Implementation of inclusion and exclusion criteria in clinical studies in OHDSI ATLAS software.

Clinical trials are essential parts of a medical study process, but studies are often cancelled due to a lack of participants. Clinical Trial Recruitment Support Systems are systems that help to increase the number of participants by seeking more suitable subjects. The software ATLAS (developed by Observational Health Data Sciences and Informatics) can support the launch of a clinical trial by building cohorts of patients who fulfill certain criteria. The correct use of medical classification systems aiming at clearly defined inclusion and exclusion criteria in the studies is an important pillar of this software. The aim of this investigation was to determine whether ATLAS can be used in a Clinical Trial Recruitment Support System to portray the eligibility criteria of clinical studies. Our analysis considered the number of criteria feasible for integration with ATLAS and identified its strengths and weaknesses. Additionally, we investigated whether nonrepresentable criteria were associated with the utilized terminology systems. We analyzed ATLAS using 223 objective eligibility criteria from 30 randomly selected trials conducted in the last 10 years. In the next step, we selected appropriate ICD, OPS, LOINC, or ATC codes to feed the software. We classified each criterion and study based on its implementation capability in the software, ensuring a clear and logical progression of information. Based on our observations, 51% of the analyzed inclusion criteria were fully implemented in ATLAS. Within our selected example set, 10% of the studies were classified as fully portrayable, and 73% were portrayed to some extent. Additionally, we conducted an evaluation of the software regarding its technical limitations and interaction with medical classification systems. To improve and expand the scope of criteria within a cohort definition in a practical setting, it is recommended to work closely with personnel involved in the study to define the criteria precisely and to carefully select terminology systems. The chosen criteria should be combined according to the specific setting. Additional work is needed to specify the significance and amount of the extracted criteria.

Strong temporal dynamics of QTL action on plant growth progression revealed through high-throughput phenotyping in canola.

A major challenge of plant biology is to unravel the genetic basis of complex traits. We took advantage of recent technical advances in high-throughput phenotyping in conjunction with genome-wide association studies to elucidate genotype-phenotype relationships at high temporal resolution. A diverse Brassica napus population from a commercial breeding programme was analysed by automated non-invasive phenotyping. Time-resolved data for early growth-related traits, including estimated biovolume, projected leaf area, early plant height and colour uniformity, were established and complemented by fresh and dry weight biomass. Genome-wide SNP array data provided the framework for genome-wide association analyses. Using time point data and relative growth rates, multiple robust main effect marker-trait associations for biomass and related traits were detected. Candidate genes involved in meristem development, cell wall modification and transcriptional regulation were detected. Our results demonstrate that early plant growth is a highly complex trait governed by several medium and many small effect loci, most of which act only during short phases. These observations highlight the importance of taking the temporal patterns of QTL/allele actions into account and emphasize the need for detailed time-resolved analyses to effectively unravel the complex and stage-specific contributions of genes affecting growth processes that operate at different developmental phases.

Inherited allelic variants and novel karyotype changes influence fertility and genome stability in Brassica allohexaploids.

Synthetic allohexaploid Brassica hybrids (2n = AABBCC) do not exist naturally, but can be synthesized by crosses between diploid and/or allotetraploid Brassica species. Using these hybrids, we aimed to identify how novel allohexaploids restore fertility and normal meiosis after formation. Chromosome inheritance, genome structure, fertility and meiotic behaviour were assessed in three segregating allohexaploid populations derived from the cross (B. napus × B. carinata) × B. juncea using a combination of molecular marker genotyping, phenotyping and cytogenetics. Plants with unbalanced A-C translocations in one direction (where a C-genome chromosome fragment replaces an A-genome fragment) but not the other (where an A-genome fragment replaces a C-genome fragment) showed significantly reduced fertility across all populations. Genomic regions associated with fertility contained several meiosis genes with putatively causal mutations inherited from the parents (copies of SCC2 in the A genome, PAIR1/PRD3, PRD1 and ATK1/KATA/KIN14a in the B genome, and MSH2 and SMC1/TITAN8 in the C genome). Reduced seed fertility associated with the loss of chromosome fragments from only one subgenome following homoeologous exchanges could comprise a mechanism for biased genome fractionation in allopolyploids. Pre-existing meiosis gene variants present in allotetraploid parents may help to stabilize meiosis in novel allohexaploids.

