The expression of the NPR1-dependent defense response pathway genes in Persea americana (Mill.) following infection with Phytophthora cinnamomi.

A plant's defense against pathogens involves an extensive set of phytohormone regulated defense signaling pathways. The salicylic acid (SA)-signaling pathway is one of the most well-studied in plant defense. The bulk of SA-related defense gene expression and the subsequent establishment of systemic acquired resistance (SAR) is dependent on the nonexpressor of pathogenesis-related genes 1 (NPR1). Therefore, understanding the NPR1 pathway and all its associations has the potential to provide valuable insights into defense against pathogens. The causal agent of Phytophthora root rot (PRR), Phytophthora cinnamomi, is of particular importance to the avocado (Persea americana) industry, which encounters considerable economic losses on account of this pathogen each year. Furthermore, P. cinnamomi is a hemibiotrophic pathogen, suggesting that the SA-signaling pathway plays an essential role in the initial defense response. Therefore, the NPR1 pathway which regulates downstream SA-induced gene expression would be instrumental in defense against P. cinnamomi. Thus, we identified 92 NPR1 pathway-associated orthologs from the P. americana West Indian pure accession genome and interrogated their expression following P. cinnamomi inoculation, using RNA-sequencing data. In total, 64 and 51 NPR1 pathway-associated genes were temporally regulated in the partially resistant (Dusa®) and susceptible (R0.12) P. americana rootstocks, respectively. Furthermore, 42 NPR1 pathway-associated genes were differentially regulated when comparing Dusa® to R0.12. Although this study suggests that SAR was established successfully in both rootstocks, the evidence presented indicated that Dusa® suppressed SA-signaling more effectively following the induction of SAR. Additionally, contrary to Dusa®, data from R0.12 suggested a substantial lack of SA- and NPR1-related defense gene expression during some of the earliest time-points following P. cinnamomi inoculation. This study represents the most comprehensive investigation of the SA-induced, NPR1-dependent pathway in P. americana to date. Lastly, this work provides novel insights into the likely mechanisms governing P. cinnamomi resistance in P. americana.

Transcriptional reprogramming during recovery from drought stress in Eucalyptus grandis.

The importance of drought as a constraint to agriculture and forestry is increasing with climate change. Genetic improvement of plants' resilience is one of the mitigation strategies to curb this threat. Although recovery from drought stress is important to long-term drought adaptation and has been considered as an indicator of dehydration tolerance in annual crops, this has not been well explored in forest trees. Thus, we aimed to investigate the physiological and transcriptional changes during drought stress and rewatering in Eucalyptus grandis W. Hill ex Maiden. We set up a greenhouse experiment where we imposed drought stress on 2-year-old seedlings and rewatered the recovery group after 17 days of drought. Our measurement of leaf stomatal conductance (gs) showed that, while gs was reduced by drought stress, it fully recovered after 5 days of rewatering. The RNA-seq analysis from stem samples revealed that genes related to known stress responses such as phytohormone and reactive oxygen species signaling were upregulated, while genes involved in metabolism and growth were downregulated due to drought stress. We observed reprogramming of signal transduction pathways and metabolic processes at 1 day of rewatering, indicating a quick response to rewatering. Our results suggest that recovery from drought stress may entail alterations in the jasmonic acid, salicylic acid, ethylene and brassinosteroid signaling pathways. Using co-expression network analysis, we identified hub genes, including the putative orthologs of ABI1, ABF2, ABF3, HAI2, BAM1, GolS2 and SIP1 during drought and CAT2, G6PD1, ADG1 and FD-1 during recovery. Taken together, by highlighting the molecular processes and identifying key genes, this study gives an overview of the mechanisms underlying the response of E. grandis to drought stress and recovery that trees may face repeatedly throughout their long life cycle. This provides a useful reference to the identification and further investigation of signaling pathways and target genes for future tree improvement.

The In Planta Gene Expression of Austropuccinia psidii in Resistant and Susceptible Eucalyptus grandis.

