Genetic analysis of yield and flesh colour in sweetpotato

Pre-breeding information on the inheritance mechanism of important sweetpotato ( Ipomoea batatas L.) agronomic traits is still limited. This study aimed at assessing the inheritance of five sweetpotato agronomic traits, viz. marketable fresh root yield (MFRY) and number (MNR), total fresh root yield (TFRY) and number (TNR) and root \u3b2-carotene content (RBCC). A 5 x 5 full diallel was performed and F1 progenies, evaluated in two environments alongside the parents. The data were subjected to ANOVA and DiallelSAS-05 Griffing\u2019s method 1. Simple Sequence Repeat (SSR) based genetic distance and cluster analysis were performed on the parental lines using Jaccard\u2019s coefficient and the unweighted pair group method with arithmetic averages (UPGMA). Significant differences (P<0.01) were detected among the genotypes for MFRY, MNR, TFRY, TNR and RBCC. Significant general and specific combining ability (P<0.01) effects were observed for all five traits. Additive gene action was predominantly involved in the inheritance of these traits. High broad sense heritability values were observed for the four yield parameters and for RBCC. The Jaccard\u2019s similarity coefficient indicated moderate to low genetic similarity distances among the parents, implying high diversity. The knowledge on the inheritance and diversity of the parental genotypes enables more effective choice of parents in breeding improved varieties.Les informations pr\ue9liminaires sur le mode de transmission des caract\ue8res agronomiques importants chez la patate douce ( Ipomoea batatas L.) sont encore tr\ue8s limit\ue9es. Cette \ue9tude vise \ue0 \ue9valuer la transmission de cinq traits agronomiques chez la patate douce. viz. Le rendement de tubercules fra\ueeches \ue0 valeur marchande (MFRY) et leur nombre (MNR), le rendement total de tubercules frais (TFRY) et leur nombre (TNR), de m\ueame que la teneur en \u3b2-carotene des tubercules (RBCC). Une s\ue9rie de croisement diallel 5 x 5 avec croisements r\ue9ciproques a \ue9t\ue9 r\ue9alis\ue9e et les descendants de g\ue9n\ue9ration F1 ont \ue9t\ue9 \ue9valu\ue9s ensemble avec les parents dans deux environnements. Les donn\ue9es collect\ue9es ont \ue9t\ue9 soumises \ue0 une analyse de variances et \ue0 une analyse DiallelSAS-05 m\ue9thode 1 de Griffing. Les distances g\ue9n\ue9tiques bas\ue9es sur des R\ue9p\ue9titions de S\ue9quences Simples (SSR) a \ue9t\ue9 calcul\ue9es et une classification num\ue9rique \ue0 \ue9t\ue9 r\ue9alis\ue9e sur les lign\ue9es parentales. Le coefficient de Jaccard et la m\ue9thode des paires-groupes non pond\ue9r\ue9s avec la moyenne arithm\ue9tique (UPGMA) ont \ue9t\ue9 utilis\ue9es \ue0 cet effet. Des diff\ue9rences significatives (P<0.01) ont \ue9t\ue9 observ\ue9es entre les g\ue9notypes pour MFRY, MNR, TFRY, TNR et RBCC. Des effets significatifs de l\u2019habilet\ue9 de combinaison g\ue9n\ue9rale (P<0.01) ont \ue9t\ue9 observ\ue9s sur tous les 5 traits. L\u2019effet additif des g\ue8nes \ue9tait pr\ue9dominant. Des valeurs d\u2019h\ue9ritabilit\ue9 au sens large ont \ue9t\ue9 observ\ue9es pour quatre param\ue8tres de rendements en tubercules et pour RBCC. Le coefficient de similarit\ue9 de Jaccard a indiqu\ue9 une des distances de similarit\ue9 g\ue9n\ue9tique faibles ou mod\ue9r\ue9es entre les parents, ce qui sugg\ue8re une grande diversit\ue9. Les connaissances sur le mode transmission et la diversit\ue9 des lign\ue9es parentales permet des choix plus efficients des parents \ue0 utiliser dans un programme d\u2019am\ue9lioration g\ue9n\ue9tique