Effect of breeding on nitrogen use efficiency-associated traits in oilseed rape.

Oilseed rape is one of the most important dicotyledonous field crops in the world, where it plays a key role in productive cereal crop rotations. However, its production requires high nitrogen fertilization and its nitrogen footprint exceeds that of most other globally important crops. Hence, increased nitrogen use efficiency (NUE) in this crop is of high priority for sustainable agriculture. We report a comprehensive study of macrophysiological characteristics associated with breeding progress, conducted under contrasting nitrogen fertilization levels in a large panel of elite oilseed rape varieties representing breeding progress over the past 20 years. The results indicate that increased plant biomass at flowering, along with increases in primary yield components, have increased NUE in modern varieties. Nitrogen uptake efficiency has improved through breeding, particularly at high nitrogen. Despite low heritability, the number of seeds per silique is associated positively with increased yield in modern varieties. Seed weight remains unaffected by breeding progress; however, recent selection for high seed oil content and for high seed yields appears to have promoted a negative correlation (r= -0.39 at high and r= -0.49 at low nitrogen) between seed weight and seed oil concentration. Overall, our results reveal valuable breeding targets to improve NUE in oilseed rape.

Sorghum root-system classification in contrasting P environments reveals three main rooting types and root-architecture-related marker-trait associations.

Background and Aims: Roots facilitate acquisition of macro- and micronutrients, which are crucial for plant productivity and anchorage in the soil. Phosphorus (P) is rapidly immobilized in the soil and hardly available for plants. Adaptation to P scarcity relies on changes in root morphology towards rooting systems well suited for topsoil foraging. Root-system architecture (RSA) defines the spatial organization of the network comprising primary, lateral and stem-derived roots and is important for adaptation to stress conditions. RSA phenotyping is a challenging task and essential for understanding root development. Methods: In this study, 19 traits describing RSA were analysed in a diversity panel comprising 194 sorghum genotypes, fingerprinted with a 90-k single-nucleotide polymorphism (SNP) array and grown under low and high P availability. Key Results: Multivariate analysis was conducted and revealed three different RSA types: (1) a small root system; (2) a compact and bushy rooting type; and (3) an exploratory root system, which might benefit plant growth and development if water, nitrogen (N) or P availability is limited. While several genotypes displayed similar rooting types in different environments, others responded to P scarcity positively by developing more exploratory root systems, or negatively with root growth suppression. Genome-wide association studies revealed significant quantitative trait loci (P < 2.9 × 10-6) on chromosomes SBI-02, SBI-03, SBI-05 and SBI-09. Co-localization of significant and suggestive (P < 5.7 × 10-5) associations for several traits indicated hotspots controlling root-system development on chromosomes SBI-02 and SBI-03. Conclusions: Sorghum genotypes with a compact, bushy and shallow root system provide potential adaptation to P scarcity in the field by allowing thorough topsoil foraging, while genotypes with an exploratory root system may be advantageous if N or water is the limiting factor, although such genotypes showed highest P uptake levels under the artificial conditions of the present study.

Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus.

Homoeologous exchanges (HEs) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence variation (PAV) is also a major contributor to genetic diversity. In this study, we show that there is an association between these two events, particularly in recent Brassica napus synthetic accessions, and that these represent a novel source of genetic diversity, which can be captured for the improvement of this important crop species. By assembling the pangenome of B. napus, we show that 38% of the genes display PAV behaviour, with some of these variable genes predicted to be involved in important agronomic traits including flowering time, disease resistance, acyl lipid metabolism and glucosinolate metabolism. This study is a first and provides a detailed characterization of the association between HEs and PAVs in B. napus at the pangenome level.

Genetic dissection of early-season cold tolerance in sorghum: genome-wide association studies for seedling emergence and survival under field and controlled environment conditions.