Austropuccinia psidii, commonly known as myrtle rust, is an obligate, biotrophic rust pathogen that causes rust disease in a broad host range of Myrtaceae species. Eucalyptus grandis, a widely cultivated hardwood Myrtaceae species, is susceptible to A. psidii infection, with this pathogen threatening both their natural range and various forest plantations across the world. This study aimed to investigate the A. psidii transcriptomic responses in resistant and susceptible E. grandis at four time points. RNA-seq reads were mapped to the A. psidii reference genome to quantify expressed genes at 12 h postinoculation and 1, 2, and 5 days postinoculation (dpi). A total of eight hundred and ninety expressed genes were found, of which 43 were candidate effector protein genes. These included rust transferred protein 1 (RTP1), expressed in susceptible hosts at 5 dpi, and a hydrolase protein gene expressed in both resistant and susceptible hosts over time. Functional categorization of expressed genes revealed processes enriched in susceptible hosts, including malate metabolic and malate dehydrogenase activity, implicating oxalic acid in disease susceptibility. These results highlight putative virulence or pathogenicity mechanisms employed by A. psidii to cause disease, and they provide the first insight into the molecular responses of A. psidii in E. grandis over time.

A Robust Disease Scoring Method to Screen Eucalyptus for Resistance Against the Aggressive Leaf Pathogen Teratosphaeria destructans.

Shoot and leaf blight caused by Teratosphaeria destructans is one of the most devastating foliar diseases on Eucalyptus. Therefore, breeding for resistance to this disease is considered urgent. Differences in susceptibility to T. destructans have been observed in the field but a robust inoculation protocol has, until recently, been unavailable and a disease scoring method for precise phenotyping has not been established. A first objective of this study was to determine the optimal conidial concentration for T. destructans inoculations on a susceptible Eucalyptus host. This concentration was then used to determine differences in susceptibility of six genotypes of Eucalyptus grandis × E. urophylla to the pathogen by assessing the percentage of infected stomata using electron microscopy and the percentage of leaf area covered by lesions (PLACL) using image processing. In addition, we developed a disease susceptibility index (SI) of six categories ranging from highly resistant (SI = 0) to highly susceptible (SI = 1.5 to 2). The more resistant genotypes were moderately resistant, with an SI value of 0.49 to 0.54 and a PLACL of 6.5 to 9%. In contrast, the more susceptible genotype scored an SI of 1.52 and PLACL of 48%. Host susceptibility was also assessed relative to the sporulation of the pathogen. This showed that the percentage of sporulation was not significantly correlated with host resistance. Overall, the results provide the basis for rigorous screening and selection of resistant genotypes to the disease caused by T. destructans using artificial inoculation.

Prevalence and associated risk factors for elevated blood pressure in young adults in South Africa.

BACKGROUND: Sub-Saharan Africa has been shown to have a high prevalence of hypertension (58% in rural black South Africans) with an accelerated course ending in end-stage renal disease. We sought to determine whether the prevalence of elevated blood pressure (EBP) in early adulthood was associated with any risk factors and/or renal target-organ damage in young adulthood, which could prevent development of these cardiorenal sequelae. METHODS: Data including risk factors for hypertension and markers of kidney damage were collected from young adults (n = 933; age 28 years; 52% female) participating in the Birth to Twenty Plus (BT20) cohort in Soweto, South Africa. Blood pressure was measured on one occasion. RESULTS: Fifty-four per cent of the study sample had EBP with more men affected (62%) than women (47%) (p < 0.001). Body mass index (BMI), hyperuricaemia and albuminuria had significant associations with EBP in men. In women, BMI, hyperuricaemia and a self-reported history of gestational hypertension had significant associations. CONCLUSIONS: Our findings suggest that the pathophysiology of EBP in young adults differs between the genders and highlights a number of modifiable factors in its development.

Multispecies comparison of host responses to Fusarium circinatum challenge in tropical pines show consistency in resistance mechanisms.

Fusarium circinatum poses a threat to both commercial and natural pine forests. Large variation in host resistance exists between species, with many economically important species being susceptible. Development of resistant genotypes could be expedited and optimised by investigating the molecular mechanisms underlying host resistance and susceptibility as well as increasing the available genetic resources. RNA-seq data, from F. circinatum inoculated and mock-inoculated ca. 6-month-old shoot tissue at 3- and 7-days postinoculation, was generated for three commercially important tropical pines, Pinus oocarpa, Pinus maximinoi and Pinus greggii. De novo transcriptomes were assembled and used to investigate the NLR and PR gene content within available pine references. Host responses to F. circinatum challenge were investigated in P. oocarpa (resistant) and P. greggii (susceptible), in comparison to previously generated expression profiles from Pinus tecunumanii (resistant) and Pinus patula (susceptible). Expression results indicated crosstalk between induced salicylate, jasmonate and ethylene signalling is involved in host resistance and compromised in susceptible hosts. Additionally, higher constitutive expression of sulfur metabolism and flavonoid biosynthesis in resistant hosts suggest involvement of these metabolites in resistance.