Meeting reports: Research on Coupled Human and Natural Systems (CHANS): Approach, Challenges, and Strategies

Understanding the complexity of human–nature interactions is central to the quest for both human well-being and global sustainability. To build an understanding of these interactions, scientists, planners, resource managers, policymakers, and communities increasingly are collaborating across wide-ranging disciplines and knowledge domains. Scientists and others are generating new integrated knowledge on top of their requisite specialized knowledge to understand complex systems in order to solve pressing environmental and social problems (e.g., Carpenter et al. 2009). One approach to this sort of integration, bringing together detailed knowledge of various disciplines (e.g., social, economic, biological, and geophysical), has become known as the study of Coupled Human and Natural Systems, or CHANS (Liu et al. 2007a, b). In 2007 a formal standing program in Dynamics of Coupled Natural and Human Systems was created by the U.S. National Science Foundation. Recently, the program supported the launch of an International Network of Research on Coupled Human and Natural Systems (CHANS-Net.org). A major kick-off event of the network was a symposium on Complexity in Human–Nature Interactions across Landscapes, which brought together leading CHANS scientists at the 2009 meeting of the U.S. Regional Association of the International Association for Landscape Ecology in Snowbird, Utah. The symposium highlighted original and innovative research emphasizing reciprocal interactions between human and natural systems at multiple spatial, temporal, and organizational scales. The presentations can be found at ‹http://chans- net.org/Symposium_2009.aspx›. The symposium was accompanied by a workshop on Challenges and Opportunities in CHANS Research. This article provides an overview of the CHANS approach, outlines the primary challenges facing the CHANS research community, and discusses potential strategies to meet these challenges, based upon the presentations and discussions among participants at the Snowbird meeting

Whole genome sequence analysis of pulmonary function and COPD in 19,996 multi-ethnic participants

Chronic obstructive pulmonary disease (COPD), diagnosed by reduced lung function, is a leading cause of morbidity and mortality. We performed whole genome sequence (WGS) analysis of lung function and COPD in a multi-ethnic sample of 11,497 participants from population- and family-based studies, and 8499 individuals from COPD-enriched studies in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program. We identify at genome-wide significance 10 known GWAS loci and 22 distinct, previously unreported loci, including two common variant signals from stratified analysis of African Americans. Four novel common variants within the regions of PIAS1, RGN (two variants) and FTO show evidence of replication in the UK Biobank (European ancestry n ~ 320,000), while colocalization analyses leveraging multi-omic data from GTEx and TOPMed identify potential molecular mechanisms underlying four of the 22 novel loci. Our study demonstrates the value of performing WGS analyses and multi-omic follow-up in cohorts of diverse ancestry

Global, regional, and national incidence, prevalence, and years lived with disability for 328 diseases and injuries for 195 countries, 1990–2016: a systematic analysis for the Global Burden of Disease Study 2016

As mortality rates decline, life expectancy increases, and populations age, non-fatal outcomes of diseases and injuries are becoming a larger component of the global burden of disease. The Global Burden of Diseases, Injuries, and Risk Factors Study 2016 (GBD 2016) provides a comprehensive assessment of prevalence, incidence, and years lived with disability (YLDs) for 328 causes in 195 countries and territories from 1990 to 2016

Global, regional, and national under-5 mortality, adult mortality, age-specific mortality, and life expectancy, 1970–2016: a systematic analysis for the Global Burden of Disease Study 2016

