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AusFarm modelling tool built using the Common Modelling Protocol.
One CSIRO Rural Decision Support - Software development - Published 08 Oct 2019
Long-term modelling scenarios under historical (1970-2017) and future climate (2018-2050) using UNSATCHEM module in HYDRUS-1D to assess the longevity of irrigation, using a range of available water re... more sources, in four main soil groups.
File extensions: .in = input file, .out = output file, .dat and .h1d are system files that can't be opened.less
Sustainable Expansion of Recycled Water-Irrigated Agriculture/Horticulture in North Adelaide Plains - HYDRUS modelling - Published 16 Sep 2019
X chromosome variants were associated to heritable fertility traits, in two bovine populations.
Fortes, Porto-Neto et al. 2019.
Background: Targeting phenotypes related to bull fertility, such as spe... more rm morphology and sperm DNA fragmentation can help identify mutations that limit reproduction capacity. Twenty-five fertility-related phenotypes were measured as indicators of bull fertility (1,099 Brahman bulls and 1,719 Tropical Composite bulls). Measurements included standard bull breeding soundness measures (e.g. sperm motility), scrotal circumference, sperm DNA fragmentation and sperm protamine deficiency. These phenotypes were used in a genome-wide association studies that aimed to detect quantitative trait loci (QTL).
Results: Genomic analyses confirmed some QTL in both breeds (Brahman and Tropical Composites) while others were breed specific. For example, only in Brahman cattle, we identified polymorphisms associated (P < 10-16) with sperm midpiece morphological abnormalities. The QTL identified and mutations occurring only in Bos indicus suggest that the gene A-kinase anchoring protein (AKAP)14 might be related to midpiece abnormalities in Brahman. Associated mutations described herein corroborate with known genes affecting spermatogenesis, including those in the AKAP and testis-expressed gene (TEX) families. Polymorphism associations suggest that AKAP14 and TEX11 are positional and functional candidate genes in chromosome X affecting bull fertility. Most significant variants and QTLs mapped to chromosome X. These results add evidence to a mammalian specialization of X that evolved to harbor genes linked to spermatogenesis, as similarly observed in mice and humans. Some variants in X may affect more than one genetically correlated trait (r2 ~ 0.33–0.51), such as sperm morphology and sperm DNA fragmentation. Correlations and shared QTL support the hypothesis that these phenotypes have the same underlying cause: faulty spermatogenesis. In addition, heritabilities for sperm DNA fragmentation and sperm protamine deficiency were moderate (h2 ~ 0.21–0.47), being the first reported estimates.
Conclusions: Genetic improvement for bull fertility is possible through selective breeding. Genomic selection for bull fertility might be more accurate if the X chromosome mutations that underlie the discovered QTL are included in the analyses. Variants associated with bull fertility accumulate in the X chromosome, as they do in humans and mice, thus, suggesting specialization of this chromosome.
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MLA: L.GEN.1818 Bull fertility update: historical data, new cohort and advanced genomics - Livestock genetics and genomics - Published 11 Sep 2019
These are behavioural data from tests conducted on individual hens that differed in their range use. The tests applied were an Open Field Test, Tonic Immobility Test, and an Attention Bias test.
UNE: A17/2342 Effects of rearing environments on ranging, adaptation to stressors and health in free-range laying hens - - Published 09 Sep 2019
SWATH-MS acquisition was used to analyse the hordein-null barley lines. This dataset was investigated in order to understand the global proteome changes upon deletion of each hordein-class.
Legacy data - - Published 21 Aug 2019
pyprecag is a Python package containing processing functions used for analysis of precision agricultural data collected by hand or using on-the-go sensors like yield monitors.
pyprecag functions und... more erpin the tools found in PAT - Precision Agriculture Tools plugin for QGIS.less
CSA1603 Simple tools for spatial analysis - key enabling technologies for Precision and Digital Viticulture (GIS Freeware RRDFP) - - Published 09 Jul 2019
PAT - Precision Agriculture Tools plugin for QGIS is a suite of tools for Precision Agriculture (PA) and Precision Viticulture (PV) data analysis.
The tools run within Quantum Geographic Information ... more System (QGIS). PAT aims to provide an easy-to-use interface for processing PA/PV data through an established workflow developed for constructing maps using on-the-go data and for the analysis of PA/PV data analysis.less
CSA1603 Simple tools for spatial analysis - key enabling technologies for Precision and Digital Viticulture (GIS Freeware RRDFP) - - Published 09 Jul 2019
SNP genotypes, collected from 11 populations and 184 Pacific oysters, as part of a published study on genetic diversity. Details of published work are:
"Assessment of genetic diversity and population ... more structure in cultured Australian Pacific oysters". Animal Genetics (In Press).less
SIP 254 FY18 - Functional Annotation of Salmon Genome - - Published 02 Jul 2019
This data collection includes the data generated under the modelling component of a GRDC project. The APSIM model was optimized using data set collected from Termora, Horsham, and Karoonda to simulate... more observed soil mineral nitrogen dynamics, water dynamics, residue recovery and crop production. The key outputs are the optimized two model parameters: the decay rate constant of humic organic carbon and carbon use efficiency of microbial decomposition. less
GRDC CSP00186 Stubble Initiative Module1 - - Published 26 Jun 2019
Scientific reference collection of physical samples of Australian soils. There are over 100,000 soil specimens in the collection: 70,000 fully archived and 30,000 stored specimens (still to be archive... more d). The specimen collection reflects the changes in research focus over the last 70 years and expects to continue this into the future.
