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Genome editing using CRISPR/Cas9 is considered the best instrument for genome engineering in plants. This methodology is based on the nuclease activity of Cas9 that is guided to specific genome sequences by single guide RNAs (sgRNAs) thus enabling researchers to engineer simple mutations or large chromosomal deletions. Current methodologies for targeted genome editing in plants using CRISPR/Cas9 are however largely inefficient, mostly due to low Cas9 activity, variable sgRNA efficiency and low heritability of genetic lesions. Here, we describe a newly developed strategy to enhance CRISPR/Cas9 efficiency in Arabidopsis thaliana focusing on the design of novel binary vectors (pUbiCAS9-Red and pEciCAS9-Red), the selection of highly efficient sgRNAs, and the use of direct plant regeneration from induced cell cultures. Our work demonstrates that by combining these three independent developments, heritable targeted chromosomal deletions of large gene clusters and intergenic regulatory sequences can be engineered at a high efficiency. Our results demonstrate that this improved CRISPR/Cas9 methodology can provide a fast, efficient and cost-effective tool to engineer targeted heritable chromosomal deletions, which will be instrumental for future high-throughput functional genomics studies in plants.

Inducible epigenetic changes in eukaryotes are believed to enable rapid adaptation to environmental fluctuations. We have found distinct regions of the Arabidopsis genome that are susceptible to DNA (de)methylation in response to hyperosmotic stress. The stress-induced epigenetic changes are associated with conditionally heritable adaptive phenotypic stress responses. However, these stress responses are primarily transmitted to the next generation through the female lineage due to widespread DNA glycosylase activity in the male germline, and extensively reset in the absence of stress. Using the CNI1/ATL31 locus as an example, we demonstrate that epigenetically targeted sequences function as distantly-acting control elements of antisense long non-coding RNAs, which in turn regulate targeted gene expression in response to stress. Collectively, our findings reveal that plants use a highly dynamic maternal ‘short-term stress memory’ with which to respond to adverse external conditions. This transient memory relies on the DNA methylation machinery and associated transcriptional changes to extend the phenotypic plasticity accessible to the immediate offspring. Most plants spend their entire lives in one fixed spot and so must be able to quickly adapt to any changes in their surroundings. For example, high levels of salt in the soil – which can be toxic to cells – triggers stress responses in plants that help them to mitigate any damage. Once the stress has passed, plants are able to retain a memory of it, which allows them to respond more quickly if they face the same stress in future. Furthermore, plants may pass on this ‘stress memory’ to their offspring. It is thought that stress memory is programmed by chemical modifications to DNA known as epigenetic marks. These marks do not alter the genetic information that is encoded by the DNA itself, but they can change the activity of particular genes. Environmental stress leads to changes in the epigenetic marks found on many plant genes, which can be directly passed on from the parent plant to its offspring. However, it was not clear whether the epigenetic marks that programme stress memory can be passed on in this way. Wibowo, Becker et al. investigated how a model plant called Arabidopsis thaliana is able to remember periods of salt stress. The experiments show that high levels of salt can trigger changes in the patterns of epigenetic marks associated with particular regions of DNA. This memory is reinforced by repetitive exposure to similar salt stress and can be passed onto offspring, primarily through the maternal line. However, this stress memory is not fixed in future generations as the epigenetic marks can be reset to their original patterns if plants find themselves growing and reproducing under non-stress conditions. In sum, the findings of Wibowo, Becker et al. show that epigenetic marks allow plants to inherit stress memory on a temporary basis while the stress is present, but to gradually lose the memory if the stress does not return. Future studies will focus on finding out if stress memory in crop plants works in the same way.

Plants differ from animals in their capability to easily regenerate fertile adult individuals from terminally differentiated cells. This unique developmental plasticity is commonly observed in nature, where many species can reproduce asexually through the ectopic initiation of organogenic or embryogenic developmental programs. While organ-specific epigenetic marks are not passed on during sexual reproduction, the fate of epigenetic marks during asexual reproduction and the implications for clonal progeny remain unclear. Here we report that organ-specific epigenetic imprints in Arabidopsis thaliana can be partially maintained during asexual propagation from somatic cells in which a zygotic program is artificially induced. The altered marks are inherited even over multiple rounds of sexual reproduction, becoming fixed in hybrids and resulting in heritable molecular and physiological phenotypes that depend on the identity of the founder tissue. Consequently, clonal plants display distinct interactions with beneficial and pathogenic microorganisms. Our results demonstrate how novel phenotypic variation in plants can be unlocked through altered inheritance of epigenetic marks upon asexual propagation.

