Late Holocene relative sea-level records from coral microatolls in Singapore.

Late Holocene relative sea-level (RSL) data are important to understand the drivers of RSL change, but there is a lack of precise RSL records from the Sunda Shelf. Here, we produced a Late Holocene RSL reconstruction from coral microatolls in Singapore, demonstrating for the first time the utility of Diploastrea heliopora microatolls as sea-level indicators. We produced 12 sea-level index points and three marine limiting data with a precision of < ± 0.2 m (2σ) and < ± 26 years uncertainties (95% highest density region). The data show a RSL fall of 0.31 ± 0.18 m between 2.8 and 0.6 thousand years before present (kyr BP), at rates between - 0.1 ± 0.3 and - 0.2 ± 0.7 mm/year. Surface profiles of the fossil coral microatolls suggest fluctuations in the rate of RSL fall: (1) stable between 2.8 and 2.5 kyr BP; (2) rising at ~ 1.8 kyr BP; and (3) stable from 0.8 to 0.6 kyr BP. The microatoll record shows general agreement with published, high-quality RSL data within the Sunda Shelf. Comparison to a suite of glacial isostatic adjustment (GIA) models indicate preference for lower viscosities in the mantle. However, more high quality and precise Late Holocene RSL data are needed to further evaluate the drivers of RSL change in the region and better constrain GIA model parameters.

ERNet: An Efficient and Reliable Human-Object Interaction Detection Network.

Human-Object Interaction (HOI) detection recognizes how persons interact with objects, which is advantageous in autonomous systems such as self-driving vehicles and collaborative robots. However, current HOI detectors are often plagued by model inefficiency and unreliability when making a prediction, which consequently limits its potential for real-world scenarios. In this paper, we address these challenges by proposing ERNet, an end-to-end trainable convolutional-transformer network for HOI detection. The proposed model employs an efficient multi-scale deformable attention to effectively capture vital HOI features. We also put forward a novel detection attention module to adaptively generate semantically rich instance and interaction tokens. These tokens undergo pre-emptive detections to produce initial region and vector proposals that also serve as queries which enhances the feature refinement process in the transformer decoders. Several impactful enhancements are also applied to improve the HOI representation learning. Additionally, we utilize a predictive uncertainty estimation framework in the instance and interaction classification heads to quantify the uncertainty behind each prediction. By doing so, we can accurately and reliably predict HOIs even under challenging scenarios. Experiment results on the HICO-Det, V-COCO, and HOI-A datasets demonstrate that the proposed model achieves state-of-the-art performance in detection accuracy and training efficiency. Codes are publicly available at https://github.com/Monash-CyPhi-AI-Research-Lab/ernet.

Performance of portable objective wound assessment tools: a systematic review.

OBJECTIVE: Accurate wound assessment is crucial for determining the progression of healing and guides treatment strategies. Portable wound assessment devices can be useful in providing an accurate evaluation in the community where most cases are treated. The objective of this review was to compare the performance of various portable wound assessment techniques used for wound healing assessment described in the literature. METHOD: In April 2020, electronic databases were searched, using appropriate search terms, for all available publications on the use of portable wound assessment devices on human and artificial wounds. The primary outcome was the reliability and reproducibility of measurement while the secondary outcome was the feasibility of the instrument. All studies underwent quality assessment of diagnostic accuracy studies (QUADAS) to examine the quality of data. RESULTS: A total of 129 articles were identified and 24 were included in the final review; 17 articles discussed two-dimensional (2D) devices; three articles discussed three-dimensional (3D) devices; and four articles discussed application-based devices. Most studies (n=8) reported on a 2D device that had an ICC of 0.92-0.99 for area measurement and a coefficient of variance of 3.1% with an error of 2.3% in human wounds and 1.55-3.7% in artificial wounds. The inter/intra observer reliability was 0.998 and 0.985, respectively with a scan time of two minutes per wound. The median QUADAS score was 12. CONCLUSION: Based on the presented evidence, 2D-based portable wound assessment devices were the most studied and demonstrated good performance. Further studies are required for 3D and application-based measurement instruments.

Cross-Ancestry Genome-Wide Association Study Defines the Extended CYP2D6 Locus as the Principal Genetic Determinant of Endoxifen Plasma Concentrations.