KEY MESSAGE: A QTL on sorghum chromosome SBI-06 putatively improves field emergence under low-temperature conditions. Low temperatures decisively limit seedling emergence and vigor during early growth of sorghum and, thus, strongly impair geographical expansion. To broaden sorghum cultivation to temperate regions, the establishment of cold-tolerant genotypes is a prioritized breeding goal. The present study aims at the quantification of seedling emergence and survival under chilling temperatures and the detection of marker-trait associations controlling temperature-related seedling establishment. A diversity set consisting of 194 biomass sorghum lines was subjected to extensive phenotyping comprising field trials and controlled environment experiments. The final emergence percentage (FEP) under field conditions was significantly reduced under cold stress. Broad-sense heritability was h 2 = 0.87 for FEP in the field and h 2 = 0.93 for seedling survival rate (SR) under controlled conditions. Correlations between FEP in the field and under controlled conditions were low; higher correlations were observed between field FEP and SR in controlled environments. Genome-wide association studies (GWAS) were conducted using 44,515 single nucleotide polymorphisms (SNPs) and revealed eight regions with suggestive marker-trait associations for FEP and SR on chromosomes SBI-01, -02, -03, -06, -09, and -10 (p < 5.7 × 10-5) and a significant association on SBI-06 for field FEP (p < 2.9 × 10-6). Although not significant under controlled conditions, SR of genotypes carrying the minor allele on the field FEP quantitative trait loci (QTL) on SBI-06 was on average 13.1% higher, while FEP under controlled conditions was on average 9.7% higher with a linearly decreasing effect with increasing temperatures (R 2 = 0.82). Promising candidate genes putatively conferring seedling cold tolerance were identified.

Transcriptome dynamic of Arabidopsis roots infected with Phytophthora parasitica identifies VQ29, a gene induced during the penetration and involved in the restriction of infection.

Little is known about the responses of plant roots to filamentous pathogens, particularly to oomycetes. To assess the molecular dialog established between the host and the pathogen during early stages of infection, we investigated the overall changes in gene expression in A. thaliana roots challenged with P. parasitica. We analyzed various infection stages, from penetration and establishment of the interaction to the switch from biotrophy to necrotrophy. We identified 3390 genes for which expression was modulated during the infection. The A. thaliana transcriptome displays a dynamic response to P. parasitica infection, from penetration onwards. Some genes were specifically coregulated during penetration and biotrophic growth of the pathogen. Many of these genes have functions relating to primary metabolism, plant growth, and defense responses. In addition, many genes encoding VQ motif-containing proteins were found to be upregulated in plant roots, early in infection. Inactivation of VQ29 gene significantly increased susceptibility to P. parasitica during the late stages of infection. This finding suggests that the gene contributes to restricting oomycete development within plant tissues. Furthermore, the vq29 mutant phenotype was not associated with an impairment of plant defenses involving SA-, JA-, and ET-dependent signaling pathways, camalexin biosynthesis, or PTI signaling. Collectively, the data presented here thus show that infection triggers a specific genetic program in roots, beginning as soon as the pathogen penetrates the first cells.

Drought-Tolerant Brassica rapa Shows Rapid Expression of Gene Networks for General Stress Responses and Programmed Cell Death Under Simulated Drought Stress.

Production of oilseed rape/canola (Brassica napus) is increasingly threatened by dry conditions while the demand for vegetable oil is increasing. Brassica rapa is a genetically diverse ancestor of B. napus, and is readily crossed with B. napus. Recently, we reported promising levels of drought tolerance in a wild type of B. rapa which could be a source of drought tolerance for B. napus. We analysed global gene expression by messenger RNA sequencing in seedlings of the drought-tolerant and a drought-sensitive genotype of B. rapa under simulated drought stress and control conditions. A subset of stress-response genes were validated by reverse transcription quantitative PCR. Gene ontology enrichment analysis and pathway enrichment analysis revealed major differences between the two genotypes in the mode and onset of stress responses in the first 12 h of treatment. Drought-tolerant plants reacted uniquely and rapidly by upregulating genes associated with jasmonic acid and salicylic acid metabolism, as well as genes known to cause endoplasmic reticulum stress and induction of programmed cell death. Conversely, active responses in drought-sensitive plants were delayed until 8 or 12 h after stress application. The results may help to identify biomarkers for selection of breeding materials with potentially improved drought tolerance.

Mapping of homoeologous chromosome exchanges influencing quantitative trait variation in Brassica napus.

