Perceptions and Prevalence of Cannabis Use in Women With Inflammatory Bowel Disease of Reproductive Age: A Cross-Sectional Study.

Background: Many patients with inflammatory bowel disease (IBD) may use cannabis for relief of symptoms. During pregnancy, however, cannabis exposure may be associated with adverse pregnancy outcomes. We aimed to determine the prevalence and perceptions of cannabis use in women with IBD. Methods: Through recruitment at Mount Sinai Hospital and online platforms such as Twitter, women with IBD (age 18-45) were asked to complete anonymous surveys on demographics, cannabis use, perception of use during pregnancy, and discussing its use with healthcare providers (HCP). Categorical variables were reported as frequencies and compared across groups with the chi-square test. Results: One-hundred and two pregnant patients with IBD were included in this study, 19 (18.6%) reported using cannabis. Current users were more likely to report constant pain in the last 12 months and discuss its use with their HCP. Fifty-three (52.0%) women were unsure of the specific risks associated with cannabis use during pregnancy, and only 15 (14.7%) had ever discussed its use with their HCP. Those who had discussed cannabis use with their HCP were more likely to have prior IBD-related surgery, perceive its use unsafe during pregnancy, and be more likely to be using cannabis. Conclusion: Many women with IBD report uncertainty of the risks of cannabis use during pregnancy and the majority have never discussed cannabis use with their providers. With the increasing legalization of cannabis in many jurisdictions, it is imperative patients and healthcare providers discuss the risks and benefits of its use, particularly during vulnerable times such as pregnancy.

Content analysis of tobacco imagery in popular music Videos, 2018-2021.

Exposure to tobacco imagery in movies and television has been identified as a key factor to youth smoking initiation (Davis, 2008; Bennett et al., 2020). This study aims to investigate the prevalence of tobacco imagery in popular music videos from 2018 to 2021. The weekly top 10 songs of 2018-2021 were identified using Billboard Charts categories (Hot 100, Hot R&B/Hip-Hop, Country, Rock & Alternative, Dance/Electronic, Pop Airplay). Content analyses of the top music videos using the Thumbs up Thumbs Down methodology were conducted to identify tobacco depictions on screen. The sample consisted of 1,008 music videos across four years; 196 of which contained tobacco imagery (19.4%). Between 2018 and 2021, the proportion of videos with tobacco imagery ranged between 12.8% and 23.0% of the total year sample. Tobacco incidences almost doubled from 280 occurrences in 2018 to 522 occurrences in 2020, but decreased by over half to 290 occurrences in 2021. Tobacco incidences varied by year and genre, with Hot 100 being the top offending genre in 2018 with 40.0% of videos containing tobacco imagery while Hot R&B/Hip-Hop was the top offending genre from 2019 to 2021 (52.7%, 52.5%, and 23.9% respectively). Cigarettes were most pervasive in 2019 (70.1% of total tobacco incidences), 2020 (45.6%), and 2021 (64.1%) music videos. Pipes were the most pervasive product in 2018 music videos (39.6%). Given the reach and frequency of exposure to music videos among young people, reducing tobacco imagery in popular music videos may prevent tobacco use among young people.

Optimizing maternal and neonatal outcomes through tight control management of inflammatory bowel disease during pregnancy: a pilot feasibility study.

A home point-of care FCP test (IBDoc) and a self-reported clinical disease activity program (IBD Dashboard) may improve routine monitoring of IBD activity during pregnancy. We aimed to evaluate the feasibility of tight control management using remote monitoring in pregnant patients with IBD. Pregnant patients (< 20 weeks) with IBD were prospectively enrolled from Mount Sinai Hospital between 2019 and 2020. Patients completed the IBDoc and IBD Dashboard at three core time points. Disease activity was measured clinically using the Harvey-Bradshaw Index (mHBI) for CD and partial Mayo (pMayo) for UC, or objectively using FCP. A feasibility questionnaire was completed in the third trimester. Seventy-seven percent of patients (24 of 31) completed the IBDoc and IBD Dashboard at all core time points. Twenty-four patients completed the feasibility questionnaires. All survey respondents strongly preferred using the IBDoc over standard lab-based testing and would use the home kit in the future. Exploratory analysis identified discordance rates of more than 50% between clinical and objective disease activity. Tight control management using remote monitoring may be feasible among pregnant patients with IBD. A combination of both clinical scores and objective disease markers may better predict disease activity.