The therapeutic efficacy of tamoxifen is predominantly mediated by its active metabolites 4-hydroxy-tamoxifen and endoxifen, whose formation is catalyzed by the polymorphic cytochrome P450 2D6 (CYP2D6). Yet, known CYP2D6 polymorphisms only partially determine metabolite concentrations in vivo. We performed the first cross-ancestry genome-wide association study with well-characterized patients of European, Middle-Eastern, and Asian descent (n = 497) to identify genetic factors impacting active and parent metabolite formation. Genome-wide significant variants were functionally evaluated in an independent liver cohort (n = 149) and in silico. Metabolite prediction models were validated in two independent European breast cancer cohorts (n = 287, n = 189). Within a single 1-megabase (Mb) region of chromosome 22q13 encompassing the CYP2D6 gene, 589 variants were significantly associated with tamoxifen metabolite concentrations, particularly endoxifen and metabolic ratio (MR) endoxifen/N-desmethyltamoxifen (minimal P = 5.4E-35 and 2.5E-65, respectively). Previously suggested other loci were not confirmed. Functional analyses revealed 66% of associated, mostly intergenic variants to be significantly correlated with hepatic CYP2D6 activity or expression (ρ = 0.35 to -0.52), and six hotspot regions in the extended 22q13 locus impacting gene regulatory function. Machine learning models based on hotspot variants (n = 12) plus CYP2D6 activity score (AS) increased the explained variability (~ 9%) compared with AS alone, explaining up to 49% (median R2 ) and 72% of the variability in endoxifen and MR endoxifen/N-desmethyltamoxifen, respectively. Our findings suggest that the extended CYP2D6 locus at 22q13 is the principal genetic determinant of endoxifen plasma concentration. Long-distance haplotypes connecting CYP2D6 with adjacent regulatory sites and nongenetic factors may account for the unexplained portion of variability.

GATA6 is predicted to regulate DNA methylation in an in vitro model of human hepatocyte differentiation.

Hepatocytes are the dominant cell type in the human liver, with functions in metabolism, detoxification, and producing secreted proteins. Although gene regulation and master transcription factors involved in the hepatocyte differentiation have been extensively investigated, little is known about how the epigenome is regulated, particularly the dynamics of DNA methylation and the critical upstream factors. Here, by examining changes in the transcriptome and the methylome using an in vitro hepatocyte differentiation model, we show putative DNA methylation-regulating transcription factors, which are likely involved in DNA demethylation and maintenance of hypo-methylation in a differentiation stage-specific manner. Of these factors, we further reveal that GATA6 induces DNA demethylation together with chromatin activation in a binding-site-specific manner during endoderm differentiation. These results provide an insight into the spatiotemporal regulatory mechanisms exerted on the DNA methylation landscape by transcription factors and uncover an epigenetic role for transcription factors in early liver development.

Hepatocellular carcinoma organoid co-cultures mimic angiocrine crosstalk to generate inflammatory tumor microenvironment.

Hepatocellular carcinoma (HCC) is the sixth most common cancer and the second leading cause of cancer worldwide. Despite approvals of several therapeutics to treat advanced HCC in the past few years, the impact of anti-angiogenic treatment on HCC patient overall survival remains limited. This suggests there may be alternative, perfusion-independent roles of endothelial cells that support tumor progression. Thus, we leveraged a well-defined hydrogel system to establish co-culture models to mimic and characterize the angiocrine crosstalk between HCC and endothelial cells in vitro. Co-cultures of HCC cell lines or patient-derived xenograft organoids with endothelial cells exhibited the upregulation of MCP-1, IL-8 and CXCL16, suggesting that the HCC-endothelial interactions established in our models recapitulate known angiocrine signaling. Additionally, by subjecting co-cultures and mono-cultures to RNA sequencing, transcriptomic analysis revealed an upregulation in the expression of genes associated with tumor necrosis factor (TNF) signaling, such as that of chemokines, suggesting that endothelial cells induce HCC cells to generate an inflammatory microenvironment by recruiting immune cells. Finally, HCC-endothelial angiocrine crosstalk in the co-culture models polarized macrophages towards a pro-inflammatory and pro-angiogenic phenotype, paralleling a tumor-associated macrophage subset previously reported in HCC. Together, these findings suggest that these HCC-endothelial co-culture models may serve as important models to understand and target the interplay between angiogenesis and the immune milieu.

Prediction of transcription factors associated with DNA demethylation during human cellular development.