Haplotype mining panel for genetic dissection and breeding in Eucalyptus.

To improve our understanding of genetic mechanisms underlying complex traits in plants, a comprehensive analysis of gene variants is required. Eucalyptus is an important forest plantation genus that is highly outbred. Trait dissection and molecular breeding in eucalypts currently relies on biallelic single-nucleotide polymorphism (SNP) markers. These markers fail to capture the large amount of haplotype diversity in these species, and thus multi-allelic markers are required. We aimed to develop a gene-based haplotype mining panel for Eucalyptus species. We generated 17 999 oligonucleotide probe sets for targeted sequencing of selected regions of 6293 genes implicated in growth and wood properties, pest and disease resistance, and abiotic stress responses. We identified and phased 195 834 SNPs using a read-based phasing approach to reveal SNP-based haplotypes. A total of 8915 target regions (at 4637 gene loci) passed tests for Mendelian inheritance. We evaluated the haplotype panel in four Eucalyptus species (E. grandis, E. urophylla, E. dunnii and E. nitens) to determine its ability to capture diversity across eucalypt species. This revealed an average of 3.13-4.52 haplotypes per target region in each species, and 33.36% of the identified haplotypes were shared by at least two species. This haplotype mining panel will enable the analysis of haplotype diversity within and between species, and provide multi-allelic markers that can be used for genome-wide association studies and gene-based breeding approaches.

COVID-19 vaccinology landscape in Africa.

More than two years after the start of COVID-19 pandemic, Africa still lags behind in terms vaccine distribution. This highlights the predicament of Africa in terms of vaccine development, deployment, and sustainability, not only for COVID-19, but for other major infectious diseases that plague the continent. This opinion discusses the challenges Africa faces in its race to vaccinate its people, and offers recommendations on the way forward. Specifically, to get out of the ongoing vaccine shortage trap, Africa needs to diversify investment not only to COVID-19 but also other diseases that burden the population. The continent needs to increase its capacity to acquire vaccines more equitably, improve access to technologies to enable local manufacture of vaccines, increase awareness on vaccines both in rural and urban areas to significantly reduce disease incidence of COVID-19 and as well as other prevalent diseases on the African continent such as HIV and TB. Such efforts will go a long way to reduce the disease burden in Africa.

Are cardiovascular health measures heritable across three generations of families in Soweto, South Africa? A cross-sectional analysis using the random family method.

OBJECTIVES: Cardiovascular disease is increasing in many low and middle-income countries, including those in Africa. To inform strategies for the prevention of cardiovascular disease in South Africa, we sought to determine the broad heritability of phenotypic markers of cardiovascular risk across three generations. DESIGN: A cross-sectional study conducted in a longitudinal family cohort. SETTING: Research unit within a tertiary hospital in a historically disadvantaged, large urban township of South Africa. PARTICIPANTS: 195 individuals from 65 biological families with all three generations including third-generation children aged 4-10 years were recruited from the longest running intergenerational cohort study in Africa, the Birth to Twenty Plus cohort. All adults (grandparents and parents) were female while children were male or female. PRIMARY AND SECONDARY OUTCOME MEASURES: The primary outcome was heritability of blood pressure (BP; brachial and central pressures). Secondary outcomes were heritability of arterial stiffness (pulse wave velocity), carotid intima media thickness (cIMT) and left ventricular mass indexed to body surface area (LVMI). RESULTS: While no significant intergenerational relationships of BP or arterial stiffness were found, there were significant relationships in LVMI across all three generations (p<0.04), and in cIMT between grandparents and parents (p=0.0166). Heritability, the proportion of phenotypic trait variation attributable to genetics, was estimated from three common statistical methods and ranged from 23% to 44% for cIMT and from 21% to 39% for LVMI. CONCLUSIONS: Structural indicators of vascular health, which are strong markers of future clinical cardiovascular outcomes, transmit between generations within African families. Identification of these markers in parents may be useful to trigger assessments of preventable risk factors for cardiovascular disease in offspring.