A resurgence of e-cigarette use among adolescents and young adults late in the COVID-19 pandemic.

BACKGROUND: Early in the COVID-19 pandemic, e-cigarette use significantly declined among young people due, in part, to losing access through social sources. As the pandemic progressed, adolescents and young adults gained opportunities to resume contact with peers. This study sought to determine whether e-cigarette use has returned to pre-pandemic levels among adolescents and young adults. METHODS: Data were drawn from a cross-sectional weekly survey of adolescents (aged 15-17) and young adults (aged 18-24) (N = 37,331). Logistic regression analyses measured odds of past 30-day e-cigarette use among respondents surveyed (a) late in the pandemic (April 2021-April 2022) compared to early in the pandemic (March-July 2020) and (b) late in the pandemic (August-December 2021) compared to prior to the pandemic (August-December 2019). RESULTS: The odds of current e-cigarette use were significantly higher later in the COVID-19 pandemic (April 2021-April 2022), compared to its initial months (March-July 2020) (OR:1.27, 95% CI: 1.17-1.38; p = 0.001). There was no significant difference in the odds of e-cigarette use for youth and younger adults late in the pandemic (August-December 2021) compared to the same time period prior to the pandemic (August-December 2019), but odds were greater for young adults aged 21 years or older (OR:1.16; 95% CI: 1.01-1.32; p = 0.030). CONCLUSIONS: E-cigarette use has returned to pre-pandemic levels among adolescents and young adults. Young adults over age 21 are more likely to use e-cigarettes than young adults of the same age surveyed prior to the pandemic. Findings have implications for targeted e-cigarette prevention and cessation efforts.

Perceived Sensory Characteristics of Blended and Ambiguous "Concept" Flavors Among Adolescent and Young Adult E-cigarette Users.

INTRODUCTION: Flavors with names describing blended tastes/sensations or with ambiguous terminology ("concept flavors") are available on the e-cigarette market. AIMS AND METHODS: This study investigates adolescent and young adult use and sensory perceptions of blended and concept flavors. Current e-cigarette users aged 15-24 years (N = 2281) completed an online convenience sample survey (October 20-November 23, 2020) and rated the sensory attributes (fruity, cooling, sweet, and minty) of their current flavor(s) using nine-point scales. T-tests compared mean sensory perception scores within and between flavors. To compare concept flavors to blends, reference categories used the average of blends with relevant descriptors: fruit (Banana Ice, Iced Mango, Melon Ice, Cool Cucumber); cooling (Banana Ice, Iced Mango, Melon Ice, Blue B Ice, Cool Cucumber, Lush Ice, and Menthol Purple); sweet (Vivid Vanilla) and mint (Mint-sation). RESULTS: Most respondents had used at least one product with blended descriptors (74.8%) or concept flavor (57.9%) in the past 30 days. All flavors had high perceived strength for at least two sensory attributes. Mint taste was not perceived to be a strong sensory characteristic for all but two flavors (Mint-sation and Winter) in the study. The most commonly used flavors used blended descriptors (Iced Mango was used by 30.2% of the sample; Banana Ice: 26.2%; Lush Ice: 23.8%; Melon Ice: 22.9%). Some concept flavors did not significantly differ from flavor blend reference categories for strength of: fruit taste (Bahama Mama and Tropic); cooling sensation (Marigold, Island Breeze, Winter); sweet taste (Bahama Mama, Honeymoon, Island Breeze, Island Cream, Meteor Milk, OMG, Royal Dagger and Tropic); and mint taste (Winter). CONCLUSIONS: Blended and concept flavors are used by most young e-cigarette users, who describe these products as fruity, sweet, and cooling. A variety of flavored products with high youth appeal are available in the U.S. market. IMPLICATIONS: This study of adolescent and young adult e-cigarette users finds evidence of the popularity of e-cigarette flavors combining a cooling sensation with fruity and sweet flavorings. Some products with this flavor profile do not use characterizing descriptors. Findings inform public health interventions intended to reduce e-cigarette use in young people.

The COVID-19 Pandemic Significantly Impacts Pregnancy Planning and Mental Health of Women With Inflammatory Bowel Disease.