DNA methylation of CpG dinucleotides is an important epigenetic modification involved in the regulation of mammalian gene expression, with each type of cell developing a specific methylation profile during its differentiation. Recently, it has been shown that a small subgroup of transcription factors (TFs) might promote DNA demethylation at their binding sites. We developed a bioinformatics pipeline to predict from genome-wide DNA methylation data TFs that promote DNA demethylation at their binding site. We applied the pipeline to International Human Epigenome Consortium methylome data and selected 393 candidate transcription factor binding motifs and associated 383 TFs that are likely associated with DNA demethylation. Validation of a subset of the candidate TFs using an in vitro assay suggested that 28 of 49 TFs from various TF families had DNA-demethylation-promoting activity; TF families, such as bHLH and ETS, contained both TFs with and without the activity. The identified TFs showed large demethylated/methylated CpG ratios and their demethylated CpGs showed significant bias toward hypermethylation in original cells. Furthermore, the identified TFs promoted demethylation of distinct sets of CpGs, with slight overlap of the targeted CpGs among TF family members, which was consistent with the results of a gene ontology (GO) term analysis of the identified TFs. Gene expression analysis of the identified TFs revealed that multiple TFs from various families are specifically expressed in human cells and tissues. Together, our results suggest that a large number of TFs from various TF families are associated with cell-type-specific DNA demethylation during human cellular development.

G-quadruplexes mark alternative lengthening of telomeres.

About 10-15% of all human cancer cells employ a telomerase-independent recombination-based telomere maintenance method, known as alternative lengthening of telomere (ALT), of which the full mechanism remains incompletely understood. While implicated in previous studies as the initiating signals for ALT telomere repair, the prevalence of non-canonical nucleic acid structures in ALT cancers remains unclear. Extending earlier reports, we observe higher levels of DNA/RNA hybrids (R-loops) in ALT-positive (ALT+) compared to telomerase-positive (TERT+) cells. Strikingly, we observe even more pronounced differences for an associated four-stranded nucleic acid structure, G-quadruplex (G4). G4 signals are found at the telomere and are broadly associated with telomere length and accompanied by DNA damage markers. We establish an interdependent relationship between ALT-associated G4s and R-loops and confirm that these two structures can be spatially linked into unique structures, G-loops, at the telomere. Additionally, stabilization of G4s and R-loops cooperatively enhances ALT-activity. However, co-stabilization at higher doses resulted in cytotoxicity in a synergistic manner. Nuclear G4 signals are significantly and reproducibly different between ALT+ and TERT+ low-grade glioma tumours. Together, we present G4 as a novel hallmark of ALT cancers with potential future applications as a convenient biomarker for identifying ALT+ tumours and as therapeutic targets.

Malaysian Stakeholder Perspectives on Suicide-Related Reporting: Findings From Focus Group Discussions.

Media guidelines on safe suicide-related reporting are within the suicide prevention armamentarium. However, implementation issues beleaguer real-world practice. This study evaluated the perspectives of the Malaysian media community, persons with lived experience of suicidal behavior (PLE), and mental health professionals (MHP) on suicide-related reporting in terms of the impact, strategies, challenges, and the implementation of guidelines on safe reporting. Three focus group discussions of purposively sampled Malaysian media practitioners (n = 8), PLE (n = 6), and MHP (n = 7) were audio-recorded, transcribed, coded and thematically analyzed. Inclusion criteria were: English fluency, no clinical depression or suicidal ideation (current), no recent previous suicide attempts or suicide bereavement. Three major themes emerged: (1) Unsafe Reporting; (2) Impact; and (3) Safe Reporting. Most described current reporting as unsafe by being potentially triggering to media users and may contribute to contagion effect. Positive impacts identified included raised awareness toward suicide and its prevention. Unsafe reporting was attributed to inadequate awareness, knowledge, and guidance, lack of empathy and accountability, job-related factors, popularity-seeking, lack of monitoring and governance, and information source(s) with unsafe content. Majority agreed on how suicide stories should be framed to produce a safe report. The media community diverged on how detailed a suicide story should be. Safe reporting challenges included difficulties in balancing beneficial versus harmful details, social media ubiquity and its citizen reporters. Participants suggested these safe reporting strategies: stakeholder engagement, educational approaches, improving governance and surveillance, and guidelines revision. Most acknowledged the relevance of guidelines but were unaware of the existence of local guidelines. Implementation challenges included the dilemma in balancing media industry needs vis-à-vis safe reporting requirements, stakeholder engagement difficulties and social media regulation. There is poor awareness regarding safe suicide-related reporting across all groups. PLE and MHP were negatively impacted by current unsafe messaging which aggravated trauma and grief reactions. Postvention support gaps for mental health professionals were highlighted. Safe reporting promotion strategies should include stakeholder engagement to increase awareness on minimizing Werther and maximizing Papageno effects. Strategic re-examination and dissemination of local media guidelines to address new media issues, and effective surveillance mechanisms, are crucial in sustainable improvement of safe reporting practices.