Genomic rearrangements arising during polyploidization are an important source of genetic and phenotypic variation in the recent allopolyploid crop Brassica napus. Exchanges among homoeologous chromosomes, due to interhomoeologue pairing, and deletions without compensating homoeologous duplications are observed in both natural B. napus and synthetic B. napus. Rearrangements of large or small chromosome segments induce gene copy number variation (CNV) and can potentially cause phenotypic changes. Unfortunately, complex genome restructuring is difficult to deal with in linkage mapping studies. Here, we demonstrate how high-density genetic mapping with codominant, physically anchored SNP markers can detect segmental homoeologous exchanges (HE) as well as deletions and accurately link these to QTL. We validated rearrangements detected in genetic mapping data by whole-genome resequencing of parental lines along with cytogenetic analysis using fluorescence in situ hybridization with bacterial artificial chromosome probes (BAC-FISH) coupled with PCR using primers specific to the rearranged region. Using a well-known QTL region influencing seed quality traits as an example, we confirmed that HE underlies the trait variation in a DH population involving a synthetic B. napus trait donor, and succeeded in narrowing the QTL to a small defined interval that enables delineation of key candidate genes.

Surviving a Genome Collision: Genomic Signatures of Allopolyploidization in the Recent Crop Species Brassica napus.

Polyploidization has played a major role in crop plant evolution, leading to advantageous traits that have been selected by humans. Here, we describe restructuring patterns in the genome of L., a recent allopolyploid species. Widespread segmental deletions, duplications, and homeologous chromosome exchanges were identified in diverse genome sequences from 32 natural and 20 synthetic accessions, indicating that homeologous exchanges are a major driver of postpolyploidization genome diversification. Breakpoints of genomic rearrangements are rich in microsatellite sequences that are known to interact with the meiotic recombination machinery. In both synthetic and natural , a subgenome bias was observed toward exchanges replacing larger chromosome segments from the C-subgenome by their smaller, homeologous A-subgenome segments, driving postpolyploidization genome size reduction. Selection in natural favored segmental deletions involving genes associated with immunity, reproduction, and adaptation. Deletions affecting mismatch repair system genes, which are assumed to control homeologous recombination, were also found to be under selection. Structural exchanges between homeologous subgenomes appear to be a major source of novel genetic diversity in de novo allopolyploids. Documenting the consequences of genomic collision by genomic resequencing gives insights into the adaptive processes accompanying allopolyploidization.

gsrc: an R package for genome structure rearrangement calling.

Summary: Genome structure rearrangements are a common phenomenon in allopolyploid species. Deletions, duplications and homeologous non-reciprocal translocations (HNRT) between the highly similar subgenomes can be observed, which are known to have a large impact on phenotypic traits. Current research is limited because these rearrangements can be located genome wide only by cost intensive sequencing approaches and not reliably in high-density array genotyping data. We developed gsrc, an R-package to detect genome structure rearrangements from genotyping data in allopolyploid species including exchanges between subgenomes. We exemplarily apply gsrc to a publicly available Brassica napus dataset. Availability and Implementation: The compiled R-package and source code are available at http://cran.r-project.org/web/packages/gsrc/ . Contact: birgit.samans@uni-giessen.de. Supplementary information: Supplementary data are available at Bioinformatics online.

Deletion of a Stay-Green Gene Associates with Adaptive Selection in Brassica napus.

Chlorophyll levels provide important information about plant growth and physiological plasticity in response to changing environments. The stay-green gene NON-YELLOWING 1 (NYE1) is believed to regulate chlorophyll degradation during senescence, concomitantly affecting the disassembly of the light-harvesting complex and hence indirectly influencing photosynthesis. We identified Brassica napus accessions carrying an NYE1 deletion associated with increased chlorophyll content, and with upregulated expression of light-harvesting complex and photosynthetic reaction center (PSI and PSII) genes. Comparative analysis of the seed oil content of accessions with related genetic backgrounds revealed that the B. napus NYE1 gene deletion (bnnye1) affected oil accumulation, and linkage disequilibrium signatures suggested that the locus has been subject to artificial selection by breeding in oilseed B. napus forms. Comparative analysis of haplotype diversity groups (haplogroups) between three different ecotypes of the allopolyploid B. napus and its A-subgenome diploid progenitor, Brassica rapa, indicated that introgression of the bnnye1 deletion from Asian B. rapa into winter-type B. napus may have simultaneously improved its adaptation to cooler environments experienced by autumn-sown rapeseed.

Species-wide genome sequence and nucleotide polymorphisms from the model allopolyploid plant Brassica napus.

