A5003354367- Genetic and phenotypic traits in livestock
- Genomics and Phylogenetic Studies
- Genetic Mapping and Diversity in Plants and Animals
- Cancer-related molecular mechanisms research
- Sugarcane Cultivation and Processing
- Genetics and Plant Breeding
- Molecular Biology Techniques and Applications
- Vector-borne infectious diseases
- Gut microbiota and health
- Ruminant Nutrition and Digestive Physiology
- Animal Virus Infections Studies
- Chromosomal and Genetic Variations
- Reproductive Physiology in Livestock
- Animal Genetics and Reproduction
- Natural Products and Biological Research
- Respiratory viral infections research
- Microbial Community Ecology and Physiology
- Microbial infections and disease research
- Environmental DNA in Biodiversity Studies
- Livestock Farming and Management
- melanin and skin pigmentation
- Effects of Environmental Stressors on Livestock
- COVID-19 epidemiological studies
- Pneumonia and Respiratory Infections
- Genomics and Rare Diseases
Agriculture and Food
2019-2024
The University of Queensland
1963-2024
ARC Centre of Excellence for Plant Success in Nature and Agriculture
2021-2024
Boston Children's Hospital
2020
Harvard University
2020
Creative Commons
2020
Agriculture Victoria
2020
The University of Melbourne
2015-2020
La Trobe University
2013-2019
Centre for Environment, Fisheries and Aquaculture Science
2017
Mammals have a large cohort of endo- and ecto- symbiotic microorganisms (the microbiome) that potentially influence host phenotypes. There been numerous exploratory studies these organisms in humans other animals, often with the aim relating microbiome to complex phenotype such as body mass index (BMI) or disease state. Here, we describe an efficient methodology for predicting traits from quantitative profiles. The method was demonstrated by inflammatory bowel (IBD) status BMI human data,...
Sugarcane is a major industrial crop cultivated in tropical and subtropical regions of the world. It primary source sugar worldwide, accounting for more than 70% world consumption. Additionally, sugarcane emerging as sustainable bioenergy. However, increase productivity from has been small compared to other crops, rate genetic gains current breeding programs tends be plateauing. In this review, some main contributors relatively slow rates gain are discussed, including (i) cycle length (ii)...
Variation of microorganism communities in the rumen cattle (Bos taurus) is great interest because possible links to economically or environmentally important traits, such as feed conversion efficiency methane emission levels. The resolution studies investigating this variation may be improved by utilizing untargeted massively parallel sequencing (MPS), that is, without targeted amplification genes. objective study was develop a method which used MPS generate "rumen metagenome profiles", and...
Abstract Background Nellore cattle ( Bos indicus ) are well-known for their adaptation to warm and humid environments. Hair length coat color may impact heat tolerance. The breed has been strongly selected white coat, but bulls generally exhibit darker hair ranging from light grey black on the head, neck, hump, knees. Given potential contribution of variation populations tropical sub-tropical environments, our aim was map positional functional candidate genetic variants associated with...
Non-additive genetic effects seem to play a substantial role in the expression of complex traits sugarcane. Including non-additive genomic prediction models significantly improves accuracy clonal performance. In recent decade, progress has been slow One reason might be that contribute substantially traits. Dense marker information provides opportunity exploit prediction. this study, series best linear unbiased (GBLUP) account for additive and were assessed improve The reproducible kernel...
The bovine rumen hosts a diverse and complex community of Eukarya, Bacteria, Archea viruses (including bacteriophage). viral population (the virome) has received little attention compared to the microbial microbiome). We used massively parallel sequencing virus like particles investigate diversity virome in thirteen lactating Australian Holstein dairy cattle all housed same location, 12 which were sampled on day. Fourteen putative sequence fragments over 30 Kbp length assembled annotated....
Introduction Respiratory disease is a major cause of morbidity and mortality in the developing world, but prospective studies temporal patterns risk factors are rare. Methods We studied people rural Western Uganda, where respiratory pervasive. followed 30 adults (ages 22–51 years; 534 observations) 234 children 3–11 1,513 between May 2019 July 2022 collected monthly data on their symptoms, for total 2,047 case records. examined associations demographic symptoms severity. Results The timing...
