought-tolerant Brachypodium were investigated using the miRNA microarray platform. A total of 205 miRNAs in control and 438 miRNAs in both drought-treated leaf and root tissues were expressed. Seven of the detected Brachypodium miRNAs were dehydration stress responsive. Expression levels of known drought-responsive miRNAs, miR896, and miR1867 were quantified by qRT-PCR in Brachypodium upon 4 h and 8 h dehydration stress applications. This was performed to compare drought responsiveness of miRNAs in closely related species. Target transcripts of selected drought responsive miRNAs, miR170, miR1850, miR896, miR406, miR528, miR390, were computationally predicted. Target transcript of miR896 was verified by retrieving a cleaved miR896 transcript from drought stress-treated leaf samples using a modified 5' RLM-RACE. Brachypodium dehydration responsive miRNA were also detected in barley and wild emmer wheat. Hence, the outcomes highlighted the conserved features of miRNA upon dehydration stress in Triticeae.

Background: Photoperiod signals provide important cues by which plants regulate their growth and development in response to predictable seasonal changes. Phytochromes, a family of red and far-red light receptors, play critical roles in regulating flowering time in response to changing photoperiods. A previous study showed that loss-offunction mutations in either PHYB or PHYC result in large delays in heading time and in the differential regulation of a large number of genes in wheat plants grown in an inductive long day (LD) photoperiod. Results: We found that under non-inductive short-day (SD) photoperiods, phyB-null and phyC-null mutants were taller, had a reduced number of tillers, longer and wider leaves, and headed later than wild-type (WT) plants. The delay in heading between WT and phy mutants was greater in LD than in SD, confirming the importance of PHYB and PHYC in accelerating heading date in LDs. Both mutants flowered earlier in SD than LD, the inverse response to that of WT plants. In both SD and LD photoperiods, PHYB regulated more genes than PHYC. We identified subsets of differentially expressed and alternatively spliced genes that were specifically regulated by PHYB and PHYC in either SD or LD photoperiods, and a smaller set of genes that were regulated in both photoperiods. We found that photoperiod had a contrasting effect on transcript levels of the flowering promoting genes VRN-A1 and PPD-B1 in phyB and phyC mutants compared to the WT. Conclusions: Our study confirms the major role of both PHYB and PHYC in flowering promotion in LD conditions. Transcriptome characterization revealed an unexpected reversion of the wheat LD plants into SD plants in the phyB-null and phyC-null mutants and identified flowering genes showing significant interactions between phytochromes and photoperiod that may be involved in this phenomenon. Our RNA-seq data provides insight into light signaling pathways in inductive and non-inductive photoperiods and a set of candidate genes to dissect the underlying developmental regulatory networks in wheat.

25Background: Photoperiod signals provide important cues by which plants regulate their growth 26 and development in response to predictable seasonal changes. Phytochromes, a family of red and 27 far-red light receptors, play critical roles in regulating flowering time in response to changing 28 photoperiods. A previous study showed that loss-of-function mutations in either PHYB or PHYC 29 result in large delays in heading time and in the differential regulation of a large number of genes 30 in wheat plants grown in an inductive long day (LD) photoperiod. 31 Results:We found that under non-inductive short-day (SD) photoperiods, phyB-null and phyC-32 null mutants were taller, had a reduced number of tillers, longer and wider leaves, and headed 33 later than wild-type plants. Unexpectedly, both mutants flowered earlier in SD than LD, the 34 inverse response to that of wild-type plants. We observed a larger number of differentially 35 expressed genes between mutants and wild-type under SD than under LD, and in both cases, the 36 number was larger for phyB than for phyC. We identified subsets of differentially expressed and 37 alternatively spliced genes that were specifically regulated by PHYB and PHYC in either SD or 38 LD photoperiods, and a smaller set of genes that were regulated in both photoperiods. We 39 observed significantly higher transcript levels of the flowering promoting genes VRN-A1, PPD-40 B1 and GIGANTEA in the phy-null mutants in SD than in LD, which suggests that they could 41 contribute to the earlier flowering of the phy-null mutants in SD than in LD. 42 Conclusions: Our study revealed an unexpected reversion of the wheat LD plants into SD plants 43in the phyB-null and phyC-null mutants and identified candidate genes potentially involved in 44 this phenomenon. Our RNA-seq data provides insight into light signaling pathways in inductive 45 and non-inductive photoperiods and a set of candidate genes to dissect the underlying 46 developmental regulatory networks in wheat. 47 Keywords: Wheat, heading date, phytochrome, FT1, FT2, FT3, PPD1, VRN1. 48 Background 49As sessile organisms, plants must be able to respond to fluctuations in their environment to 50 maximize their reproductive success. To achieve this, plants have evolved a series of regulatory 51 mechanisms to ensure that critical stages of their development coincide with optimal 52 environmental conditions. One important determinant of reproductive success is flowering time, 53 which is strongly influenced by seasonal changes in photoperiod and temperature [1]. In cereal 54 crops, these cues are fundamental to ensure the plant does not flower too early, to prevent 55 exposure of sensitive reproductive tissues to late-spring frosts, or too late, so as to minimize 56 exposure to damaging high temperatures during grain filling [2]. There is a direct link between 57 reproductive success and grain production, so characterizing the regulatory networks underlying 58 flowering time is critical to support the development of resilient crop varieties, ...

Linking mitochondrial DNA (mtDNA) mutations to patient outcomes remains a formidable challenge. The multicopy nature and potential heteroplasmy of the mitochondrial genome, differential distribution of mutant mtDNAs among various tissues, genetic interactions among alleles, and environmental effects currently hamper clinical efforts to diagnose mitochondrial disease. Multiple sequence alignments are often deployed to estimate the potential significance of mitochondrial variants. However, factors including sample set bias, alignment errors, and sequencing errors currently limit the utility of multiple sequence alignments in pathogenicity prediction. Here, we describe an approach to assessment of site-specific conservation and variant acceptability that is reliant upon ancestral phylogenetic predictions and minimizes current alignment limitations. Using the output of our approach, we deploy machine learning in order to predict the pathogenicity of thousands of human mtDNA variants not yet linked to disease. Our work demonstrates that a substantial portion of mtDNA variants not yet characterized as harmful are, in fact, likely to be deleterious. Our findings will be of direct relevance to those at risk of mitochondria-associated illness, but the general applications of our methodology also extend beyond the context of mitochondrial disorders.