Over-expression of miR172 causes loss of spikelet determinacy and floral organ abnormalities in rice (Oryza sativa)

<p>Abstract</p> <p>Background</p> <p>Regulation of gene expression by microRNAs (miRNAs) plays a crucial role in many developmental and physiological processes in plants. miRNAs act to repress expression of their target genes via mRNA cleavage or translational repression. Dozens of miRNA families have been identified in rice, 21 of which are conserved between rice and Arabidopsis. miR172 is a conserved miRNA family which has been shown to regulate expression of <it>APETALA2 </it>(<it>AP2</it>)-like transcription factors in Arabidopsis and maize. The rice genome encodes five <it>AP2</it>-like genes predicted to be targets of miR172. To determine whether these rice <it>AP2</it>-like genes are regulated by miR172 and investigate the function of the target genes, we studied the effect of over-expressing two members of the miR172 family on rice plant development.</p> <p>Results</p> <p>Analysis of miR172 expression showed that it is most highly expressed in late vegetative stages and developing panicles. Analyses of expression of three miR172 targets showed that <it>SUPERNUMERARY BRACT </it>(<it>SNB</it>) and <it>Os03g60430 </it>have high expression in developing panicles. Expression of miR172 was not inversely correlated with expression of its targets although miR172-mediated cleavage of <it>SNB </it>was detected by 5' rapid amplification of cDNA ends (RACE). Over-expression of miR172b in rice delayed the transition from spikelet meristem to floral meristem, and resulted in floral and seed developmental defects, including changes to the number and identity of floral organs, lower fertility and reduced seed weight. Plants over-expressing miR172b not only phenocopied the T-DNA insertion mutant of <it>SNB </it>but showed additional defects in floret development not seen in the <it>snb </it>mutant. However <it>SNB </it>expression was not reduced in the miR172b over-expression plants.</p> <p>Conclusions</p> <p>The phenotypes resulting from over-expression of miR172b suggests it represses <it>SNB </it>and at least one of the other miR172 targets, most likely <it>Os03g60430</it>, indicating roles for other <it>AP2</it>-like genes in rice floret development. miR172 and the <it>AP2</it>-like genes had overlapping expression patterns in rice and their expression did not show an obvious negative correlation. There was not a uniform decrease in the expression of the <it>AP2</it>-like miR172 target mRNAs in the miR172b over-expression plants. These observations are consistent with miR172 functioning via translational repression or with expression of the <it>AP2</it>-like genes being regulated by a negative feedback loop.</p

ALTERED MERISTEM PROGRAM 1 Is involved in Development of Seed Dormancy in Arabidopsis

Mutants in the rice PLASTOCHRON 3 and maize VIVIPAROUS 8 genes have been shown to have reduced dormancy and ABA levels. In this study we used several mutants in the orthologous gene ALTERED MERISTEM PROGRAM 1 (AMP1) to determine its role in seed dormancy in Arabidopsis. Here we report that there are accession-specific effects of mutations in AMP1. In one accession, amp1 mutants produce seeds with higher dormancy, while those in two other accessions produce seeds of lower dormancy. These accession-specific effects of mutating AMP1 were shown to extend to ABA levels. We assayed global gene transcription differences in seeds of wild-type and mutant from two accessions demonstrating opposing phenotypes. The transcript changes observed indicate that the amp1 mutation shifts the seed transcriptome from a dormant into an after-ripened state. Specific changes in gene expression in the mutants give insight into the direct and indirect effects that may be contributing to the opposing dormancy phenotypes observed, and reveal a role for AMP1 in the acquisition and/or maintenance of seed dormancy in Arabidopsis

Selection and mutation on microRNA target sequences during rice evolution

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) posttranscriptionally down-regulate gene expression by binding target mRNAs. Analysis of the evolution of miRNA binding sites is helpful in understanding the co-evolution between miRNAs and their targets. To understand this process in plants a comparative analysis of miRNA-targeted duplicated gene pairs derived from a well-documented whole genome duplication (WGD) event in combination with a population genetics study of six experimentally validated miRNA binding sites in rice (<it>O. sativa</it>) was carried out.</p> <p>Results</p> <p>Of the 1,331 pairs of duplicate genes from the WGD, 41 genes (29 pairs) were computationally predicted to be miRNA targets. Sequence substitution analysis indicated that the synonymous substitution rate was significantly lower in the miRNA binding sites than their 5' and 3' flanking regions. Of the 29 duplicated gene pairs, 17 have only one paralog been targeted by a miRNA. This could be due to either gain of a miRNA binding site after the WGD or because one of the duplicated genes has escaped from being a miRNA target after the WGD (loss of miRNA binding site). These possibilities were distinguished by separating miRNAs conserved in both dicots and monocot plants from rice-specific miRNAs and by phylogenetic analysis of miRNA target gene families. The gain/loss rate of miRNA binding sites was estimated to be 3.0 × 10^-9gain/loss per year. Most (70.6%) of the gains/losses were due to nucleotide mutation. By analysis of cultivated (<it>O. sativa</it>; <it>n </it>= 30) and wild (<it>O. rufipogon</it>; <it>n </it>= 15) rice populations, no segregating site was observed in six miRNA binding sites whereas 0.12–0.20 SNPs per 21-nt or 1.53–1.80 × 10^-3of the average pairwise nucleotide diversity (π) were found in their flanking regions.</p> <p>Conclusion</p> <p>Both molecular evolution and population genetics support the hypothesis that conservation of miRNA binding sites is maintained by purifying selection through elimination of deleterious alleles. Nucleotide mutations play a major role in the gain/loss of miRNA binding sites during evolution.</p