ExoSTING, an extracellular vesicle loaded with STING agonists, promotes tumor immune surveillance.

Cyclic dinucleotide (CDN) agonists of the STimulator of InterferoN Genes (STING) pathway have shown immune activation and tumor clearance in pre-clinical models. However, CDNs administered intratumorally also promote STING activation leading to direct cytotoxicity of many cell types in the tumor microenvironment (TME), systemic inflammation due to rapid tumor extravasation of the CDN, and immune ablation in the TME. These result in a failure to establish immunological memory. ExoSTING, an engineered extracellular vesicle (EV) exogenously loaded with CDN, enhances the potency of CDN and preferentially activates antigen presenting cells in the TME. Following intratumoral injection, exoSTING was retained within the tumor, enhanced local Th1 responses and recruitment of CD8+ T cells, and generated systemic anti-tumor immunity to the tumor. ExoSTING at therapeutically active doses did not induce systemic inflammatory cytokines, resulting in an enhanced therapeutic window. ExoSTING is a novel, differentiated therapeutic candidate that leverages the natural biology of EVs to enhance the activity of CDNs.

SHP2 blockade enhances anti-tumor immunity via tumor cell intrinsic and extrinsic mechanisms.

SHP2 is a ubiquitous tyrosine phosphatase involved in regulating both tumor and immune cell signaling. In this study, we discovered a novel immune modulatory function of SHP2. Targeting this protein with allosteric SHP2 inhibitors promoted anti-tumor immunity, including enhancing T cell cytotoxic function and immune-mediated tumor regression. Knockout of SHP2 using CRISPR/Cas9 gene editing showed that targeting SHP2 in cancer cells contributes to this immune response. Inhibition of SHP2 activity augmented tumor intrinsic IFNγ signaling resulting in enhanced chemoattractant cytokine release and cytotoxic T cell recruitment, as well as increased expression of MHC Class I and PD-L1 on the cancer cell surface. Furthermore, SHP2 inhibition diminished the differentiation and inhibitory function of immune suppressive myeloid cells in the tumor microenvironment. SHP2 inhibition enhanced responses to anti-PD-1 blockade in syngeneic mouse models. Overall, our study reveals novel functions of SHP2 in tumor immunity and proposes that targeting SHP2 is a promising strategy for cancer immunotherapy.

Hydrogels to engineer tumor microenvironments in vitro.

In recent years, hydrogel-based three-dimensional tumor models have become increasingly mainstream for cancer research. Hydrogels enable recapitulation of biochemical and biophysical cues in the tumor microenvironment (TME) for the culture of cancer and stromal cells. While there is increasing insight into how cancer-stromal interactions support tumor progression and drug resistance, much remains to be understood for the successful development of therapeutic targets that are capable of controlling tumors in patients. This review aims to first describe both acellular and cellular characteristics of the TME, focusing on cancer cell interactions with the extracellular matrix, fibroblasts, endothelial cells and immune cells. We will then discuss hydrogel systems that have been developed in the past four years to mimic these interactions in the TME and finally propose future directions in the field of in vitro tumor modeling.

Effectiveness of a Malaysian Media Intervention Workshop: Safe Reporting on Suicide.

Background: Suicide remains an important cause of premature deaths and draws much media attention. However, unsafe reporting and portrayal of suicides by the media have been associated with increased risk of suicidal behavior. Current evidence suggests that media capacity-building could potentially prevent suicide. However, there are still knowledge gaps in terms of a lack of data on effective strategies for improving awareness and safe reporting of suicide-related media content. This study aims to investigate the effectiveness of a workshop conducted with members of the media community on the safe reporting of suicide-related content. Methods: An interventional single-arm pre and post pilot study was conducted on a sample of the Malaysian media community recruited through purposive and snowball sampling. The media safe reporting workshop was conducted by a suicide prevention expert with a media industry background. Thirty participants completed a self-reported evaluation questionnaire on their awareness and knowledge of reporting on suicide-related media content; before and after the interventional workshop. Results: There was a significant difference between the total scores before and after the intervention, with a large effect size. Post-intervention scores were significantly improved in 8 items, namely those related to the reporting of: (i) the content of any suicide note; (ii) headlines with methods of suicide; (iii) headlines with the location of suicide; (iv) cases of suspected suicide despite the unconfirmed cause of death; (v) suicide news to cater to readers' interests; (vi) cause of suicide; (vii) details of the location of suicide; and (viii) the negative impact to media community when reporting suicide stories. In particular, there was an improvement in the majority of items for people from the media community with no lived experience of suicidal behavior. Conclusion: The media safe reporting workshop is a potentially effective intervention for improving awareness and knowledge measures relating to safe reporting on suicide among the media community, with a more pronounced effect in those without lived experience of suicidal behavior. Limitations in the sample size, generalizability, short-term evaluation, and lack of a control group warrant future larger, longer-term controlled, and more representative studies.