BACKGROUND AND GOALS: The coronavirus disease 2019 (COVID-19) pandemic has significantly impacted daily life, particularly in those with inflammatory bowel disease (IBD). We aimed to determine the impact of the pandemic on the pregnancy planning and mental health of women with IBD. METHODS: Women with IBD (age 18 to 45 y) were asked to complete anonymous surveys on the impact of the COVID-19 pandemic on pregnancy planning and mental health symptoms such as stress (Perceived Stress Scale), depression (Patient Health Questionnaire-9), and anxiety (Generalized Anxiety Disorder-7). Univariate and multivariable analyses were conducted to identify risk factors associated with stress, depression, and anxiety during the pandemic. RESULTS: Seventy-three women with IBD were included (mean age: 32.1). Of 39 patients who were preconception, 20 (51.3%) reported a significant impact of the pandemic on pregnancy planning, with common reasons for not planning conception being fear of transmission of the virus to the fetus, lack of social supports, and no desire to be in hospital during pregnancy. Over half of all women reported an increase in stress and depression symptoms during the pandemic, with over half also reporting symptoms of anxiety. On multivariable linear regression analyses, increased anxiety levels were a significant predictor of increased stress and depression symptoms during the pandemic. Urban residence and younger age were significant predictors of increased anxiety symptoms during the pandemic. CONCLUSION: A significant proportion of women with IBD experienced an impact of the COVID-19 pandemic on pregnancy planning and mental health illnesses such as stress, depression, and anxiety.

Relative increases in direct-to-consumer menthol ads following 2020 FDA guidance on flavoured e-cigarettes.

OBJECTIVE: To examine potential changes in email and direct mail advertisements for flavoured e-cigarettes following the 2020 Food and Drug Administration (FDA) flavour guidance. METHODS: Digital copies of e-cigarette advertisements were obtained from Mintel Comperemedia (November 2019-May 2020) and coded for the presence of flavours. Χ2 tests were used to determine changes in the prevalence of email and direct mail advertisements for e-cigarettes with menthol, non-menthol and no flavours. RESULTS: Following FDA guidance, the relative proportion of menthol-flavoured e-cigarette advertisements sent via email significantly increased from 22.5% to 52.2%. No changes were found for e-cigarette advertisements mentioning no flavours, nor non-menthol-flavoured e-cigarettes, sent via email or direct mail. CONCLUSIONS: The 2020 FDA flavour guidance was followed by an increased proportion of direct-to-consumer email advertisements of menthol-flavoured e-cigarette products.

Evaluation of In-Field Inoculation Methods for Characterization of Macadamia Germplasm to Husk Spot Incidence and Severity.

Husk spot, a fungal disease of macadamia pericarps (Pseudocercospora macadamiae), induces premature abscission in several major commercial cultivars. Breeding for resistance to husk spot is a priority of the Australian macadamia industry. Due to the large tree size of macadamia and high numbers of progeny in breeding populations, inoculating for resistance screening is laborious and time consuming. Previously utilized methods included direct applications of P. macadamiae suspensions and the hanging of bags of diseased husks above developing fruit in tree canopies. In this study, both methods were modified to allow for efficient application in large-scale breeding populations, and their efficacy was evaluated. Two quantities of diseased husk per bag, 'large' (75 g) and 'small' (30 g), and two concentrations of sprayed P. macadamiae suspensions, 'stock' (5 × 105 propagules/ml) and 'dilute' (2.5 × 105 propagules/ml), were tested across two fruiting seasons. Treatments were compared against a control (sterile water) in commercial cultivars A38 and A4. Husk spot incidence and severity produced by small bags were significantly affected by season. A significant season effect was less common for other treatments. All four treatments infected over 50% of target fruit in each season, but the highest husk spot incidence across both seasons (≥85%) was produced from large bags. Overall, the large bags were the most reliable method for infection of target fruit. Results also demonstrate the importance of considering the effect of season when selecting husk spot inoculation methods.

A Novel Decision Aid Improves Quality of Reproductive Decision-Making and Pregnancy Knowledge for Women with Inflammatory Bowel Disease.