Brassica napus (oilseed rape, canola) is one of the world's most important sources of vegetable oil for human nutrition and biofuel, and also a model species for studies investigating the evolutionary consequences of polyploidisation. Strong bottlenecks during its recent origin from interspecific hybridisation, and subsequently through intensive artificial selection, have severely depleted the genetic diversity available for breeding. On the other hand, high-throughput genome profiling technologies today provide unprecedented scope to identify, characterise and utilise genetic diversity in primary and secondary crop gene pools. Such methods also enable implementation of genomic selection strategies to accelerate breeding progress. The key prerequisite is availability of high-quality sequence data and identification of high-quality, genome-wide sequence polymorphisms representing relevant gene pools. We present comprehensive genome resequencing data from a panel of 52 highly diverse natural and synthetic B. napus accessions, along with a stringently selected panel of 4.3 million high-confidence, genome-wide SNPs. The data is of great interest for genomics-assisted breeding and for evolutionary studies on the origins and consequences in allopolyploidisation in plants.

Microspore culture reveals complex meiotic behaviour in a trigenomic Brassica hybrid.

BACKGROUND: Development of synthetic allohexaploid Brassica (2n = AABBCC) would be beneficial for agriculture, as allelic contributions from three genomes could increase hybrid vigour and broaden adaptation. Microspore culture of a near-allohexaploid hybrid derived from the cross (B. napus × B. carinata) × B. juncea was undertaken in order to assess the frequency and distribution of homologous and homoeologous crossovers in this trigenomic hybrid. SNP and SSR molecular markers were used to detect inheritance of A, B and C genome alleles in microspore-derived (MD) progeny. SNP allele copy number was also assessed. The MD progeny were also compared to progeny derived by self-pollination and open-pollination for fertility (estimated by self-pollinated seed set and pollen viability) and DNA ploidy (measured by flow cytometry). RESULTS: In the trigenomic hybrid, homologous chromosome pairs A(j)-A(n), B(j)-B(c) and C(n)-C(c) had similar meiotic crossover frequencies and segregation to that previously observed in established Brassica species, as demonstrated by marker haplotype analysis of the MD population. Homoeologous pairing between chromosomes A1-C1, A2-C2 and A7-C6 was detected at frequencies of 12-18 %, with other homoeologous chromosome regions associating from 8 % (A3-C3) to 0-1 % (A8-C8, A8-C9) of the time. Copy number analysis revealed eight instances of additional chromosomes and 20 instances of chromosomes present in one copy in somatically doubled MD progeny. Presence of chromosome A6 was positively correlated with self-pollinated seed set and pollen viability in the MD population. Many MD progeny were unable to produce self-pollinated seed (76 %) or viable pollen (53 %), although one MD plant produced 198 self-pollinated seeds. Average fertility was significantly lower in progeny obtained by microspore culture than progeny obtained by self-pollination or open-pollination, after excluding MD progeny which had not undergone chromosome doubling. CONCLUSIONS: Based on SNP data analysis of the microspore-derived progeny, crossover frequency per chromosome in the allohexaploid hybrid was found to be similar to that in established Brassica species, suggesting that the higher chromosome number did not significantly disrupt cellular regulation of meiosis. SNP allele copy number analysis revealed the occurrence not only of homoeologous duplication/deletion events but also other cryptic duplications and deletions that may have been the result of mitotic instability. Microspore culture simplified the assessment of chromosome behaviour in the allohexaploid hybrid but yielded progeny with lower fertility and a greater range of ploidy levels compared to progeny obtained by self- or open-pollination.

Species- and genome-wide dissection of the shoot ionome in Brassica napus and its relationship to seedling development.

Knowing the genetic basis of the plant ionome is essential for understanding the control of nutrient transport and accumulation. The aim of this research was to (i) study mineral nutrient concentrations in a large and diverse set of Brassica napus, (ii) describe the relationships between the shoot ionome and seedling development, and (iii) identify genetic regions associated with variation of the shoot ionome. The plant material under study was a germplasm set consisting of 509 inbred lines that was genotyped by a 6K single nucleotide polymorphism (SNP) array and phenotyped by analyzing the concentrations of eleven mineral nutrients in the shoots of 30 days old seedlings. Among mineral concentrations, positive correlations were found, whereas mineral concentrations were mainly negatively correlated with seedling development traits from earlier studies. In a genome-wide association mapping approach, altogether 29 significantly associated loci were identified across seven traits after correcting for multiple testing. The associations included a locus with effects on the concentrations of Cu, Mn, and Zn on chromosome C3, and a genetic region with multiple associations for Na concentration on chromosome A9. This region was situated within an association hotspot close to SOS1, a key gene for Na tolerance in plants.

