Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution

Waist-hip ratio (WHR) is a measure of body fat distribution and a predictor of metabolic consequences independent of overall adiposity. WHR is heritable, but few genetic variants influencing this trait have been identified. We conducted a meta-analysis of 32 genome-wide association studies for WHR adjusted for body mass index (comprising up to 77,167 participants), following up 16 loci in an additional 29 studies (comprising up to 113,636 subjects). We identified 13 new loci in or near RSPO3, VEGFA, TBX15-WARS2, NFE2L3, GRB14, DNM3-PIGC, ITPR2-SSPN, LY86, HOXC13, ADAMTS9, ZNRF3-KREMEN1, NISCH-STAB1 and CPEB4 (P = 1.9 × 10−9 to P = 1.8 × 10−40) and the known signal at LYPLAL1. Seven of these loci exhibited marked sexual dimorphism, all with a stronger effect on WHR in women than men (P for sex difference = 1.9 × 10−3 to P = 1.2 × 10−13). These findings provide evidence for multiple loci that modulate body fat distribution independent of overall adiposity and reveal strong gene-by-sex interactions.

Quantitative Trait Loci for CD4:CD8 Lymphocyte Ratio Are Associated with Risk of Type 1 Diabetes and HIV-1 Immune Control

Abnormal expansion or depletion of particular lymphocyte subsets is associated with clinical manifestations such as HIV progression to AIDS and autoimmune disease. We sought to identify genetic predictors of lymphocyte levels and reasoned that these may play a role in immune-related diseases. We tested 2.3 million variants for association with five lymphocyte subsets, measured in 2538 individuals from the general population, including CD4+ T cells, CD8+ T cells, CD56+ natural killer (NK) cells, and the derived measure CD4:CD8 ratio. We identified two regions of strong association. The first was located in the major histocompatibility complex (MHC), with multiple SNPs strongly associated with CD4:CD8 ratio (rs2524054, p = 2.1 × 10−28). The second region was centered within a cluster of genes from the Schlafen family and was associated with NK cell levels (rs1838149, p = 6.1 × 10−14). The MHC association with CD4:CD8 replicated convincingly (p = 1.4 × 10−9) in an independent panel of 988 individuals. Conditional analyses indicate that there are two major independent quantitative trait loci (QTL) in the MHC region that regulate CD4:CD8 ratio: one is located in the class I cluster and influences CD8 levels, whereas the second is located in the class II cluster and regulates CD4 levels. Jointly, both QTL explained 8% of the variance in CD4:CD8 ratio. The class I variants are also strongly associated with durable host control of HIV, and class II variants are associated with type-1 diabetes, suggesting that genetic variation at the MHC may predispose one to immune-related diseases partly through disregulation of T cell homeostasis.

Rapid microsatellite marker development for African mahogany ( Khaya senegalensis, Meliaceae) using next-generation sequencing and assessment of its intra-specific genetic diversity.

Khaya senegalensis (African mahogany or dry-zone mahogany) is a high-value hardwood timber species with great potential for forest plantations in northern Australia. The species is distributed across the sub-Saharan belt from Senegal to Sudan and Uganda. Because of heavy exploitation and constraints on natural regeneration and sustainable planting, it is now classified as a vulnerable species. Here, we describe the development of microsatellite markers for K. senegalensis using next-generation sequencing to assess its intra-specific diversity across its natural range, which is a key for successful breeding programs and effective conservation management of the species. Next-generation sequencing yielded 93943 sequences with an average read length of 234bp. The assembled sequences contained 1030 simple sequence repeats, with primers designed for 522 microsatellite loci. Twenty-one microsatellite loci were tested with 11 showing reliable amplification and polymorphism in K. senegalensis. The 11 novel microsatellites, together with one previously published, were used to assess 73 accessions belonging to the Australian K. senegalensis domestication program, sampled from across the natural range of the species. STRUCTURE analysis shows two major clusters, one comprising mainly accessions from west Africa (Senegal to Benin) and the second based in the far eastern limits of the range in Sudan and Uganda. Higher levels of genetic diversity were found in material from western Africa. This suggests that new seed collections from this region may yield more diverse genotypes than those originating from Sudan and Uganda in eastern Africa.