Dynamic modeling and target loads of sulfur and nitrogen for surface waters in Finland, Norway, Sweden, and the United Kingdom

The target load concept is an extension of the critical load concept of air pollution inputs to ecosystems. The advantage of target loads over critical loads is that one can define the deposition and the point in time (target year) when the critical (chemical) limit is no longer violated. This information on the timing of recovery requires dynamic modelling. Using a well-documented dynamic model, target loads for acidic deposition were determined for 848 surface waters across Finland, Norway, Sweden and the United Kingdom for the target year 2050. In the majority of sites (n = 675), the critical ANC-limit was predicted to be achieved by 2050; however, for 127 sites target loads were determined. In addition, 46 sites were infeasible, i.e., even a deposition reduction to zero would not achieve the limit by 2050. The average maximum target load for sulphur was 38% lower than the respective critical load across the study lakes (n = 127). Target loads on a large regional scale can inform effects-based emission reduction policies; the current assessment suggests that reductions beyond the Gothenburg Protocol are required to ensure surface water recovery from acidification by 2050

Sequence variation and selection of small RNAs in domesticated rice

<p>Abstract</p> <p>Background</p> <p>Endogenous non-coding small RNAs (21-24 nt) play an important role in post-transcriptional gene regulation in plants. Domestication selection is the most important evolutionary force in shaping crop genomes. The extent of polymorphism at small RNA loci in domesticated rice and whether small RNA loci are targets of domestication selection have not yet been determined.</p> <p>Results</p> <p>A polymorphism survey of 94 small RNA loci (88 <it>MIRNAs</it>, four <it>TAS3 </it>loci and two miRNA-like long hairpins) was conducted in domesticated rice, generating 2 Mb of sequence data. Many mutations (substitution or insertion/deletion) were observed at small RNA loci in domesticated rice, e.g. 12 mutation sites were observed in the mature miRNA sequences of 11 <it>MIRNAs </it>(12.5% of the investigated <it>MIRNAs</it>). Several small RNA loci showed significant signals for positive selection and/or potential domestication selection.</p> <p>Conclusions</p> <p>Sequence variation at miRNAs and other small RNAs is higher than expected in domesticated rice. Like protein-coding genes, non-coding small RNA loci could be targets of domestication selection and play an important role in rice domestication and improvement.</p

Vernalization-Repression of Arabidopsis FLC Requires Promoter Sequences but Not Antisense Transcripts

The repression of Arabidopsis FLC expression by vernalization (extended cold) has become a model for understanding polycomb-associated epigenetic regulation in plants. Antisense and sense non-coding RNAs have been respectively implicated in initiation and maintenance of FLC repression by vernalization. We show that the promoter and first exon of the FLC gene are sufficient to initiate repression during vernalization; this initial repression of FLC does not require antisense transcription. Long-term maintenance of FLC repression requires additional regions of the gene body, including those encoding sense non-coding transcripts

Longitudinal clusters of pain and stiffness in polymyalgia rheumatica: 2-year results from the PMR Cohort study

Objectives. To investigate potential subgroups of primary care diagnosed patients with polymyalgia rheumatica (PMR) based on self-reported pain and stiffness severity over time.Methods. 652 people with an incident PMR diagnosis were recruited from English general practices and completed a baseline postal questionnaire. They were followed-up with a further six questionnaires over a two-year period. 446 people completed 2-year follow-up. Pain and stiffness were reported on 0-10 numerical rating scales. Latent class growth analysis was used to estimate the joint trajectories of pain and stiffness overtime. A combination ofstatistical and clinical considerations was used to choose the number of clusters. Characteristics of the classes were described. Results. Five clusters were identified. One cluster represented the profile of ‘classical’ PMR symptoms and one represented sustained symptoms that may not be PMR. The other three clusters displayed a partial recovery, a recovery followed by worsening and a slow, but sustained recovery. Those displaying classical PMR symptoms were in better overall health at diagnosis than the other groups.Conclusions. PMR is a heterogeneous condition, with a number of phenotypes. The spectrum of presentation, as well as varying responses to treatment, may be related to underlying health status at diagnosis. Future research should seek to stratify patients at diagnosis to identify those likely to have a poor recovery and in need of an alternative treatment pathway. Clinicians should be aware of the different experiences of patients and monitor symptoms closely, even where there is initial improvement

The histone modification H3 lysine 27 tri-methylation has conserved gene regulatory roles in the triplicated genome of Brassica rapa L

© The Author(s) 2019. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. Brassica rapa L. is an important vegetable and oilseed crop. We investigated the distribution of the histone mark tri-methylation of H3K27 (H3K27me3) in B. rapa and its role in the control of gene expression at two stages of development (2-day cotyledons and 14-day leaves) and among paralogs in the triplicated genome. H3K27me3 has a similar distribution in two inbred lines, while there was variation of H3K27me3 sites between tissues. Sites that are specific to 2-day cotyledons have increased transcriptional activity, and low levels of H3K27me3 in the gene body region. In 14-day leaves, levels of H3K27me3 were associated with decreased gene expression. In the triplicated genome, H3K27me3 is associated with paralogs that have tissue-specific expression. Even though B. rapa and Arabidopsis thaliana are not closely related within the Brassicaceae, there is conservation of H3K27me3-marked sites in the two species. Both B. rapa and A. thaliana require vernalization for floral initiation with FLC being the major controlling locus. In all four BrFLC paralogs, low-temperature treatment increases H3K27me3 at the proximal nucleation site reducing BrFLC expression. Following return to normal temperature growth conditions, H3K27me3 spreads along all four BrFLC paralogs providing stable repression of the gene