Obesity, hypertension, and tobacco use associated with left ventricular remodeling and hypertrophy in South African women: Birth to Twenty Plus Cohort.

BACKGROUND: Left ventricular hypertrophy (LVH) is a marker of increased risk in developing future life-threatening cardiovascular disease (CVD), however, it is unclear how CVD risk factors, such as obesity, blood pressure (BP), and tobacco use, are associated with left ventricular (LV) remodeling and LVH in urban African populations. Therefore, we aimed to identify the prevalence of LVH as well as the health factors associated with LV remodeling and LVH, within black South African adult women and their pre-pubescent children. METHODS: Black female adults (n = 123; age: 29-68 years) and their children (n = 64; age: 4-10; 55% female) were recruited from the Birth to Twenty Plus Cohort in Soweto, South Africa. Tobacco and alcohol use, physical activity, presence of diabetes mellitus, heart disease, and medication were self-reported. Height, weight, and blood pressure were measured in triplicate to determine the prevalence of obesity and hypertension respectively. Echocardiography was used to assess LV mass at end-diastole, based on linear measurements, and indexed to body surface area to determine LVH. RESULTS: Hypertension and obesity prevalences were 35.8% and 59.3% for adults and 45.3% and 6.3% for children. Self-reported tobacco use in adults was 22.8%. LVH prevalence was 35.8% in adults (75% eccentric: 25% concentric), and 6.3% in children. Concentric remodeling was observed in 15.4% of adults, however, concentric remodeling was only found in one child. In adults, obesity [OR: 2.54 (1.07-6.02; p = 0.02)] and hypertension [3.39 (1.08-10.62; p = 0.04)] significantly increased the odds of LVH, specifically eccentric LVH, while concentric LVH was associated with self-reported tobacco use [OR: 4.58 (1.18-17.73; p = 0.03)]. Although no logistic regression was run within children, of the four children LVH, three had elevated blood pressure and the child with normal blood pressure was overweight. CONCLUSIONS: The association between obesity, hypertension, tobacco use, and LVH in adults, and the 6% prevalence of LVH in children, calls for stronger public health efforts to control risk factors and monitor children who are at risk.

Fungal Communities of Eucalyptus grandis Leaves Are Influenced by the Insect Pest Leptocybe invasa.

Fungal communities in above-ground tree tissues are hyperdiverse and are influenced by biotic interactions with other organisms living in or on these tissues. These biotic interactions are, however, still poorly understood. In this study, we aimed to understand how insect-associated gall formation on Eucalyptus foliage correlates with the diversity of foliar fungal communities in surrounding healthy leaf tissue, as well as the co-occurrence patterns among the members of the fungal community. We used ITS metabarcoding to characterise the foliar fungal communities of 179 individual E. grandis trees. These trees were assigned to infestation levels of the wasp Leptocybe invasa (Eulophidae: Hymenoptera), which causes gall formation on shoot tips and leaves of its host. Fungal community networks were calculated using a Pearson correlation coefficient. The composition and diversity of fungal communities were influenced by the severity of L. invasa infestations. We identified potential Eucalyptus pathogens with high sequence abundance at all disease severity levels, but network analysis indicated that the co-occurrence of potential pathogens between no to mild and medium to heavy infestation differed significantly. A better understanding of microbial interactions, especially the role of pathogens, can be useful for controlling disease- and beneficial host-associated microbial communities.

Genome-wide association study identifies SNP markers and putative candidate genes for terpene traits important for Leptocybe invasa resistance in Eucalyptus grandis.

Terpenes are an important group of plant specialized metabolites influencing, amongst other functions, defence mechanisms against pests. We used a genome-wide association study to identify single nucleotide polymorphism (SNP) markers and putative candidate genes for terpene traits. We tested 15,387 informative SNP markers derived from genotyping 416 Eucalyptus grandis individuals for association with 3 terpene traits, 1,8-cineole, γ-terpinene, and p-cymene. A multilocus mixed model analysis identified 21 SNP markers for 1,8-cineole on chromosomes 2, 4, 6, 7, 8, 9, 10, and 11, that individually explained 3.0%-8.4% and jointly 42.7% of the phenotypic variation. Association analysis of γ-terpinene found 32 significant SNP markers on chromosomes 1, 2, 4, 5, 6, 9, and 11, explaining 3.4-15.5% and jointly 54.5% of phenotypic variation. For p-cymene, 28 significant SNP markers were identified on chromosomes 1, 2, 3, 5, 6, 7, 10, and 11, explaining 3.4-16.1% of the phenotypic variation and jointly 46.9%. Our results show that variation underlying the 3 terpene traits is influenced by a few minor loci in combination with a few major effect loci, suggesting an oligogenic nature of the traits.