BACKGROUND: Women with inflammatory bowel disease (IBD) with poor IBD-specific reproductive knowledge experience more childlessness and fear of IBD medications in pregnancy. The Pregnancy in IBD Decision Aid (PIDA), developed by an international multidisciplinary team, offers personalized online decision support regarding pregnancy in IBD. AIMS: Assess the impact of PIDA on quality of reproductive decision-making and pregnancy-related knowledge among preconception (PC) and pregnant patients with IBD, and evaluate acceptability to patients and clinicians. METHODS: PC and pregnant patients with IBD aged 18-45 completed questionnaires pre- and post-PIDA to assess quality of decision-making (Decisional Conflict Scale (DCS); Decision Self-Efficacy Scale (DSES) and IBD-in-pregnancy knowledge (Crohn's and Colitis Pregnancy Knowledge Score (CCPKnow)). Paired t test assessed for differences pre- and post-PIDA. Patients and clinicians completed acceptability surveys. RESULTS: DCS and DSES were completed by 74 patients (42 Crohn's disease, 32 ulcerative colitis); 41 PC and 33 pregnant. DCS improved significantly post-PIDA in PC patients regarding pregnancy planning (t(40) = 4.83, p < 0.0001, Cohen's dz = 0.75) and in pregnant patients regarding medication management (t(32) = 2.37, p = 0.0242, dz = 0.41). DSES for PC patients improved significantly post-PIDA (t(40) = -3.56, p = 0.001, dz = -0.56). CCPKnow improved significantly post-PIDA in PC (t(42) = 4.93, p < 0.0001, dz = -0.75) and pregnant patients (t(32) = 5.1, p < 0.0001, dz = -0.89). PIDA was deemed optimal for length, readability, and content amount and considered highly useful by patients (n = 73) and clinicians (n = 14). CONCLUSIONS: Patients using PIDA developed an improved quality of reproductive decision-making and IBD-in-pregnancy knowledge. PIDA is an accessible tool that can empower women with IBD to make values-congruent, evidence-based decisions regarding pregnancy and may reduce voluntary childlessness.

Finding the facts in an infodemic: framing effective COVID-19 messages to connect people to authoritative content.

The public's need for timely and trusted COVID-19 information remains high. Governments and global health agencies such as the WHO have sought to disseminate accurate and timely information to counteract misinformation and disinformation that has arisen as part of an 'infodemic'-the overabundance of information on COVID-19-some accurate and some not. In early 2020, WHO began a collaboration with Google to run online public service announcements on COVID-19, in the form of search ads displayed above results of Google Search queries. Web-based text ads can drive online searchers of COVID-19 information to authoritative COVID-19 content but determining what message is most effective is a challenge. WHO wanted to understand which message framing, that is, the way in which ad information is worded for the public, leads searchers to click through to WHO content. WHO tested 71 text ads in English across four COVID-19 topics using a mix of message frames: descriptive, collective, gain, loss, appeals to values and emphasising reasons. Between 11 September 2020 and 23 November 2020, there were 13 million views of the experimental WHO text ads leading to 1.4 million click-throughs to the WHO website. Within the set of 71 ads, there was a large spread between the most effective and least effective messages; for messages on COVID-19, the best performing framings were more than twice as effective as the worst performing framings (18.7% vs 8.5% engagement rate). Health practitioners can apply the messaging tactics WHO found to be successful to rapidly optimise messages for their own public health campaigns and better reach the public with authoritative information. Similar collaboration between big technology companies and governments and global health agencies has the potential to advance public health.

Influence of Flavors and Nicotine Concentration on Nicotine Dependence in Adolescent and Young Adult E-Cigarette Users.

Objective: The objective of this study is to examine the relationships between e-cigarette flavors, nicotine concentration, and their interaction on measures of nicotine dependence.Methods: Survey data are drawn from a cross-sectional convenience sample of past 30-day e-cigarette users aged 15 to 24 years (N = 2037) collected between October 2020 and November 2020. Participants were asked to provide information about the e-cigarette products they used most regularly. Only those with available information on flavors (fruit, mint, menthol/ice, and tobacco), nicotine concentration (0-2.9%, 3-4.9%, and 5% or greater), and time to first vape after waking (within 30 minutes, greater than 30 minutes) were included in analyses (N = 1430). Generalized linear regression models were used with log link and binary distribution to assess the relationship between flavors, nicotine concentration, and nicotine dependence. Effect modification by nicotine concentration was assessed using an interaction term for flavors by nicotine concentration. Models were adjusted for age, race/ethnicity, gender, and financial situation.Findings: Fruit, mint, and menthol flavor user groups had a very similar dose-response relationship between nicotine concentration and prevalence of vaping within 30 minutes. These groups showed that the prevalence of vaping within 30 minutes gradually increased as nicotine concentration increased. Meanwhile, tobacco flavor user groups demonstrated a decrease in prevalence of vaping within 30 minutes, as nicotine concentration increased.Conclusion: Results highlight the need for understanding how e-cigarette product characteristics like flavors and nicotine concentration can facilitate nicotine dependence to e-cigarettes. Findings suggest that comprehensive e-cigarette product regulation of all flavors and reducing nicotine concentration will help to reduce the risk for nicotine dependence among young people.