Although plants are able to withstand a range of environmental conditions, spikes in ambient temperature can impact plant fertility causing reductions in seed yield and notable economic losses 1 , 2 . Therefore, understanding the precise molecular mechanisms that underpin plant fertility under environmental constraints is critical to safeguarding future food production 3 . Here, we identified two Argonaute-like proteins whose activities are required to sustain male fertility in maize plants under high temperatures. We found that MALE-ASSOCIATED ARGONAUTE-1 and -2 associate with temperature-induced phased secondary small RNAs in pre-meiotic anthers and are essential to controlling the activity of retrotransposons in male meiocyte initials. Biochemical and structural analyses revealed how male-associated Argonaute activity and its interaction with retrotransposon RNA targets is modulated through the dynamic phosphorylation of a set of highly conserved, surface-located serine residues. Our results demonstrate that an Argonaute-dependent, RNA-guided surveillance mechanism is critical in plants to sustain male fertility under environmentally constrained conditions, by controlling the mutagenic activity of transposons in male germ cells. MALE-ASSOCIATED ARGONAUTE-1 and -2 promote heat-induced phasiRNA production, which represses heat-activated retrotransposons and protects male fertility. This activity is regulated by heat-mediated hypophosphorylation of the Argonaute proteins.

The Casparian Strip (CS) constitutes a physical diffusion barrier to water and nutrients in plant roots, and is formed by the polar deposition of lignin polymer in the endodermis. This precise pattern of lignin deposition is thought to be mediated by the scaffolding activity of membrane-bound Casparian Strip domain proteins (CASPs). However, we show that endodermis-specific receptor-like kinase 1 (ERK1) and ROP Binding Kinase1 (RBK1) are also involved in this intricate process, with the former playing an essential role both in the localization of CASP1 and in lignin deposition. We further characterised ERK1 and determined its subcellular localisation in the cytoplasm and nucleus of the endodermis, as well as provide evidence for its involvement in a signalling pathway together with the circadian clock regulator, Time for Coffee (TIC). We also show that disruption to CS organisation and increased suberisation in the endodermis due to loss of function of either ERK1 or TIC collectively leads to an altered root microbiome composition. Thus, our work reveals additional players in the complex cascade of signalling events operating in the root endodermis to establish both the CS diffusion barrier and the microbial composition of the rhizosphere.

Plants differ from animals in their capability to easily regenerate fertile adult individuals from terminally differentiated cells. This unique developmental plasticity is commonly observed in nature where many species can reproduce asexually through the ectopic initiation of organogenic or embryogenic developmental programs. However, it is not currently known if this developmental reprogramming is coupled to a global epigenomic resetting, or what impact it has on the phenotype of the clonal progeny. Here we show that plants asexually propagated via induction of a zygotic developmental program do not fully reset cell-specific epigenetic imprints. These imprints are instead inherited even over multiple rounds of sexual reproduction, becoming fixed in hybrids and resulting in heritable molecular and physiological phenotypes that depend on the founder cell used. Our results demonstrate how novel phenotypic variation in plants can be unlocked through the incomplete reprogramming of cell-specific epigenetic marks during asexual propagation.

ABSTRACT Although plants are able to withstand a range of environmental conditions, spikes in ambient temperature can impact plant fertility causing reductions in seed yield and significant economic losses1,2. Therefore, understanding the precise molecular mechanisms that underpin plant fertility under environmental constraints is critical to safeguard future food production3. Here, we identified two Argonaute-like proteins whose activities are required to sustain male fertility in maize plants under high temperatures. We found that MALE-ASSOCIATED ARGONAUTE 1 and 2 (MAGO1 and MAGO2) associate with temperature-induced phased secondary small RNAs in pre-meiotic anthers and are essential to control the activity of retrotransposons in male meiocyte initials. Biochemical and structural analyses revealed how MAGO2 activity and its interaction with retrotransposon RNA targets are modulated through the dynamic phosphorylation of a set of highly conserved surface-located serine residues. Our results demonstrate that an Argonaute-dependent RNA-guided surveillance mechanism is critical in plants to sustain male fertility under environmentally constrained conditions by controlling the mutagenic activity of transposons in male germ cells. Competing Interest Statement The authors have declared no competing interest.

