101 results match your criteria: "Centre for AgriBiosciences[Affiliation]"

Article Synopsis
  • Genotype imputation helps in obtaining sequence genotypes for analyses like genome-wide association studies (GWAS), but assessing imputation accuracy is crucial to avoid false positives.
  • The study compared three imputation programs—Beagle 5.2, Minimac4, and IMPUTE5—and found that high-density genotypes yield better accuracy than low-density, with notable differences in how each software estimates imputation performance.
  • The findings highlight the need for customized Rsq thresholds when filtering data and indicate that INDEL variants tend to have lower accuracy than SNPs; also, the accuracy of X chromosome imputation varies significantly between different regions.
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Bioinformatic pipelines are becoming increasingly complex with the ever-accumulating amount of Next-generation sequencing (NGS) data. Their orchestration is difficult with a simple Bash script, but bioinformatics workflow managers such as Nextflow provide a framework to overcome respective problems. This study used Nextflow to develop a bioinformatic pipeline for detecting expression quantitative trait loci (eQTL) using a DSL2 Nextflow modular syntax, to enable sharing the huge demand for computing power as well as data access limitation across different partners often associated with eQTL studies.

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The nitidulid beetle Carpophilus truncatus is rapidly becoming a major pest of nut crops around the world. This insect first infested Australian almonds in 2013 and has since escalated to be the preeminent insect pest for the industry. Data pertaining to C.

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Background: Mastitis is a disease that incurs significant costs in the dairy industry. A promising approach to mitigate its negative effects is to genetically improve the resistance of dairy cattle to mastitis. A meta-analysis of genome-wide association studies (GWAS) across multiple breeds for clinical mastitis (CM) and its indicator trait, somatic cell score (SCS), is a powerful method to identify functional genetic variants that impact mastitis resistance.

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Most genetic variants associated with fertility in mammals fall in non-coding regions of the genome and it is unclear how these variants affect fertility. Here we use genome-wide association summary statistics for Heifer puberty (pubertal or not at 600 days) from 27,707 Bos indicus, Bos taurus and crossbred cattle; multi-trait GWAS signals from 2119 indicine cattle for four fertility traits, including days to calving, age at first calving, pregnancy status, and foetus age in weeks (assessed by rectal palpation of the foetus); and expression quantitative trait locus for whole blood from 489 indicine cattle, to identify 87 putatively functional genes affecting cattle fertility. Our analysis reveals a significant overlap between the set of cattle and previously reported human fertility-related genes, impling the existence of a shared pool of genes that regulate fertility in mammals.

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The integration of genomic prediction with crop growth models enabled the estimation of missing environmental variables which improved the prediction accuracy of grain yield. Since the invention of whole-genome prediction (WGP) more than two decades ago, breeding programmes have established extensive reference populations that are cultivated under diverse environmental conditions. The introduction of the CGM-WGP model, which integrates crop growth models (CGM) with WGP, has expanded the applications of WGP to the prediction of unphenotyped traits in untested environments, including future climates.

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A common regulatory haplotype doubles lactoferrin concentration in milk.

Genet Sel Evol

March 2024

Research & Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand.

Background: Bovine lactoferrin (Lf) is an iron absorbing whey protein with antibacterial, antiviral, and antifungal activity. Lactoferrin is economically valuable and has an extremely variable concentration in milk, partly driven by environmental influences such as milking frequency, involution, or mastitis. A significant genetic influence has also been previously observed to regulate lactoferrin content in milk.

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To comprehensively evaluate the impact of agricultural management practices on soil productivity, it is imperative to conduct a thorough analysis of soil bacterial ecology. Deep-banding nutrient-rich amendments is a soil management practice that aims to improve plant growth and soil structure by addressing the plant-growth constraints posed by dense-clay subsoils. However, the response of bacterial communities to deep-banded amendments has not been thoroughly studied.

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Queensland fruit fly, Bactrocera tryoni, Froggatt (Diptera: Tephritidae) is Australia's primary fruit fly pest species. Integrated Pest Management (IPM) has been adopted to sustainably manage this polyphagous species with a reduced reliance on chemical pesticides. At present, control measures are aimed at the adult stages of the fly, with no IPM tools available to target larvae once they exit the fruit and pupate in the soil.