The starting collection, which was received at the founding of the Soil Archive in 2003, has been complemented by more recent submissions from other agencies and current CSIRO projects from a range of Business Units (predominantly Agriculture & Food, Land & Water). Researchers can submit their soil specimens to the Soil Archive. These soil specimens will need to be accompanied by the collected soil data. For more information, see our website.
The sub sample collection of the Soil Archive holds 43,000 specimens of fine earth (< 2 mm) (10 gram duplicates of the larger specimens) that are suitable to near-infrared spectroscopic analysis. less
Legacy data - Australian Soil Resource Information System - Published 25 Jun 2019
This data collection include the APSIM simulation outputs and the relevant data assessment on the trade-offs between crop yield, soil sequestration and N2O emissions under different nitrogen managemen... more t scenarios at 613 sites across Australian cropping regions. At each site, the model was run for 100 years under different N applications rates, while crop yield, soil carbon stock, N2O emissions from the soil were output. Based on the these dataset, the best N management practices were identified. less
Potential soil carbon sequestrati - - Published 20 Jun 2019
This data collection includes APSIM simulation of crop yield, nitrogen and water management, soil nitrogen and carbon dynamics in Huang-Huai-Hai Plain, China. A winter-wheat and summer maize double cr... more opping system was simulated under a series of management scenarios including nitrogen and water management. less
Scientific benchmarks for sustainable agricultural intensification - - Published 20 Jun 2019
Data related to Naval-Sanchez et al. 2019 "Selection Signatures in heat-resistant cattle reveal missense mutations in damage response gene HELB".
Samples:
Whole genome sequences from the 1000 Bull Gen... more omes Project (Run6, Bos taurus, and Bos indicus) for breeds chosen as a reference for imputation were retrieved (Daetwyler et al. 2014; Hayes and Daetwyler 2018). This results in 440 whole-genome sequences across 18 cattle breeds.
Breeds were grouped in accordance to their phenotypes and reported genomic crosses as taurine (humpless), indicine (with hump), admixed or African sanga, the two latter being stabilized composite breeds (Rege J 1999; Hanotte et al. 2002; Rege J et al. 2007; Mwai et al. 2015; Felius, Marleen et al. 2016).
The dataset contains 186 European Taurine, 102 Asiatic indicine and 80 cross-bred genomes as well as a set of African samples composed of 12 taurine, 41 sanga and 19 indicine.
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Genomic Analytics in the Realm of Big Data (OCE Post-Doc) - - Published 17 Jun 2019
LC-MS/MS discovery characterisation of 20 rye cultivars after gluten enrichment (using IPA/DTT) and tryptic digestion.Data set includes raw MS data and ProteinPilot results files. The samples were als... more o analysed with a quantitative LC-MRM-MS method (rye peptide markers) with all raw data uploaded for: (1) 20 rye cultivars; (2) 16 cereals and pseudocereals; (3) a range of food products (10 breakfast cereals and 7 snack foods); (4) repeat analysis on spelt after contamination was noted in batch 1.less
Livestock - Testing & Services - - Published 31 May 2019
History: rotation phase for each plot from 1925 to 1993.
Grain yield: for each plot from 1925 to 1993.
Total dry matter: for each plot from 1925 to 1991.
Pasture cuts: for each plot from 1950 to 1991.... more
Pasture composition: for each plot from 1950 to 1991.
Monthly climate data: from 1925 to 1993.