The Application of Near Infrared Spectroscopy for the Assessment of Avocado Quality Attributes, Infrared Spectroscopy. Chapter 14

Quality and safety evaluation of agricultural products has become an increasingly important consideration in market/commercial viability and systems for such evaluations are now demanded by customers, including distributors and retailers. Unfortunately, most horticultural products struggle with delivering adequate and consistent quality to the consumer. Removing inconsistencies and providing what the consumer expects is a key factor for retaining and expanding both domestic and international markets. Most commercial quality classification systems for fruit and vegetables are based on external features of the product, for example: shape, colour, size, weight and blemishes. However, the external appearance of most fruit is generally not an accurate guide to the internal or eating quality of the fruit. Internal quality of fruit is currently subjectively judged on attributes such as volatiles, firmness, and appearance. Destructive subjective measures such as internal flesh colour, or objective measures such as extraction of juice to measure sweetness (oBrix) or assessment of dry matter (DM) content are also used, although obviously not for every fruit – just a sample to represent the whole consignment. For avocado fruit, external colour is not a maturity characteristic, and its smell is too weak and appears later in its maturity stage (Gaete-Garreton et al., 2005). Since maturity is a major component of avocado quality and palatability, it is important to harvest mature fruit, so as to ensure that fruit will ripen properly and have acceptable eating quality. Currently, commercial avocado maturity estimation is based on destructive assessment of the %DM, and sometimes percent oil, both of which are highly correlated with maturity (Clark et al., 2003; Mizrach & Flitsanov, 1999). Avocados Australia Limited (AAL (2008)) recommend a minimum maturity standard for its growers of 23 %DM (greater than 10% oil content) for the ‘Hass’ cultivar, although consumer studies indicate a preference for at least 25 %DM (Harker et al., 2007).

A neutron diffraction investigation of the structure of PBO-PBCL2 glasses

Neutron diffraction techniques have been employed to investigate the structure of PbO-PbCl2 glasses as a function of composition in the nominal range PbO.PbCl2 to 9PbO.PbCl2. It is concluded that, whereas the first Pb-O distance is well defined, the distribution of Pb-Cl distances is much broader, in agreement with a previous EXAFS study.

AQUAMAN: a web-based decision support system for irrigation scheduling in peanuts

Peanut (Arachis hypogaea L.) is an economically important legume crop in irrigated production areas of northern Australia. Although the potential pod yield of the crop in these areas is about 8 t ha(-1), most growers generally obtain around 5 t ha(-1), partly due to poor irrigation management. Better information and tools that are easy to use, accurate, and cost-effective are therefore needed to help local peanut growers improve irrigation management. This paper introduces a new web-based decision support system called AQUAMAN that was developed to assist Australian peanut growers schedule irrigations. It simulates the timing and depth of future irrigations by combining procedures from the food and agriculture organization (FAO) guidelines for irrigation scheduling (FAO-56) with those of the agricultural production systems simulator (APSIM) modeling framework. Here, we present a description of AQUAMAN and results of a series of activities (i.e., extension activities, case studies, and a survey) that were conducted to assess its level of acceptance among Australian peanut growers, obtain feedback for future improvements, and evaluate its performance. Application of the tool for scheduling irrigations of commercial peanut farms since its release in 2004-2005 has shown good acceptance by local peanuts growers and potential for significantly improving yield. Limited comparison with the farmer practice of matching the pan evaporation demand during rain-free periods in 2006-2007 and 2008-2009 suggested that AQUAMAN enabled irrigation water savings of up to 50% and the realization of enhanced water and irrigation use efficiencies.

Effects of seasonal variability on FT-NIR prediction of dry matter content for whole Hass avocado fruit

Fourier Transform (FT)-near infra-red spectroscopy (NIRS) was investigated as a non-invasive technique for estimating percentage (%) dry matter of whole intact 'Hass' avocado fruit. Partial least squares (PLS) calibration models were developed from the diffuse reflectance spectra to predict % dry matter, taking into account effects of seasonal variation. It is found that seasonal variability has a significant effect on model predictive performance for dry matter in avocados. The robustness of the calibration model, which in general limits the application for the technique, was found to increase across years (seasons) when more seasonal variability was included in the calibration set. The R-v(2) and RMSEP for the single season prediction models predicting on an independent season ranged from 0.09 to 0.61 and 2.63 to 5.00, respectively, while for the two season models predicting on the third independent season, they ranged from 0.34 to 0.79 and 2.18 to 2.50, respectively. The bias for single season models predicting an independent season was as high as 4.429 but <= 1.417 for the two season combined models. The calibration model encompassing fruit from three consecutive years yielded predictive statistics of R-v(2) = 0.89, RMSEP = 1.43% dry matter with a bias of -0.021 in the range 16.1-39.7% dry matter for the validation population encompassing independent fruit from the three consecutive years. Relevant spectral information for all calibration models was obtained primarily from oil, carbohydrate and water absorbance bands clustered in the 890-980, 1005-1050, 1330-1380 and 1700-1790 nm regions. These results indicate the potential of FT-NIRS, in diffuse reflectance mode, to non-invasively predict the % dry matter of whole 'Hass' avocado fruit and the importance of the development of a calibration model that incorporates seasonal variation. Crown Copyright (c) 2012 Published by Elsevier B.V. All rights reserved.