Capturing sequence variation among flowering-time regulatory gene homologs in the allopolyploid crop species Brassica napus.

Flowering, the transition from the vegetative to the generative phase, is a decisive time point in the lifecycle of a plant. Flowering is controlled by a complex network of transcription factors, photoreceptors, enzymes and miRNAs. In recent years, several studies gave rise to the hypothesis that this network is also strongly involved in the regulation of other important lifecycle processes ranging from germination and seed development through to fundamental developmental and yield-related traits. In the allopolyploid crop species Brassica napus, (genome AACC), homoeologous copies of flowering time regulatory genes are implicated in major phenological variation within the species, however the extent and control of intraspecific and intergenomic variation among flowering-time regulators is still unclear. To investigate differences among B. napus morphotypes in relation to flowering-time gene variation, we performed targeted deep sequencing of 29 regulatory flowering-time genes in four genetically and phenologically diverse B. napus accessions. The genotype panel included a winter-type oilseed rape, a winter fodder rape, a spring-type oilseed rape (all B. napus ssp. napus) and a swede (B. napus ssp. napobrassica), which show extreme differences in winter-hardiness, vernalization requirement and flowering behavior. A broad range of genetic variation was detected in the targeted genes for the different morphotypes, including non-synonymous SNPs, copy number variation and presence-absence variation. The results suggest that this broad variation in vernalization, clock and signaling genes could be a key driver of morphological differentiation for flowering-related traits in this recent allopolyploid crop species.

Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.

Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.

Uniformity of nucleosome preservation pattern in Mammalian sperm and its connection to repetitive DNA elements.

Nucleosome-to-protamine exchange during mammalian spermiogenesis is essential for compaction and protection of paternal DNA. It is interesting that, depending on the species, 1% to 15% of nucleosomes are retained, but the generalizability and biological function of this retention are unknown. Here, we show concordantly in human and bovine that nucleosomes remained in sperm chromatin predominantly within distal intergenic regions and introns and associated with centromere repeats and retrotransposons (LINE1 and SINEs). In contrast, nucleosome depletion concerned particularly exons, 5'-UTR, 3'-UTR, TSS, and TTS and was associated with simple and low-complexity repeats. Overlap of human and bovine genes exhibiting nucleosome preservation in the promoter and gene body revealed a significant enrichment of signal transduction and RNA- and protein-processing factors. Our study demonstrates the genome-wide uniformity of the nucleosome preservation pattern in mammalian sperm and its connection to repetitive DNA elements and suggests a function in preimplantation processes for paternally derived nucleosomes.

N-Acyl-Homoserine Lactone Primes Plants for Cell Wall Reinforcement and Induces Resistance to Bacterial Pathogens via the Salicylic Acid/Oxylipin Pathway.

The ability of plants to monitor their surroundings, for instance the perception of bacteria, is of crucial importance. The perception of microorganism-derived molecules and their effector proteins is the best understood of these monitoring processes. In addition, plants perceive bacterial quorum sensing (QS) molecules used for cell-to-cell communication between bacteria. Here, we propose a mechanism for how N-acyl-homoserine lactones (AHLs), a group of QS molecules, influence host defense and fortify resistance in Arabidopsis thaliana against bacterial pathogens. N-3-oxo-tetradecanoyl-l-homoserine lactone (oxo-C14-HSL) primed plants for enhanced callose deposition, accumulation of phenolic compounds, and lignification of cell walls. Moreover, increased levels of oxylipins and salicylic acid favored closure of stomata in response to Pseudomonas syringae infection. The AHL-induced resistance seems to differ from the systemic acquired and the induced systemic resistances, providing new insight into inter-kingdom communication. Consistent with the observation that short-chain AHLs, unlike oxo-C14-HSL, promote plant growth, treatments with C6-HSL, oxo-C10-HSL, or oxo-C14-HSL resulted in different transcriptional profiles in Arabidopsis. Understanding the priming induced by bacterial QS molecules augments our knowledge of plant reactions to bacteria and suggests strategies for using beneficial bacteria in plant protection.