In tropically-adapted beef heifers, application of genomic prediction for age at puberty has been limited due to low accuracies. Our aim was investigate novel methods pre-selecting whole-genome sequence (WGS) variants and alternative analysis methodologies; including best linear unbiased (GBLUP) with multiple relationship matrices (MGRM) Bayesian (BayesR) analyses, determine if accuracy can be improved.Genotypes phenotypes were obtained from two research herds. total, 868 Brahman 960...
Abstract Background It has been challenging to implement genomic selection in multi-breed tropical beef cattle populations. If commercial (often crossbred) animals could be used the reference population for these evaluations, this allow very large In systems, such often have no pedigree information. Here we investigate potential models data, using marker heterozygosity (to model heterosis) and breed composition derived from genetic markers, as covariates model. Models treated effects either...
Sugarcane smut and Pachymetra root rots are two serious diseases of sugarcane, with susceptible infected crops losing over 30% yield. A heritable component to both has been demonstrated, suggesting selection could improve disease resistance. Genomic accelerate gains even further, enabling early resistant seedlings for breeding clonal propagation. In this study we evaluated four types algorithms genomic predictions performance These were: best linear unbiased prediction (GBLUP), including...
Background: Alendronate sodium and raloxifene hydrochloride were recently approved for the prevention of postmenopausal osteoporosis, but data on their clinical efficacy are limited.We compared these drugs with hormone replacement therapy (HRT) to help women physicians guide treatment decisions.Objective: To understand how they can best choose most beneficial after menopause based individual risk profile. Methods:We developed a decision analytic Markov model compare effects alendronate...
Extensively grazed cattle are often mustered only once a year. Therefore, birthdates typically unknown or inaccurate. Birthdates would be useful for deriving important traits (growth rate; calving interval), breed registrations, and making management decisions. Epigenetic clocks use methylation of DNA to predict an individual’s age. An epigenetic clock could provide solution the challenges industry birthdate recording. Here we derived first tropically adapted using portable sequencing...
Abstract Animal metagenomic studies, in which host-associated microbiomes are profiled, an increasingly important contribution to our understanding of the physiological functions, health and susceptibility diseases livestock. One major challenges these studies is host DNA contamination, limits sequencing capacity for content reduces accuracy profiling. This first study comparing effectiveness different methods profiling bovine vaginal samples. We compared new method Oxford Nanopore...
Abstract Reverse zoonotic respiratory diseases threaten great apes across Sub-Saharan Africa. Studies of wild chimpanzees have identified the causative agents most disease outbreaks as “common cold” paediatric human pathogens, but reverse transmission pathways remained unclear. Between May 2019 and August 2021, we conducted a prospective cohort study 234 children aged 3–11 years in communities bordering Kibale National Park, Uganda, 30 adults who were forest workers regularly entered park....
Most genetic variants associated with fertility in mammals fall non-coding regions of the genome and it is unclear how these affect fertility. Here we use genome-wide association summary statistics for Heifer puberty (pubertal or not at 600 days) from 27,707 Bos indicus, taurus crossbred cattle; multi-trait GWAS signals 2119 indicine cattle four traits, including days to calving, age first pregnancy status, foetus weeks (assessed by rectal palpation foetus); expression quantitative trait...
Abstract Motivation Trimming and filtering tools are useful in DNA sequencing analysis because they increase the accuracy of sequence alignments thus reliability results. Oxford nanopore technologies (ONT) trimming currently rudimentary, generally only reads based on whole read average quality. This results discarding that contain regions high-quality sequence. Here, we propose Prowler, a trimmer uses window-based approach inspired by algorithms used to trim short data. Importantly, retain...
Food insecurity is highly prevalent in the United States. Even best of times, some 10% U.S. population self-reports food annual census instrument, and 23.3 million Americans use community-based emergency system. Unemployed or underemployed individuals, elderly, single parents, substance abusers, uninsured underinsured individuals with medical illnesses are at increased risk for insecurity. This article discusses clinical approaches to food-insecure individuals. Measurement tools developed...