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A compendium of genetic regulatory effects across pig tissues.

Nat Genet

January 2024

Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.

Article Synopsis
  • The FarmGTEx project aims to create a public database of genetic variants in livestock to connect genetic differences with physical traits, benefiting both animal breeding and human health research.
  • The pilot phase, PigGTEx, involved analyzing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples from pigs, leading to the development of a genotype imputation panel and associations between millions of genetic variants and transcriptomic traits across 34 different tissues.
  • The study highlights the tissue-specific regulatory effects of these variants, revealing molecular mechanisms affecting 207 complex pig traits while also demonstrating the relevance of pigs as models for understanding human gene expression and genetic regulation.
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Article Synopsis
  • Many QTLs are found in non-coding regions and are believed to influence gene regulation, impacting gene expression and RNA splicing.
  • A study examined the contributions of eVariants (which affect gene expression) and sVariants (which influence RNA splicing) from 16 tissues in ~120,000 cattle, showing they explain 69.2% of heritability for various traits.
  • The research highlights that these regulatory variants substantially affect phenotypes, with eVariants and sVariants particularly explaining 24% of heritability, which is notably higher than expected from random variants.
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Root systems of most land plants are colonised by arbuscular mycorrhiza fungi. The symbiosis supports nutrient acquisition strategies predominantly associated with plant access to inorganic phosphate. The nutrient acquisition is enhanced through an extensive network of external fungal hyphae that extends out into the soil, together with the development of fungal structures forming specialised interfaces with root cortical cells.

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Allele specific expression (ASE) is widespread in many species including cows. Therefore, regulatory regions which control gene expression should show cis-regulatory variation which mirrors this differential expression within the animal. ChIP-seq peaks for histone modifications and transcription factors measure activity at functional regions and the height of some peaks have been shown to correlate across tissues with the expression of particular genes, suggesting these peaks are putative regulatory regions.

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Article Synopsis
  • A novel potexvirus called "Adenium obesum virus X" (AobVX) was discovered in Adenium obesum plants imported into Australia from China and analyzed at quarantine facilities.
  • The virus has a complete genome of 6781 nucleotides and likely encodes several essential potexvirus proteins across five open reading frames.
  • AobVX's RNA-dependent RNA polymerase shows significant similarity to related viruses, marking the first documented case of a positive-sense single-stranded RNA virus linked to the Potexvirus genus in this plant species.
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MYB-bHLH-TTG1 in a Multi-tiered Pathway Regulates Arabidopsis Seed Coat Mucilage Biosynthesis Genes Including PECTIN METHYLESTERASE INHIBITOR14 Required for Homogalacturonan Demethylesterification.

Plant Cell Physiol

August 2023

Department of Animal, Plant and Soil Sciences, AgriBio, Centre for AgriBiosciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Melbourne, Victoria 3086, Australia.

MYB-bHLH-TTG1 (MBW) transcription factor (TF) complexes regulate Arabidopsis seed coat biosynthesis pathways via a multi-tiered regulatory mechanism. The MYB genes include MYB5, MYB23 and TRANSPARENT TESTA2 (TT2), which regulate GLABRA2 (GL2), HOMEODOMAIN GLABROUS2 (HDG2) and TRANSPARENT TESTA GLABRA2 (TTG2). Here, we examine the role of PECTIN METHYLESTERASE INHIBITOR14 (PMEI14) in seed coat mucilage pectin methylesterification and provide evidence in support of multi-tiered regulation of seed coat mucilage biosynthesis genes including PMEI14.

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Running crop growth models (CGM) coupled with whole genome prediction (WGP) as a CGM-WGP model introduces environmental information to WGP and genomic relatedness information to the genotype-specific parameters modelled through CGMs. Previous studies have primarily used CGM-WGP to infer prediction accuracy without exploring its potential to enhance CGM and WGP. Here, we implemented a heading and maturity date wheat phenology model within a CGM-WGP framework and compared it with CGM and WGP.

