A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement

Hexaploid oat ( L., 2 = 6 = 42) is a member of the Poaceae family and has a large genome (∼12.5 Gb) containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density consensus linkage map that is representative of the majority of commonly grown oat varieties. Data from a cDNA-derived single-nucleotide polymorphism (SNP) array and genotyping-by-sequencing (GBS) were collected from the progeny of 12 biparental recombinant inbred line populations derived from 19 parents representing oat germplasm cultivated primarily in North America. Linkage groups from all mapping populations were compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster were then merged into 21 consensus chromosomes, generating a framework consensus map of 7202 markers spanning 2843 cM. An additional 9678 markers were placed on this map with a lower degree of certainty. Assignment to physical chromosomes with high confidence was made for nine chromosomes. Comparison of homeologous regions among oat chromosomes and matches to orthologous regions of rice ( L.) reveal that the hexaploid oat genome has been highly rearranged relative to its ancestral diploid genomes as a result of frequent translocations among chromosomes. Heterogeneous chromosome rearrangements among populations were also evident, probably accounting for the failure of some linkage groups to match the consensus. This work contributes to a further understanding of the organization and evolution of hexaploid grass genomes

Association of Food Insecurity with Early Childhood Caries

Objectives The aim of this study was to examine the association of food insecurity on the prevalence of dental caries in preschool children. Methods Eighty-two children, aged 12-71 months old, from the Marquette University School of Dentistry Community South Clinic and their caregivers participated in this cross-sectional study. Following informed consent, parents completed the validated six-item US Department of Agriculture food insecurity questionnaire and questions regarding demographic information and family structure. Upon clinical examination caries was recorded using the decayed, missing, filled teeth (dmft) index based on the International Caries Detection and Assessment System criteria. Results The correlation between dmft and food insecurity was found statistically significant (P = 0.002, R2 = 0.115), and children of higher food insecurity demonstrated higher levels of dental caries. Food insecurity was also positively correlated with parental age (P = 0.034), whereby higher levels of food insecurity were associated with the father being less than 25 years of age. Results from the questionnaire revealed that 58.5 percent of the families were fully secure, 11.0 percent had marginal, 24.4 percent had low, and 6.1 percent had very low food security. Results from clinical examination reported dmft 4.09 ± 4.38, dt 2.20 ± 2.83, and ft 1.83 ± 2.95. Most of the children (79.7 percent) were Hispanic, 53.1 percent were female and the median age of the sample was 48 months. Conclusions Results of the present study suggest that preschool children with food insecurity have higher levels of dental caries

Association of Obesity and Diabetes with SARS-Cov-2 Infection and Symptoms in the COVID-19 Community Research Partnership

OBJECTIVE: Obesity and diabetes are established risk factors for severe SARS-CoV-2 outcomes, but less is known about their impact on susceptibility to COVID-19 infection and general symptom severity. We hypothesized that those with obesity or diabetes would be more likely to self-report a positive SARS-CoV-2 test, and among those with a positive test, have greater symptom severity and duration. METHODS: Among 44,430 COVID-19 Community Research Partnership participants, we evaluated the association of self-reported and electronic health record obesity and diabetes with a self-reported positive COVID-19 test at any time. Among the 2,663 participants with a self-reported positive COVID-19 test during the study, we evaluated the association of obesity and diabetes with self-report of symptom severity, duration, and hospitalization. Logistic regression models were adjusted for age, sex, race/ethnicity, socioeconomic status, and healthcare worker status. RESULTS: We found a positive graded association between Body Mass Index (BMI) category and positive COVID-19 test (Overweight OR = 1.14 [1.05-1.25]; Obesity I OR = 1.29 [1.17-2.42]; Obesity II OR = 1.34 [1.19-1.50]; Obesity III OR = 1.53 [1.35-1.73]), and a similar but weaker association with COVID-19 symptoms and severity among those with a positive test. Diabetes was associated with COVID-19 infection but not symptoms after adjustment, with some evidence of an interaction between obesity and diabetes. CONCLUSIONS: While the limitations of this health system convenience sample include generalizability and selection around test-seeking, the strong graded association of BMI and diabetes with self-reported COVID-19 infection suggests that obesity and diabetes may play a role in risk for symptomatic SARS-CoV-2 beyond co-occurrence with socioeconomic factors

Whole Genome Sequencing Identifies CRISPLD2 as a Lung Function Gene in Children With Asthma

BackgroundAsthma is a common respiratory disorder with a highly heterogeneous nature that remains poorly understood. The objective was to use whole genome sequencing (WGS) data to identify regions of common genetic variation contributing to lung function in individuals with a diagnosis of asthma.MethodsWGS data were generated for 1,053 individuals from trios and extended pedigrees participating in the family-based Genetic Epidemiology of Asthma in Costa Rica study. Asthma affection status was defined through a physician's diagnosis of asthma, and most participants with asthma also had airway hyperresponsiveness (AHR) to methacholine. Family-based association tests for single variants were performed to assess the associations with lung function phenotypes.ResultsA genome-wide significant association was identified between baseline FEV1/FVC ratio and a single-nucleotide polymorphism in the top hit cysteine-rich secretory protein LCCL domain-containing 2 (CRISPLD2) (rs12051168; P = 3.6 × 10-8 in the unadjusted model) that retained suggestive significance in the covariate-adjusted model (P = 5.6 × 10-6). Rs12051168 was also nominally associated with other related phenotypes: baseline FEV1 (P = 3.3 × 10-3), postbronchodilator (PB) FEV1 (7.3 × 10-3), and PB FEV1/FVC ratio (P = 2.7 × 10-3). The identified baseline FEV1/FVC ratio and rs12051168 association was meta-analyzed and replicated in three independent cohorts in which most participants with asthma also had confirmed AHR (combined weighted z-score P = .015) but not in cohorts without information about AHR.ConclusionsThese findings suggest that using specific asthma characteristics, such as AHR, can help identify more genetically homogeneous asthma subgroups with genotype-phenotype associations that may not be observed in all children with asthma. CRISPLD2 also may be important for baseline lung function in individuals with asthma who also may have AHR