Paediatric Hypertension in Africa: A Systematic Review and Meta-Analysis.

BACKGROUND: The burden of cardiovascular disease (CVD) and hypertension is rapidly increasing in low- and middle-income countries. This is evident not only in adults, but also in children. Recent estimates of prevalence in children are lacking, particularly in Africa. As such, we conducted a systematic review and meta-analysis to provide updated estimates of paediatric hypertension in Africa. METHODS: We searched PubMed and EBSCO to identify articles published from January 2017 to November 2020. Studies were assessed for quality. We combined results for meta-analyses using a random effects model (Freeman-Tukey arcsine transformation). Heterogeneity was quantified using the I2 statistic. FINDINGS: In the narrative synthesis of 53 studies, publication bias was low for 28, moderate for 24, and high for one study. Hypertension prevalence ranged substantially (0·2%-38·9%). Meta-analysis included 41 studies resulting in data on 52918 participants aged 3 to 19 years from ten countries. The pooled prevalence for hypertension (systolic/diastolic BP≥95th percentile) was 7·45% (95%CI 5·30-9·92, I2=98.96%), elevated blood pressure (BP, systolic/diastolic BP≥90th percentile and <95th percentile) 11·38% (95%CI 7·94-15·33, I2=98.97%) and combined hypertension/elevated BP 21·74% (95%CI 15·5-28·69, I2=99.48%). Participants categorized as overweight/with obesity had a higher prevalence of hypertension (18·5% [95%CI 10·2-28·5]) than those categorized as underweight/normal (1·0% [95%CI 0·1-2·6], 4·8% [95%CI 2·9-7·1], p<0·001). There were significant differences in hypertension prevalence when comparing BP measurement methods and classification guidelines. INTERPRETATION: Compared to a previous systematic review conducted in 2017, this study suggests a continued increase in prevalence of paediatric hypertension in Africa, and highlights the potential role of increasing overweight/obesity. FUNDING: This research was funded in part by the Wellcome Trust [Grant number:214082/Z/18/Z]. LJW and SAN are supported by the DSI-NRF Centre of Human Development at the University of the Witwatersrand.

Comparison of the Infection Biology of Teratosphaeria destructans and Teratosphaeria epicoccoides on Eucalyptus.

Leaf blight caused by Teratosphaeria destructans is one of the most important diseases of Eucalyptus planted in the subtropics and tropics. In contrast, the better-known T. epicoccoides, though also a primary pathogen of Eucalyptus, causes less damage to trees in these areas. Although T. destructans is an aggressive pathogen, nothing is known about its infection biology. In this study, the conditions for infection and disease development caused by T. destructans and T. epicoccoides were evaluated and compared on a Eucalyptus grandis × E. urophylla hybrid clone. The optimal temperature for germination ranged from 25 to 30°C for T. destructans and 15 to 20°C for T. epicoccoides. The germination of these pathogens was favored under conditions of light and high levels of RH. Penetration by T. destructans and T. epicoccoides occurred via stomata, and the hyphae colonized the intercellular spaces of infected leaves. Symptoms were clearly visible 3 weeks after inoculation by both pathogens, and reproductive structures started to develop in substomatal cavities at 4 weeks after inoculation. The results of this study will facilitate the establishment of rapid screening trials based on artificial inoculations aimed at reducing the impact of disease caused by T. destructans.

Pulse wave velocity in South African women and children: comparison between the Mobil-O-Graph and SphygmoCor XCEL devices.