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Scab, caused by the biotrophic fungal pathogen Venturia inaequalis, is the most economically important disease of apples. During infection, colonizes the subcuticular host environment, where it develops specialized infection structures called runner hyphae and stromata. These structures are thought to be involved in nutrient acquisition and effector (virulence factor) delivery, but also give rise to conidia that further the infection cycle.

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Spatial and temporal variability in benthic flux denitrification efficiency occurs across Port Phillip Bay, Australia. Here, we assess the capacity for untargeted metatranscriptomics to resolve spatiotemporal differences in the microbial contribution to benthic nitrogen cycling. The most abundant sediment transcripts assembled were associated with the archaeal nitrifier Nitrosopumilus.

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Urban population structure and dispersal of an Australian mosquito (Aedes notoscriptus) involved in disease transmission.

Heredity (Edinb)

February 2023

Pest and Environmental Adaptation Research Group, School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia.

Dispersal is a critical parameter for successful pest control measures as it determines the rate of movement across target control areas and influences the risk of human exposure. We used a fine-scale spatial population genomic approach to investigate the dispersal ecology and population structure of Aedes notoscriptus, an important disease transmitting mosquito at the Mornington Peninsula, Australia. We sampled and reared Ae.

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The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi.

BMC Biol

November 2022

Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand.

Background: Scab, caused by the biotrophic fungus Venturia inaequalis, is the most economically important disease of apples worldwide. During infection, V. inaequalis occupies the subcuticular environment, where it secretes virulence factors, termed effectors, to promote host colonization.

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Crop growth models (CGM) can predict the performance of a cultivar in untested environments by sampling genotype-specific parameters. As they cannot predict the performance of new cultivars, it has been proposed to integrate CGMs with whole genome prediction (WGP) to combine the benefits of both models. Here, we used a CGM-WGP model to predict the performance of new wheat (Triticum aestivum) genotypes.

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Temporal profiling resolves the drivers of microbial nitrogen cycling variability in coastal sediments.

Sci Total Environ

January 2023

La Trobe University, AgriBio Centre for AgriBiosciences, 5 Ring Road Bundoora, Australia; Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, 5 Ring Road Bundoora, Australia.

Here we describe the potential for sediment microbial nitrogen-cycling gene (DNA) and activity (RNA) abundances to spatially resolve coastal areas impacted by seasonal variability in external nutrient inputs. Three sites were chosen within a nitrogen-limited embayment, Port Phillip Bay (PPB), Australia that reflect variability in both proximity to external nutrient inputs and the dominant form of available nitrogen. At three sediment depths (0-1; 1-5; 5-10 cm) across a 2 year study key genes involved in nitrification (archaeal amoA and bacterial β-amoA), nitrite reduction (clade I nirS and cluster I nirK, archaeal nirK-a), anaerobic oxidation of ammonium (anammox 16S rRNA phylogenetic marker) and nitrogen fixation (nifH) were quantified.

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Article Synopsis
  • Cases of Buruli ulcer, linked to Mycobacterium ulcerans, have notably increased in Victoria, Australia, prompting research into environmental transmission.
  • Analysis of samples from properties with Buruli ulcer cases revealed links to specific environmental features, including certain native plants, soil alkalinity, and common ringtail possums.
  • While ringtail possums may be key hosts for the bacteria, differences in environmental risk factors between positive properties and actual cases suggest that human behavior and other factors also play a role in how the disease spreads.
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A multi-tissue atlas of regulatory variants in cattle.

Nat Genet

September 2022

Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA.

Article Synopsis
  • * The authors present the Cattle Genotype-Tissue Expression atlas (CattleGTEx), which utilizes data from over 7,000 RNA-sequencing samples to explore gene expression in more than 100 tissues.
  • * They analyze the genetic associations related to gene expression and alternative splicing, linking these findings to 43 important traits in cattle to understand the molecular mechanisms involved in livestock genetics.
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Heat tolerance is the ability of an animal to maintain production and reproduction levels under hot and humid conditions and is now a trait of economic relevance in dairy systems worldwide because of an escalating warming climate. The Australian dairy population is one of the excellent study models for enhancing our understanding of the biology of heat tolerance because they are predominantly kept outdoors on pastures where they experience direct effects of weather elements (e.g.

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