The Genomic Impact of Selection for Virulence against Resistance in the Potato Cyst Nematode, Globodera pallida.

Although the use of natural resistance is the most effective management approach against the potato cyst nematode (PCN) Globodera pallida, the existence of pathotypes with different virulence characteristics constitutes a constraint towards this goal. Two resistance sources, GpaV (from Solanum vernei) and H3 from S. tuberosum ssp. andigena CPC2802 (from the Commonwealth Potato Collection) are widely used in potato breeding programmes in European potato industry. However, the use of resistant cultivars may drive strong selection towards virulence, which allows the increase in frequency of virulent alleles in the population and therefore, the emergence of highly virulent nematode lineages. This study aimed to identify Avirulence (Avr) genes in G. pallida populations selected for virulence on the above resistance sources, and the genomic impact of selection processes on the nematode. The selection drive in the populations was found to be specific to their genetic background. At the genomic level, 11 genes were found that represent candidate Avr genes. Most of the variant calls determining selection were associated with H3-selected populations, while many of them seem to be organised in genomic islands facilitating selection evolution. These phenotypic and genomic findings combined with histological studies performed revealed potential mechanisms underlying selection in G. pallida.

Methodological quality of systematic reviews on treatments for osteoporosis: A cross-sectional study.

PURPOSE: Systematic reviews (SRs) provide the best evidence on the effectiveness of treatment strategies for osteoporosis. Carefully conducted SRs provide high-quality evidence for supporting decision-making, but the trustworthiness of conclusions can be hampered by limitation in rigor. We aimed to appraise the methodological quality of a representative sample of SRs on osteoporosis treatments in a cross-sectional study. METHODS: Cochrane Database of Systematic Reviews, EMBASE, MEDLINE, and PsycINFO were searched for SRs on osteoporotic treatments. AMSTAR (A MeaSurement Tool to Assess systematic Reviews) 2 was used to evaluate methodological quality of SRs. Associations between bibliographical characteristics and methodological quality ratings were explored using multivariate regression analyses. RESULTS: A total of 101 SRs were appraised. Overall, one (1.0%) was rated "high quality", three (3.0%) were rated "moderate quality", eleven (10.9%) were rated "low quality", and eighty-six (85.1%) were rated "critically low quality". Ninety-nine (98.0%) did not explain study design selection, eighty-five (84.2%) did not provide a list of excluded studies (84.2%), and eighty-five (84.2%) did not report funding sources of included studies. SRs published in 2018 or after were associated with higher overall quality [adjusted odds ratio (AOR): 5.48; 95% confidence interval (CI): 1.12-26.89], while SRs focused on pharmacological interventions were associated with lower overall quality [AOR: 0.24; 95% CI: 0.06-0.96]. CONCLUSION: The methodological quality of the included SRs is far from satisfactory. Future reviewers must strengthen rigor by improving literature search comprehensiveness, registering and publishing a priori protocols, and optimising study selection and data extraction. Better transparency in reporting conflicts of interest among reviewers, as well as sources of funding among included primary studies, are also needed.

Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development.

Lineage-specific gene expression is modulated by a balance between transcriptional activation and repression during animal development. Knowledge about enhancer-centered transcriptional activation has advanced considerably, but silencers and their roles in normal development remain poorly understood. Here, we performed chromatin interaction analyses of Polycomb repressive complex 2 (PRC2), a key inducer of transcriptional gene silencing, to uncover silencers, their molecular identity and associated chromatin connectivity. Systematic analysis of cis-regulatory silencer elements reveals their chromatin features and gene-targeting specificity. Deletion of certain PRC2-bound silencers in mice results in transcriptional derepression of their interacting genes and pleiotropic developmental phenotypes, including embryonic lethality. While some PRC2-bound elements function as silencers in pluripotent cells, they can transition into active tissue-specific enhancers during development, highlighting their regulatory versatility. Our study characterizes the molecular profile of silencers and their associated chromatin architectures, and suggests the possibility of targeted reactivation of epigenetically silenced genes.