Relatedness communicated in lemur scent

Lemurs are the most olfactory-oriented of primates, yet there is still only a basic level of understanding of what their scent marks communicate. We analyzed scent secretions from Milne-Edwards' sifakas (Propithecus edwardsi) collected in their natural habitat of Ranomafana National Park, Madagascar. We sought to test whether the scent mark could signal genetic relatedness in addition to species, sex, season, and individuality. We not only found correlations (r (2) = 0.38, P = 0.017) between the total olfactory fingerprint and genetic relatedness but also between relatedness and specific components of the odor, despite the complex environmental signals from differences in diet and behavior in a natural setting. To the best of our knowledge, this is the first demonstration of an association between genetic relatedness and chemical communication in a wild primate population. Furthermore, we found a variety of compounds that were specific to each sex and each sampling period. This research shows that scent marks could act as a remote signal to avoid inbreeding, optimize mating opportunities, and potentially aid kin selection.

Prediction of breeding values for average fruit weight in mango using a multivariate individual mixed model

Mango is an important horticultural fruit crop and breeding is a key strategy to improve ongoing sustainability. Knowledge of breeding values of potential parents is important for maximising progress from breeding. This study successfully employed a mixed linear model methods incorporating a pedigree to predict breeding values for average fruit weight from highly unbalanced data for genotypes planted over three field trials and assessed over several harvest seasons. Average fruit weight was found to be under strong additive genetic control. There was high correlation between hybrids propagated as seedlings and hybrids propagated as scions grafted onto rootstocks. Estimates of additive genetic correlation among trials ranged from 0.69 to 0.88 with correlations among harvest seasons within trials greater than 0.96. These results suggest that progress from selection for broad adaptation can be achieved, particularly as no repeatable environmental factor that could be used to predict G x E could be identified. Predicted breeding values for 35 known cultivars are presented for use in ongoing breeding programs.

Estimating Resource Requirements to Staff a Response to a Medium to Large Outbreak of Foot and Mouth Disease in Australia

A recent report to the Australian Government identified concerns relating to Australia's capacity to respond to a medium to large outbreak of FMD. To assess the resources required, the AusSpread disease simulation model was used to develop a plausible outbreak scenario that included 62 infected premises in five different states at the time of detection, 28 days after the disease entered the first property in Victoria. Movements of infected animals and/or contaminated product/equipment led to smaller outbreaks in NSW, Queensland, South Australia and Tasmania. With unlimited staff resources, the outbreak was eradicated in 63 days with 54 infected premises and a 98% chance of eradication within 3 months. This unconstrained response was estimated to involve 2724 personnel. Unlimited personnel was considered unrealistic, and therefore, the course of the outbreak was modelled using three levels of staffing and the probability of achieving eradication within 3 or 6 months of introduction determined. Under the baseline staffing level, there was only a 16% probability that the outbreak would be eradicated within 3 months, and a 60% probability of eradication in 6 months. Deployment of an additional 60 personnel in the first 3 weeks of the response increased the likelihood of eradication in 3 months to 68%, and 100% in 6 months. Deployment of further personnel incrementally increased the likelihood of timely eradication and decreased the duration and size of the outbreak. Targeted use of vaccination in high-risk areas coupled with the baseline personnel resources increased the probability of eradication in 3 months to 74% and to 100% in 6 months. This required 25 vaccination teams commencing 12 days into the control program increasing to 50 vaccination teams 3 weeks later. Deploying an equal number of additional personnel to surveillance and infected premises operations was equally effective in reducing the outbreak size and duration.