E-cigarette device and liquid characteristics and E-cigarette dependence: A pilot study of pod-based and disposable E-cigarette users.

BACKGROUND: E-cigarette device and liquid characteristics, such as electrical power output and liquid nicotine concentration, determine the rate at which nicotine is emitted from the e-cigarette (i.e., nicotine flux), and thus are likely to influence user nicotine dependence. We hypothesize that nicotine flux would be associated with the E-cigarette Dependence Scale (EDS) among pod-based and disposable e-cigarette products. METHODS: Data were obtained from online panel participants between 18 and 65 years of age, who had indicated that they were either former or current e-cigarette users and resided within the United States (N = 1036). To be included in these analyses, participants had to provide information regarding device type (pod-based or disposable), power (watts), and nicotine concentration (mg/mL), from which we could determine nicotine flux (µg/s) (N = 666). To assess the relationship between nicotine flux and EDS, a series of multivariable linear regressions were conducted. Each model was separated by device type and adjusted for by age and past 30-day e-cigarette use. RESULTS: Greater nicotine flux was associated with higher EDS scores among pod-based e-cigarette users (beta = 0.19, SE = 0.09, p-value = 0.043), but not users of disposable e-cigarettes. Neither power nor nicotine concentration were associated with EDS scores among users of either e-cigarette device type. CONCLUSION: Results support the hypothesis that nicotine flux is positively associated with nicotine dependence in a sample of current users of pod-based and disposable e-cigarettes.

Shared decision making in pregnancy in inflammatory bowel disease: design of a patient orientated decision aid.

BACKGROUND: Research has indicated a lack of disease-specific reproductive knowledge among patients with Inflammatory Bowel Disease (IBD) and this has been associated with increased "voluntary childlessness". Furthermore, a lack of knowledge may contribute to inappropriate medication changes during or after pregnancy. Decision aids have been shown to support decision making in pregnancy as well as in multiple other chronic diseases. A published decision aid for pregnancy in IBD has not been identified, despite the benefit of pre-conception counselling and patient desire for a decision support tool. This study aimed to develop and test the feasibility of a decision aid encompassing reproductive decisions in the setting of IBD. METHODS: The International Patient Decision Aid Standards were implemented in the development of the Pregnancy in IBD Decision Aid (PIDA). A multi-disciplinary steering committee was formed. Patient and clinician focus groups were conducted to explore themes of importance in the reproductive decision-making processes in IBD. A PIDA prototype was designed; patient interviews were conducted to obtain further insight into patient perspectives and to test the prototype for feasibility. RESULTS: Issues considered of importance to patients and clinicians encountering decisions regarding pregnancy in the setting of IBD included fertility, conception timing, inheritance, medications, infant health, impact of surgery, contraception, nutrition and breastfeeding. Emphasis was placed on the provision of preconception counselling early in the disease course. Decisions relating to conception and medications were chosen as the current focus of PIDA, however content inclusion was broad to support use across preconception, pregnancy and post-partum phases. Favourable and constructive user feedback was received. CONCLUSIONS: The novel development of a decision aid for use in pregnancy and IBD was supported by initial user testing.

Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population.