Tumor Intrinsic Efficacy by SHP2 and RTK Inhibitors in KRAS-Mutant Cancers.

KRAS, an oncogene mutated in nearly one third of human cancers, remains a pharmacologic challenge for direct inhibition except for recent advances in selective inhibitors targeting the G12C variant. Here, we report that selective inhibition of the protein tyrosine phosphatase, SHP2, can impair the proliferation of KRAS-mutant cancer cells in vitro and in vivo using cell line xenografts and primary human tumors. In vitro, sensitivity of KRAS-mutant cells toward the allosteric SHP2 inhibitor, SHP099, is not apparent when cells are grown on plastic in 2D monolayer, but is revealed when cells are grown as 3D multicellular spheroids. This antitumor activity is also observed in vivo in mouse models. Interrogation of the MAPK pathway in SHP099-treated KRAS-mutant cancer models demonstrated similar modulation of p-ERK and DUSP6 transcripts in 2D, 3D, and in vivo, suggesting a MAPK pathway-dependent mechanism and possible non-MAPK pathway-dependent mechanisms in tumor cells or tumor microenvironment for the in vivo efficacy. For the KRASG12C MIAPaCa-2 model, we demonstrate that the efficacy is cancer cell intrinsic as there is minimal antiangiogenic activity by SHP099, and the effects of SHP099 is recapitulated by genetic depletion of SHP2 in cancer cells. Furthermore, we demonstrate that SHP099 efficacy in KRAS-mutant models can be recapitulated with RTK inhibitors, suggesting RTK activity is responsible for the SHP2 activation. Taken together, these data reveal that many KRAS-mutant cancers depend on upstream signaling from RTK and SHP2, and provide a new therapeutic framework for treating KRAS-mutant cancers with SHP2 inhibitors.

Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi.

Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes of two common DSE of semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced and analyzed with another 32 ascomycetes of different lifestyles. Cadophora sp. (Helotiales) and P. macrospinosa (Pleosporales) have genomes of 70.46 Mb and 54.99 Mb with 22,766 and 18,750 gene models, respectively. The majority of DSE-specific protein clusters lack functional annotation with no similarity to characterized proteins, implying that they have evolved unique genetic innovations. Both DSE possess an expanded number of carbohydrate active enzymes (CAZymes), including plant cell wall degrading enzymes (PCWDEs). Those were similar in three other DSE, and contributed a signal for the separation of root endophytes in principal component analyses of CAZymes, indicating shared genomic traits of DSE fungi. Number of secreted proteases and lipases, aquaporins, and genes linked to melanin synthesis were also relatively high in our fungi. In spite of certain similarities between our two DSE, we observed low levels of convergence in their gene family evolution. This suggests that, despite originating from the same habitat, these two fungi evolved along different evolutionary trajectories and display considerable functional differences within the endophytic lifestyle.

Potato late blight field resistance from QTL dPI09c is conferred by the NB-LRR gene R8.

Following the often short-lived protection that major nucleotide binding, leucine-rich-repeat (NB-LRR) resistance genes offer against the potato pathogen Phytophthora infestans, field resistance was thought to provide a more durable alternative to prevent late blight disease. We previously identified the QTL dPI09c on potato chromosome 9 as a more durable field resistance source against late blight. Here, the resistance QTL was fine-mapped to a 186 kb region. The interval corresponds to a larger, 389 kb, genomic region in the potato reference genome of Solanum tuberosum Group Phureja doubled monoploid clone DM1-3 (DM) and from which functional NB-LRRs R8, R9a, Rpi-moc1, and Rpi_vnt1 have arisen independently in wild species. dRenSeq analysis of parental clones alongside resistant and susceptible bulks of the segregating population B3C1HP showed full sequence representation of R8. This was independently validated using long-range PCR and screening of a bespoke bacterial artificial chromosome library. The latter enabled a comparative analysis of the sequence variation in this locus in diverse Solanaceae. We reveal for the first time that broad spectrum and durable field resistance against P. infestans is conferred by the NB-LRR gene R8, which is thought to provide narrow spectrum race-specific resistance.