Postoperative surgical site infections are one of the most frequent complications after open abdominal surgery, and triclosan-coated sutures were developed to reduce their occurrence. The aim of the PROUD trial was to obtain reliable data for the effectiveness of triclosan-coated PDS Plus sutures for abdominal wall closure, compared with non-coated PDS II sutures, in the prevention of surgical site infections. This multicentre, randomised controlled group-sequential superiority trial was done in 24 German hospitals. Adult patients (aged ≥18 years) who underwent elective midline abdominal laparotomy for any reason were eligible for inclusion. Exclusion criteria were impaired mental state, language problems, and participation in another intervention trial that interfered with the intervention or outcome of this trial. A central web-based randomisation tool was used to randomly assign eligible participants by permuted block randomisation with a 1:1 allocation ratio and block size 4 before mass closure to either triclosan-coated sutures (PDS Plus) or uncoated sutures (PDS II) for abdominal fascia closure. The primary endpoint was the occurrence of superficial or deep surgical site infection according to the Centers for Disease Control and Prevention criteria within 30 days after the operation. Patients, surgeons, and the outcome assessors were masked to group assignment. Interim and final analyses were by modified intention to treat. This trial is registered with the German Clinical Trials Register, number DRKS00000390. Between April 7, 2010, and Oct 19, 2012, 1224 patients were randomly assigned to intervention groups (607 to PDS Plus, and 617 to PDS II), of whom 1185 (587 PDS Plus and 598 PDS II) were analysed by intention to treat. The study groups were well balanced in terms of patient and procedure characteristics. The occurrence of surgical site infections did not differ between the PDS Plus group (87 [14·8%] of 587) and the PDS II group (96 [16·1%] of 598; OR 0·91, 95% CI 0·66–1·25; p=0·64). Serious adverse events also did not differ between the groups—146 of 583 (25·0%) patients treated with PDS Plus had at least one serious adverse event, compared with 138 of 602 (22·9%) patients treated with PDS II; p=0·39). Triclosan-coated PDS Plus did not reduce the occurrence of surgical site infection after elective midline laparotomy. Innovative, multifactorial strategies need to be developed and assessed in future trials to reduce surgical site infections. Johnson & Johnson Medical Limited.

Rabies is a neglected zoonotic disease that causes around 59,000 deaths per year globally. In Africa, rabies virus is mostly maintained in populations of free‐roaming domestic dogs (FRDD) that are predominantly owned. Characterizing the roaming behavior of FRDD can provide relevant information to understand disease spread and inform prevention and control interventions. To estimate the home range (HR) of FRDD and identify predictors of HR size, we studied 168 dogs in seven different areas of Blantyre city, Malawi, tracking them with GPS collars for 1–4 days. The median core HR (HR50) of FRDD in Blantyre city was 0.2 ha (range: 0.08–3.95), while the median extended HR (HR95) was 2.14 ha (range: 0.52–23.19). Multivariable linear regression models were built to identify predictors of HR size. Males presented larger HR95 than females. Dogs living in houses with a higher number of adults had smaller HR95, while those living in houses with higher number of children had larger HR95. Animals that received products of animal origin in their diets had larger HR95, and only in the case of females, animals living in low‐income areas had larger HR50 and HR95. In contrast, whether male dogs were castrated or not was not found to be associated with HR size. The results of this study may help inform rabies control and prevention interventions in Blantyre city, such as designing risk‐based surveillance activities or rabies vaccination campaigns targeting certain FRDD subpopulations. Our findings can also be used in rabies awareness campaigns, particularly to illustrate the close relationship between children and their dogs. In Africa, rabies virus is mostly maintained in populations of free‐roaming domestic dogs (FRDD) that are predominantly owned. Characterizing the roaming behavior of FRDD can provide relevant information to understand disease spread and inform prevention and control interventions. In our study, we tracked with GPS collars 168 FRDD in Blantyre city, Malawi, to estimate their home range and identify predictors of HR size.