BACKGROUND: Improving yield prediction and selection efficiency is critical for tree breeding. This is vital for macadamia trees with the time from crossing to production of new cultivars being almost a quarter of a century. Genomic selection (GS) is a useful tool in plant breeding, particularly with perennial trees, contributing to an increased rate of genetic gain and reducing the length of the breeding cycle. We investigated the potential of using GS methods to increase genetic gain and accelerate selection efficiency in the Australian macadamia breeding program with comparison to traditional breeding methods. This study evaluated the prediction accuracy of GS in a macadamia breeding population of 295 full-sib progeny from 32 families (29 parents, reciprocals combined), along with a subset of parents. Historical yield data for tree ages 5 to 8 years were used in the study, along with a set of 4113 SNP markers. The traits of focus were average nut yield from tree ages 5 to 8 years and yield stability, measured as the standard deviation of yield over these 4 years. GBLUP GS models were used to obtain genomic estimated breeding values for each genotype, with a five-fold cross-validation method and two techniques: prediction across related populations and prediction across unrelated populations. RESULTS: Narrow-sense heritability of yield and yield stability was low (h2 = 0.30 and 0.04, respectively). Prediction accuracy for yield was 0.57 for predictions across related populations and 0.14 when predicted across unrelated populations. Accuracy of prediction of yield stability was high (r = 0.79) for predictions across related populations. Predicted genetic gain of yield using GS in related populations was 474 g/year, more than double that of traditional breeding methods (226 g/year), due to the halving of generation length from 8 to 4 years. CONCLUSIONS: The results of this study indicate that the incorporation of GS for yield into the Australian macadamia breeding program may accelerate genetic gain due to reduction in generation length, though the cost of genotyping appears to be a constraint at present.

E-Cigarette Use Among Youths and Young Adults During the COVID-19 Pandemic: United States, 2020.

Objectives. To determine whether the COVID-19 pandemic affected e-cigarette use among young people in the United States.Methods. Data came from a weekly cross-sectional online survey of youths and young adults (aged 15-24 years). Logistic regression analyses measured odds of past-30-day e-cigarette use (n = 5752) following widespread stay-at-home directives (March 14-June 29, 2020), compared with the pre‒COVID-19 period (January 1-March 13, 2020). Logistic regression among a subsample of current e-cigarette users (n = 779) examined factors associated with reduced use following stay-at-home orders.Results. Odds of current e-cigarette use were significantly lower during the COVID-19 pandemic compared with the pre‒COVID-19 period among youths aged 15 to 17 years (odds ratio [OR] = 0.72; 95% confidence interval [CI] = 0.54, 0.96) and young adults aged 18 to 20 years (OR = 0.65; 95% CI = 0.52, 0.81). E-cigarette users with reduced access to retail environments had higher odds of reporting reduced e-cigarette use (OR = 1.51; 95% CI = 1.07, 2.14).Conclusions. COVID-19 stay-at-home directives present barriers to e-cigarette access and are associated with a decline in e-cigarette use among young people.Public Health Implications. Findings support the urgent implementation of interventions that reduce underage access to e-cigarettes to accelerate a downward trajectory of youth and young adult e-cigarette use.

Genome-wide association studies for yield component traits in a macadamia breeding population.

BACKGROUND: Breeding for new macadamia cultivars with high nut yield is expensive in terms of time, labour and cost. Most trees set nuts after four to five years, and candidate varieties for breeding are evaluated for at least eight years for various traits. Genome-wide association studies (GWAS) are promising methods to reduce evaluation and selection cycles by identifying genetic markers linked with key traits, potentially enabling early selection through marker-assisted selection. This study used 295 progeny from 32 full-sib families and 29 parents (18 phenotyped) which were planted across four sites, with each tree genotyped for 4113 SNPs. ASReml-R was used to perform association analyses with linear mixed models including a genomic relationship matrix to account for population structure. Traits investigated were: nut weight (NW), kernel weight (KW), kernel recovery (KR), percentage of whole kernels (WK), tree trunk circumference (TC), percentage of racemes that survived from flowering through to nut set, and number of nuts per raceme. RESULTS: Seven SNPs were significantly associated with NW (at a genome-wide false discovery rate of < 0.05), and four with WK. Multiple regression, as well as mapping of markers to genome assembly scaffolds suggested that some SNPs were detecting the same QTL. There were 44 significant SNPs identified for TC although multiple regression suggested detection of 16 separate QTLs. CONCLUSIONS: These findings have important implications for macadamia breeding, and highlight the difficulties of heterozygous populations with rapid LD decay. By coupling validated marker-trait associations detected through GWAS with MAS, genetic gain could be increased by reducing the selection time for economically important nut characteristics. Genomic selection may be a more appropriate method to predict complex traits like tree size and yield.

Ultra-high-throughput DArTseq-based silicoDArT and SNP markers for genomic studies in macadamia.