BACKGROUND: Detailed assessments of mortality patterns, particularly age-specific mortality, represent a crucial input that enables health systems to target interventions to specific populations. Understanding how all-cause mortality has changed with respect to development status can identify exemplars for best practice. To accomplish this, the Global Burden of Diseases, Injuries, and Risk Factors Study 2016 (GBD 2016) estimated age-specific and sex-specific all-cause mortality between 1970 and 2016 for 195 countries and territories and at the subnational level for the five countries with a population greater than 200 million in 2016. METHODS: We have evaluated how well civil registration systems captured deaths using a set of demographic methods called death distribution methods for adults and from consideration of survey and census data for children younger than 5 years. We generated an overall assessment of completeness of registration of deaths by dividing registered deaths in each location-year by our estimate of all-age deaths generated from our overall estimation process. For 163 locations, including subnational units in countries with a population greater than 200 million with complete vital registration (VR) systems, our estimates were largely driven by the observed data, with corrections for small fluctuations in numbers and estimation for recent years where there were lags in data reporting (lags were variable by location, generally between 1 year and 6 years). For other locations, we took advantage of different data sources available to measure under-5 mortality rates (U5MR) using complete birth histories, summary birth histories, and incomplete VR with adjustments; we measured adult mortality rate (the probability of death in individuals aged 15-60 years) using adjusted incomplete VR, sibling histories, and household death recall. We used the U5MR and adult mortality rate, together with crude death rate due to HIV in the GBD model life table system, to estimate age-specific and sex-specific death rates for each location-year. Using various international databases, we identified fatal discontinuities, which we defined as increases in the death rate of more than one death per million, resulting from conflict and terrorism, natural disasters, major transport or technological accidents, and a subset of epidemic infectious diseases; these were added to estimates in the relevant years. In 47 countries with an identified peak adult prevalence for HIV/AIDS of more than 0·5% and where VR systems were less than 65% complete, we informed our estimates of age-sex-specific mortality using the Estimation and Projection Package (EPP)-Spectrum model fitted to national HIV/AIDS prevalence surveys and antenatal clinic serosurveillance systems. We estimated stillbirths, early neonatal, late neonatal, and childhood mortality using both survey and VR data in spatiotemporal Gaussian process regression models. We estimated abridged life tables for all location-years using age-specific death rates. We grouped locations into development quintiles based on the Socio-demographic Index (SDI) and analysed mortality trends by quintile. Using spline regression, we estimated the expected mortality rate for each age-sex group as a function of SDI. We identified countries with higher life expectancy than expected by comparing observed life expectancy to anticipated life expectancy on the basis of development status alone. FINDINGS: Completeness in the registration of deaths increased from 28% in 1970 to a peak of 45% in 2013; completeness was lower after 2013 because of lags in reporting. Total deaths in children younger than 5 years decreased from 1970 to 2016, and slower decreases occurred at ages 5-24 years. By contrast, numbers of adult deaths increased in each 5-year age bracket above the age of 25 years. The distribution of annualised rates of change in age-specific mortality rate differed over the period 2000 to 2016 compared with earlier decades: increasing annualised rates of change were less frequent, although rising annualised rates of change still occurred in some locations, particularly for adolescent and younger adult age groups. Rates of stillbirths and under-5 mortality both decreased globally from 1970. Evidence for global convergence of death rates was mixed; although the absolute difference between age-standardised death rates narrowed between countries at the lowest and highest levels of SDI, the ratio of these death rates-a measure of relative inequality-increased slightly. There was a strong shift between 1970 and 2016 toward higher life expectancy, most noticeably at higher levels of SDI. Among countries with populations greater than 1 million in 2016, life expectancy at birth was highest for women in Japan, at 86·9 years (95% UI 86·7-87·2), and for men in Singapore, at 81·3 years (78·8-83·7) in 2016. Male life expectancy was generally lower than female life expectancy between 1970 and 2016, an

Polygenic transcriptome risk scores for COPD and lung function improve cross-ethnic portability of prediction in the NHLBI TOPMed program