Soil carbon data: measured total organic carbon (by combustion) and size fractions (by MIR-PLSR prediction) and delta 14C values for select plots for 1963, 1973, 1983 and 1993 for each of 0-10 cm and 10-22.5 cm depths.less
1179.2 Uncertainty quantification in soi - Soil carbon measurement - Published 23 May 2019
Proteomics data collected as part of the manuscript by Tanner et al (2019) Frontiers in Plant Science
Abstract: The temporal pattern of accumulation of hordein storage proteins in developing barley gr... more ains was studied by enzyme-linked immunosorbent assay (ELISA), western blot and liquid chromatography tandem mass spectrometry (LC-MS/MS). Hordein accumulation was compared to the pattern seen for two abundant control proteins, serpin Z4 (an early accumulator) and lipid transferase protein (LTP1, a late accumulator). Hordeins were detected from six days post-anthesis (DPA) and peaked at 30 DPA. Changes in fresh weight indicate that desiccation begins at 20 DPA and by 37 DPA fresh weight had decreased by 35%. ELISA analysis of hordein content, expressed on a protein basis, increased to a maximum at 30 DPA followed by a 17% decrease by 37 DPA. The accumulation of 39 tryptic and 29 chymotryptic hordein peptides representing all classes of hordein was studied by LC-MS/MS. Most peptides increased to a maximum at 30 DPA, and either remained at the maximum or did not decrease significantly. Only five tryptic peptides, members of the related B1- and γ1-hordeins decreased significantly by 21-51% at 37 DPA. Thus, the concentration of some specific peptides was reduced while remaining members of the same family were not affected. The N-terminal signal region was removed by proteolysis during co-translation. In addition to a suite of previously characterised hordeins, two novel barley B-hordein isoforms mapping to wheat low molecular weight glutenins (LMW-GS-like B-hordeins), and two avenin-like proteins (ALPs) sharing homology with wheat ALPs, were identified. These identified isoforms have not previously been mapped in the barley genome. Cereal storage proteins provide significant nutritional content for human consumption and seed germination. In barley, the bulk of the storage proteins comprise the hordein family and the final hordein concentration affects the quality of baked and brewed products. It is therefore important to study the accumulation of hordeins as this knowledge may assist plant breeding for improved health outcomes (by minimizing triggering of detrimental immune responses), nutrition and food processing properties. less
Livestock - Testing & Services - - Published 03 Apr 2019
This data collection contains behavioural and cortisol data for 28 Merino ewes. The study aimed to determine the impact of chronic stress on the emotional states of sheep, assessed through judgement b... more ias and attention bias tests. Stress was induced pharmacologically by administering Synacthen. Judgement bias was assessed during acute (one injection), chronic (21 daily injections) and acute-on-chronic (2 min isolation after 28 daily injections) stress. Attention bias was assessed during chronic stress only (22 daily injections). Cortisol responses were assessed on days 1 and 29 to confirm the effects of the Synacthen.less
SIP 36-1: Resilience in livestock - - Published 12 Mar 2019
Supporting 16S and ITS Illumina MiSeq data for the paper "Vineyard soil microbiome composition related to rotundone concentration in Australian cool climate ‘peppery’ Shiraz grapes" by Vadakattu et al... more .less
AWRI: Rotundone - - Published 26 Feb 2019
This data collection contains behavioural and temperature data for 80 sheep during a modified attention bias test. Prior to testing sheep were treated with drugs to induce short-term anxiety-like, cal... more m-like and euphoric-like states. The work aimed to determine whether the modified test could be used to measure the induced states.less
SIP 326: Developing measures of positive affective states in livestock - - Published 12 Feb 2019
These data are historic weather records for Australia obtained from the Bureau of Meteorology, then processed for use with the GrazPlan suite of decision support tools (MetAccess, GrassGro and AusFarm... more ). The raw data must not be redistributed without the consent of the Bureau of Meteorology.less
SIP 60 APSIM Development - - Published 09 Feb 2019
A selection of photographs from those taken by Stanley Fowler (1895-1961).
With the co-operation of the Royal Australian Air Force, in 1936-39 and 1942-46 he undertook a series of aerial observations ... more of pelagic stock in coastal waters. His photographs number over 10,000.
This collection includes photographs of landforms, coastal areas, vessels, equipment and people from South Australia, Queensland, Victoria, Tasmania and Flinders Island. It also includes photographs of the research vessel, "Warreen", in which the C.S.I.R.'s decision to purchase Fowler had been instrumental.less
Legacy data - Stanley Fowler Images - Published 06 Feb 2019
We introduce a synthetic dataset of 10,000 top down images of Arabidopsis plants. Leaf instance segmentation labels for each image are also presented. This dataset was designed to accompany the real d... more ataset provided with the Leaf Segmentation Challenge of the Computer Vision Problems in Plant Phenotyping. Furthermore, we release a leaf instance segmentation pre-trained model based on the Mask-RCNN architecture.less
Legacy data - - Published 10 Jan 2019
We are currently limited in our ability to predict when and where invertebrate pest densities will reach high levels and cause yield loss in grain crops across Australia. This is partly due to a lack ... more of fundamental knowledge around pest and beneficial species distribution and the factors that influence population abundance. This collection will generate new knowledge about the life-cycle and biology of a range of pest and beneficial species across southern and western regions, which will enable pathways for better insecticide-use decision-making and the proactive management of pests.less
GRDC: CSE00059 New knoweldge to improve - Critical knowledge gaps for pests and beneficials in Australian grain production systems - Published 11 Dec 2018
GrazFeed is a decision support tool developed by CSIRO to help graziers improve the profitability of livestock production, through more efficient use of pastures and supplementary feeds.
GrazFeed is r... more egarded as the industry benchmark for the nutrition of grazing animals in temperate Australia. It is based on the Australian Feeding Standards (1990).less
SIP 60 APSIM Development - Software Development - Published 01 Nov 2018
This collection contains three types of data files:
1) Canopy temperature files in csv format
2) Weather data corresponding to canopy temperature sensor location csv format
3) Agronomic data correspon... more ding to canopy temperature sensor location in csv formatless
Legacy data - Canopy Temperature - Published 22 Oct 2018