Macadamia (Macadamia integrifolia, M. tetraphylla and hybrids) is an Australian native nut crop and has a significant economic value in the food industries worldwide. Long juvenility along with traditional breeding strategies impede quick genetic improvement of this crop. The existing cultivars constitute only second to fourth generation of the wild germplasm in the rainforest. The utilisation of molecular markers for genomic selection and genome-wide association studies may accelerate genetic gains. Identification of a robust, reproducible, and cost-effective marker system is instrumental in increasing the efficiency of genomic studies. This study is the first to report the potential of two ultra-high-throughput diversity array technology (DArT) markers (silicoDArT and SNP) in macadamia. Both markers were used to identify the genetic diversity and population structure in 80 macadamia cultivars. Parentage analysis of 25 scions in a rootstock trial was conducted to confirm plant identity where recorded identities did not corroborate with phenotypic field observations. A total of 22,280 silicoDArT and 7,332 SNP markers were reported, of which 11,526 silicoDArT and 3,956 SNP markers were used for analyses after screening with quality control parameters including >95% call rate, >95% reproducibility, and >0.05 one ratio. The average polymorphic information content (PIC) values of silicoDArT and SNP markers were 0.29 and 0.21, respectively. Genetic variance among the cultivars ranged from 0.003 to 0.738 in silicoDArT and 0.004 to 0.412 in SNP markers. Four distinct population groups were identified from SNP data analysis. Most of the accessions used in this study were descended from two or more populations. Cluster analysis clearly separated genotypes of distinct origins, such as the Hawaii Agricultural Experiment Station and Hidden Valley Plantation accessions. Two wild accessions of Macadamia jansenii and M. ternifolia were found to be distantly related to the cultivars. Wild germplasm individuals and their hybrids with cv. '660' formed separate clusters, suggesting that crossing between wild and cultivated genepools can extend genetic diversity. DArTseq-based SNP markers were successfully utilized to confirm the genetic identity of 25 scions in a rootstock trial. Our study suggests that DArT platforms are a robust system for the facilitation of genomic studies with regard to macadamia.

A regulatory toolbox of MiniPromoters to drive selective expression in the brain.

The Pleiades Promoter Project integrates genomewide bioinformatics with large-scale knockin mouse production and histological examination of expression patterns to develop MiniPromoters and related tools designed to study and treat the brain by directed gene expression. Genes with brain expression patterns of interest are subjected to bioinformatic analysis to delineate candidate regulatory regions, which are then incorporated into a panel of compact human MiniPromoters to drive expression to brain regions and cell types of interest. Using single-copy, homologous-recombination "knockins" in embryonic stem cells, each MiniPromoter reporter is integrated immediately 5' of the Hprt locus in the mouse genome. MiniPromoter expression profiles are characterized in differentiation assays of the transgenic cells or in mouse brains following transgenic mouse production. Histological examination of adult brains, eyes, and spinal cords for reporter gene activity is coupled to costaining with cell-type-specific markers to define expression. The publicly available Pleiades MiniPromoter Project is a key resource to facilitate research on brain development and therapies.

A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation.

As part of a larger project to sequence the Populus genome and generate genomic resources for this emerging model tree, we constructed a physical map of the Populus genome, representing one of the few such maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2802 contigs, was constructed from fingerprinted bacterial artificial chromosome (BAC) clones. The map represents approximately 9.4-fold coverage of the Populus genome, which has been estimated from the genome sequence assembly to be 485 +/- 10 Mb in size. BAC ends were sequenced to assist long-range assembly of whole-genome shotgun sequence scaffolds and to anchor the physical map to the genome sequence. Simple sequence repeat-based markers were derived from the end sequences and used to initiate integration of the BAC and genetic maps. A total of 2411 physical map contigs, representing 97% of all clones assigned to contigs, were aligned to the sequence assembly (JGI Populus trichocarpa, version 1.0). These alignments represent a total coverage of 384 Mb (79%) of the entire poplar sequence assembly and 295 Mb (96%) of linkage group sequence assemblies. A striking result of the physical map contig alignments to the sequence assembly was the co-localization of multiple contigs across numerous regions of the 19 linkage groups. Targeted sequencing of BAC clones and genetic analysis in a small number of representative regions showed that these co-aligning contigs represent distinct haplotypes in the heterozygous individual sequenced, and revealed the nature of these haplotype sequence differences.