While polygenic risk scores (PRSs) enable early identification of genetic risk for chronic obstructive pulmonary disease (COPD), predictive performance is limited when the discovery and target populations are not well matched. Hypothesizing that the biological mechanisms of disease are shared across ancestry groups, we introduce a PrediXcan-derived polygenic transcriptome risk score (PTRS) to improve cross-ethnic portability of risk prediction. We constructed the PTRS using summary statistics from application of PrediXcan on large-scale GWASs of lung function (forced expiratory volume in 1 s [FEV1] and its ratio to forced vital capacity [FEV1/FVC]) in the UK Biobank. We examined prediction performance and cross-ethnic portability of PTRS through smoking-stratified analyses both on 29,381 multi-ethnic participants from TOPMed population/family-based cohorts and on 11,771 multi-ethnic participants from TOPMed COPD-enriched studies. Analyses were carried out for two dichotomous COPD traits (moderate-to-severe and severe COPD) and two quantitative lung function traits (FEV1 and FEV1/FVC). While the proposed PTRS showed weaker associations with disease than PRS for European ancestry, the PTRS showed stronger association with COPD than PRS for African Americans (e.g., odds ratio [OR] = 1.24 [95% confidence interval [CI]: 1.08–1.43] for PTRS versus 1.10 [0.96–1.26] for PRS among heavy smokers with ≥ 40 pack-years of smoking) for moderate-to-severe COPD. Cross-ethnic portability of the PTRS was significantly higher than the PRS (paired t test p < 2.2 × 10−16 with portability gains ranging from 5% to 28%) for both dichotomous COPD traits and across all smoking strata. Our study demonstrates the value of PTRS for improved cross-ethnic portability compared to PRS in predicting COPD risk

Multiethnic Meta-Analysis Identifies RAI1 as a Possible Obstructive Sleep Apnea-related Quantitative Trait Locus in Men.

Obstructive sleep apnea (OSA) is a common heritable disorder displaying marked sexual dimorphism in disease prevalence and progression. Previous genetic association studies have identified a few genetic loci associated with OSA and related quantitative traits, but they have only focused on single ethnic groups, and a large proportion of the heritability remains unexplained. The apnea-hypopnea index (AHI) is a commonly used quantitative measure characterizing OSA severity. Because OSA differs by sex, and the pathophysiology of obstructive events differ in rapid eye movement (REM) and non-REM (NREM) sleep, we hypothesized that additional genetic association signals would be identified by analyzing the NREM/REM-specific AHI and by conducting sex-specific analyses in multiethnic samples. We performed genome-wide association tests for up to 19,733 participants of African, Asian, European, and Hispanic/Latino American ancestry in 7 studies. We identified rs12936587 on chromosome 17 as a possible quantitative trait locus for NREM AHI in men (N = 6,737; P = 1.7 × 10 &lt;sup&gt;-8&lt;/sup&gt; ) but not in women (P = 0.77). The association with NREM AHI was replicated in a physiological research study (N = 67; P = 0.047). This locus overlapping the RAI1 gene and encompassing genes PEMT1, SREBF1, and RASD1 was previously reported to be associated with coronary artery disease, lipid metabolism, and implicated in Potocki-Lupski syndrome and Smith-Magenis syndrome, which are characterized by abnormal sleep phenotypes. We also identified gene-by-sex interactions in suggestive association regions, suggesting that genetic variants for AHI appear to vary by sex, consistent with the clinical observations of strong sexual dimorphism

Whole-genome sequencing in diverse subjects identifies genetic correlates of leukocyte traits: The NHLBI TOPMed program

Many common and rare variants associated with hematologic traits have been discovered through imputation on large-scale reference panels. However, the majority of genome-wide association studies (GWASs) have been conducted in Europeans, and determining causal variants has proved challenging. We performed a GWAS of total leukocyte, neutrophil, lymphocyte, monocyte, eosinophil, and basophil counts generated from 109,563,748 variants in the autosomes and the X chromosome in the Trans-Omics for Precision Medicine (TOPMed) program, which included data from 61,802 individuals of diverse ancestry. We discovered and replicated 7 leukocyte trait associations, including (1) the association between a chromosome X, pseudo-autosomal region (PAR), noncoding variant located between cytokine receptor genes (CSF2RA and CLRF2) and lower eosinophil count; and (2) associations between single variants found predominantly among African Americans at the S1PR3 (9q22.1) and HBB (11p15.4) loci and monocyte and lymphocyte counts, respectively. We further provide evidence indicating that the newly discovered eosinophil-lowering chromosome X PAR variant might be associated with reduced susceptibility to common allergic diseases such as atopic dermatitis and asthma. Additionally, we found a burden of very rare FLT3 (13q12.2) variants associated with monocyte counts. Together, these results emphasize the utility of whole-genome sequencing in diverse samples in identifying associations missed by European-ancestry-driven GWASs