How weed control and fertilisation influence tree physiological processes and growth at early establishment in an exotic F1 hybrid pine plantation of subtropical Australia

Purpose This study investigated how nitrogen (N) nutrition and key physiological processes varied under changed water and nitrogen competition resulting from different weed control and fertilisation treatments in a 2-year-old F1 hybrid (Pinus elliottii Engelm var. elliottii × P. caribaea var. hondurensis Barr. ex Golf.) plantation on a grey podzolic soil type, in Southeast Queensland. Materials and methods The study integrated a range of measures including growth variables (diameter at ground level (DGL), diameter at breast height (DBH) and height (H)), foliar variables (including foliar N concentration, foliar δ13C and δ15N) and physiological variables (including photosynthesis (An), stomatal conductance (gs), transpiration (E), intrinsic water use efficiency (WUEi) (A/gs) and xylem pressure potential (ΨXPP)) to better understand the mechanisms influencing growth under different weed control and fertilisation treatments. Five levels of weed control were applied: standard (routine), luxury, intermediate, mechanical and nil weed control, all with routine fertilisation plus an additional treatment, routine weed control and luxury fertilisation. Relative weed cover was assessed at 0.8, 1.1 and 1.6 years after plantation establishment to monitor the effectiveness of weed control treatments. Soil investigation included soil ammonium (NH4 +-N), nitrate (NO3 −-N), potentially mineralizable N (PMN), gravimetric soil moisture content (MC), hot water extractable organic carbon (HWETC), hot water extractable total N (HWETN), total C, total N, stable C isotope composition (δ13C), stable N isotope composition (δ15N), total P and extractable K. Results and discussion There were significant relationships between foliar N concentrations and relative weed cover and between tree growth and foliar N concentration or foliar δ15N, but initial site preparation practices also increased soil N transformations in the planting rows reducing the observable effects of weed control on foliar δ15N. A positive relationship between foliar N concentration and foliar δ13C or photosynthesis indicated that increased N availability to trees positively influenced non-stomatal limitations to photosynthesis. However, trees with increased foliar N concentrations and photosynthesis were negatively related to xylem pressure potential in the afternoons which enhanced stomatal limitations to photosynthesis and WUEi. Conclusions Luxury and intermediate weed control and luxury fertilisation positively influenced growth at early establishment by reducing the competition for water and N resources. This influenced fundamental key physiological processes such as the relationships between foliar N concentration, A n, E, gs and ΨXPP. Results also confirmed that time from cultivation is an important factor influencing the effectiveness of using foliar δ15N as an indicator of soil N transformations.

Hendra Virus and Horse Owners – Risk Perception and Management

Hendra virus is a highly pathogenic novel paramyxovirus causing sporadic fatal infection in horses and humans in Australia. Species of fruit-bats (genus Pteropus), commonly known as flying-foxes, are the natural host of the virus. We undertook a survey of horse owners in the states of Queensland and New South Wales, Australia to assess the level of adoption of recommended risk management strategies and to identify impediments to adoption. Survey questionnaires were completed by 1431 respondents from the target states, and from a spectrum of industry sectors. Hendra virus knowledge varied with sector, but was generally limited, with only 13% of respondents rating their level of knowledge as high or very high. The majority of respondents (63%) had seen their state’s Hendra virus information for horse owners, and a similar proportion found the information useful. Fifty-six percent of respondents thought it moderately, very or extremely likely that a Hendra virus case could occur in their area, yet only 37% said they would consider Hendra virus if their horse was sick. Only 13% of respondents stabled their horses overnight, although another 24% said it would be easy or very easy to do so, but hadn’t done so. Only 13% and 15% of respondents respectively had horse feed bins and water points under solid cover. Responses varied significantly with state, likely reflecting different Hendra virus history. The survey identified inconsistent awareness and/or adoption of available knowledge, confusion in relation to Hendra virus risk perception, with both over-and under-estimation of true risk, and lag in the uptake of recommended risk minimisation strategies, even when these were readily implementable. However, we also identified frustration and potential alienation by horse owners who found the recommended strategies impractical, onerous and prohibitively expensive. The insights gained from this survey have broader application to other complex risk-management scenarios.

Relatedness communicated in lemur scent

Lemurs are the most olfactory-oriented of primates, yet there is still only a basic level of understanding of what their scent marks communicate. We analyzed scent secretions from Milne-Edwards' sifakas (Propithecus edwardsi) collected in their natural habitat of Ranomafana National Park, Madagascar. We sought to test whether the scent mark could signal genetic relatedness in addition to species, sex, season, and individuality. We not only found correlations (r 2 = 0.38, P = 0.017) between the total olfactory fingerprint and genetic relatedness but also between relatedness and specific components of the odor, despite the complex environmental signals from differences in diet and behavior in a natural setting. To the best of our knowledge, this is the first demonstration of an association between genetic relatedness and chemical communication in a wild primate population. Furthermore, we found a variety of compounds that were specific to each sex and each sampling period. This research shows that scent marks could act as a remote signal to avoid inbreeding, optimize mating opportunities, and potentially aid kin selection. © 2013 Springer-Verlag Berlin Heidelberg.