BACKGROUND: Carotid-femoral pulse wave velocity (PWV) is the gold-standard noninvasive measure of arterial stiffness. Data comparing tonometry-based devices such as the SphygmoCor XCEL to simpler brachial-cuff-based estimates of PWV, such as from the Mobil-O-Graph in African populations are sparse. We therefore aimed to compare PWV measured by the Mobil-O-Graph and the SphygmoCor XCEL device in a sample of South African women and children. METHODS: Women (n = 85) 29 years [interquartile range (IQR): 29-69] and their children/grandchildren (n = 27) 7 years (IQR: 4-11) were recruited for PWV measurement with Mobil-O-Graph and SphygmoCor XCEL on the same day. Wilcoxon signed-rank test, regression analysis, spearman correlation and Bland-Altman plots were used for PWV comparison between devices. RESULTS: For adults, the SphygmoCor XCEL device had a significantly higher PWV (7.3 m/s, IQR: 6.4-8.5) compared with the Mobil-O-Graph (5.9 m/s, IQR: 5.0-8.1, P = 0.001) with a correlation coefficient of 0.809 (P ≤ 0.001). Bland--Altman analysis indicated an acceptable level of agreement but significant bias (mean difference PWV: 0.90 ±â€Š1.02 m/s; limits of agreement: -1.10 to 2.90). The odds of having a PWV difference more than 1 m/s decreased with a higher age [odds ratio (OR): 0.95, 95% confidence interval (95% CI) = 0.92-0.98] and increased with greater height (OR: 1.10, 95% CI = 1.01-1.21, P = 0.03) in multivariable analysis. In children, the Bland-Altman indicated an excellent level of agreement (-0.03 ±â€Š0.63 m/s; limits of agreement: -1.26 to 1.21), but no correlation was found (rs = 0.08, P = 0.71). CONCLUSION: Particularly in younger and taller women, the Mobil-O-Graph significantly underestimated PWV compared with the SphygmoCor. Although no correlation was found between the two devices for children, further research is required due to the small sample size. Furthermore, the clinical value of both methods in young African populations requires further investigation.

A genome-wide SNP genotyping resource for tropical pine tree species.

We performed gene and genome targeted SNP discovery towards the development of a genome-wide, multispecies genotyping array for tropical pines. Pooled RNA-seq data from shoots of seedlings from five tropical pine species was used to identify transcript-based SNPs resulting in 1.3 million candidate Affymetrix SNP probe sets. In addition, we used a custom 40 K probe set to perform capture-seq in pooled DNA from 81 provenances representing the natural ranges of six tropical pine species in Mexico and Central America resulting in 563 K candidate SNP probe sets. Altogether, 300 K RNA-seq (72%) and 120 K capture-seq (28%) derived SNP probe sets were tiled on a 420 K screening array that was used to genotype 576 trees representing the 81 provenances and commercial breeding material. Based on the screening array results, 50 K SNPs were selected for commercial SNP array production including 20 K polymorphic SNPs for P. patula, P. tecunumanii, P. oocarpa and P. caribaea, 15 K for P. greggii and P. maximinoi, 13 K for P. elliottii and 8K for P. pseudostrobus. We included 9.7 K ancestry informative SNPs that will be valuable for species and hybrid discrimination. Of the 50 K SNP markers, 25% are polymorphic in only one species, while 75% are shared by two or more species. The Pitro50K SNP chip will be useful for population genomics and molecular breeding in this group of pine species that, together with their hybrids, represent the majority of fast-growing tropical and subtropical pine plantations globally.

Coronavirus Disease 2019 Diagnostics: Key to Africa's Recovery.

With the coronavirus disease of 2019 (COVID-19) becoming a full-blown outbreak in Africa, coupled with many other challenges faced on the African continent, it is apparent that Africa continues to need diagnostics to enable case identification and recovery to this and future challenges. With the slow vaccination rates across the continent, reliable diagnostic tests will be in demand, likely for years to come. Thus, access to reliable diagnostic tools to detect the severe acute respiratory syndrome of the coronavirus-2 (SARS-CoV-2), the virus responsible for COVID-19, remain a critical pillar to monitor and contain new waves of COVID-19. Increasing the local capacity to manufacture and roll-out vaccines and decentralized COVID-19 testing are paramount for fighting the pandemic in Africa.

qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE).

BACKGROUND: Affordable high-throughput DNA and RNA sequencing technologies are allowing genomic analysis of plant and animal populations and as a result empowering new systems genetics approaches to study complex traits. The availability of intuitive tools to browse and analyze the resulting large-scale genetic and genomic datasets remain a significant challenge. Furthermore, these integrative genomics approaches require innovative methods to dissect the flow and interconnectedness of biological information underlying complex trait variation. The Plant Genome Integrative Explorer (PlantGenIE.org) is a multi-species database and domain that houses online tools for model and woody plant species including Eucalyptus. Since the Eucalyptus Genome Integrative Explorer (EucGenIE) is integrated within PlantGenIE, it shares genome and expression analysis tools previously implemented within the various subdomains (ConGenIE, PopGenIE and AtGenIE). Despite the success in setting up integrative genomics databases, online tools for systems genetics modelling and high-resolution dissection of complex trait variation in plant populations have been lacking. RESULTS: We have developed qtlXplorer ( https://eucgenie.org/QTLXplorer ) for visualizing and exploring systems genetics data from genome-wide association studies including quantitative trait loci (QTLs) and expression-based QTL (eQTL) associations. This module allows users to, for example, find co-located QTLs and eQTLs using an interactive version of Circos, or explore underlying genes using JBrowse. It provides users with a means to build systems genetics models and generate hypotheses from large-scale population genomics data. We also substantially upgraded the EucGenIE resource and show how it enables users to combine genomics and systems genetics approaches to discover candidate genes involved in biotic stress responses and wood formation by focusing on two multigene families, laccases and peroxidases. CONCLUSIONS: qtlXplorer adds a new dimension, population genomics, to the EucGenIE and PlantGenIE environment. The resource will be of interest to researchers and molecular breeders working in Eucalyptus and other woody plant species. It provides an example of how systems genetics data can be integrated with functional genetics data to provide biological insight and formulate hypotheses. Importantly, integration within PlantGenIE enables novel comparative genomics analyses to be performed from population-scale data.

Insect egg-induced physiological changes and transcriptional reprogramming leading to gall formation.

Gall-inducing insects and their hosts present some of the most intricate plant-herbivore interactions. Oviposition on the host is often the first cue of future herbivory and events at this early time point can affect later life stages. Many gallers are devastating plant pests, yet little information regarding the plant-insect molecular interplay exists, particularly following egg deposition. We studied the physiological and transcriptional responses of Eucalyptus following oviposition by the gall-inducing wasp, Leptocybe invasa, to explore potential mechanisms governing defence responses and gall development. RNA sequencing and microscopy were used to explore a susceptible Eucalyptus-L. invasa interaction. Infested and control material was compared over time (1-3, 7 and 90 days post oviposition) to examine the transcriptional and morphological changes. Oviposition induces accumulation of reactive oxygen species and phenolics which is reflected in the transcriptome analysis. Gene expression supports phytohormones and 10 transcription factor subfamilies as key regulators. The egg and oviposition fluid stimulate cell division resulting in gall development. Eucalyptus responses to oviposition are apparent within 24 hr. Putative defences include the oxidative burst and barrier reinforcement. However, egg and oviposition fluid stimuli may redirect these responses towards gall development.

The Threat of the Combined Effect of Biotic and Abiotic Stress Factors in Forestry Under a Changing Climate.

Plants encounter several biotic and abiotic stresses, usually in combination. This results in major economic losses in agriculture and forestry every year. Climate change aggravates the adverse effects of combined stresses and increases such losses. Trees suffer even more from the recurrence of biotic and abiotic stress combinations owing to their long lifecycle. Despite the effort to study the damage from individual stress factors, less attention has been given to the effect of the complex interactions between multiple biotic and abiotic stresses. In this review, we assess the importance, impact, and mitigation strategies of climate change driven interactions between biotic and abiotic stresses in forestry. The ecological and economic importance of biotic and abiotic stresses under different combinations is highlighted by their contribution to the decline of the global forest area through their direct and indirect roles in forest loss and to the decline of biodiversity resulting from local extinction of endangered species of trees, emission of biogenic volatile organic compounds, and reduction in the productivity and quality of forest products and services. The abiotic stress factors such as high temperature and drought increase forest disease and insect pest outbreaks, decrease the growth of trees, and cause tree mortality. Reports of massive tree mortality events caused by "hotter droughts" are increasing all over the world, affecting several genera of trees including some of the most important genera in plantation forests, such as Pine, Poplar, and Eucalyptus. While the biotic stress factors such as insect pests, pathogens, and parasitic plants have been reported to be associated with many of these mortality events, a considerable number of the reports have not taken into account the contribution of such biotic factors. The available mitigation strategies also tend to undermine the interactive effect under combined stresses. Thus, this discussion centers on mitigation strategies based on research and innovation, which build on models previously used to curb individual stresses.