Design and role of an information nucleus in sheep breeding programs

2010 ◽  
Vol 50 (12) ◽  
pp. 998 ◽  
Author(s):  
J. H. J. van der Werf ◽  
B. P. Kinghorn ◽  
R. G. Banks
Keyword(s):  
Large Scale ◽  
Research Centre ◽  
Cooperative Research ◽  
Breeding Programs ◽  
Sheep Breeding ◽  
Genome Association ◽  
Current Design ◽  
Australian Sheep ◽  
Whole Genome Association ◽  
Design Factors

The Australian sheep Cooperative Research Centre has initiated an information nucleus with the aim to estimate genetic parameters for new traits, to undertake a large-scale whole-genome association study and to enhance the breeding values of breeding animals in commercial studs. This paper presents the rationale behind the current design factors to meet the main objectives. It then discusses the potential design of an information nucleus if it were a sustainable part of commercial sheep-breeding programs in the long term. Advantages of such an information nucleus are summarised and quantified where possible.

A CASE STUDY OF A CARBON DIOXIDE WELL TEST

2007 ◽  
Vol 47 (1) ◽  
pp. 239
Author(s):  
J.Q. Xu ◽  
G. Weir ◽  
L. Paterson ◽  
I. Black ◽  
S. Sharma
Keyword(s):  
Carbon Dioxide ◽  
Natural Gas ◽  
Large Scale ◽  
Surface Flow ◽  
Phase Changes ◽  
Co2 Production ◽  
Research Centre ◽  
Well Test ◽  
Cooperative Research ◽  
Gas Well

This paper reports on the planning, procedure, results and analysis of a carbon dioxide (CO2) well test performed on Buttress–1, a well located in the Otway Basin, Victoria, Australia. A large-scale pilot study of CO2 sequestration is planned by the Australian Cooperative Research Centre for Greenhouse Gas Technologies (CO2CRC) in this area, which will involve, inter alia, taking CO2 from the Buttress reservoir and injecting it into a nearby depleted gas field. Understanding the production characteristics of this well is important to the success of this pilot, which forms part of a more extensive study to establish viable means to mitigate CO2 emissions to the atmosphere. This general backdrop forms the motivation for this study.Testing comprised of a standard suite of draw-downs and build-ups to determine reservoir/well characteristics, such as the well deliverability, the non-Darcy skin coefficient and the average reservoir permeability and volume.Compared to the wealth of experience developed over many years in testing oil and gas wells, the collective experience in CO2 well testing is extremely limited. The distinguishing features between this test and those of a typical natural gas well test need to be emphasised. Although, in general, flow testing a CO2 well should be similar to testing a natural gas well, differences in the thermodynamic properties of CO2 affect the analysis of the well test considerably. In particular, the non-Darcy skin effect is more pronounced and the wellbore and surface flow can involve dramatic phase changes, such as the formation of ice. Also, since CO2 is more compressible than a typical natural gas, the accurate measurement of the flow rate becomes more challenging. It is also apparent that the use of pseudo pressure, as opposed to simpler methods of dealing with the pressure dependency of key properties, is essential to the successful analysis of the pressure response to the CO2 production.

Genetic parameters for lamb autopsy traits

2014 ◽  
Vol 54 (6) ◽  
pp. 736 ◽  
Author(s):  
D. J. Brown ◽  
R. M. Jones ◽  
G. N. Hinch
Keyword(s):  
Genetic Correlations ◽  
Selection Criterion ◽  
Research Centre ◽  
Cooperative Research ◽  
Crown Rump Length ◽  
Australian Sheep ◽  
Lamb Survival ◽  
Fleece Weight ◽  
Indicator Traits ◽  
Overall Mortality

Heritabilities and genetic correlations were estimated between individual and composite autopsy traits for lambs autopsied in the Australian Sheep Cooperative Research Centre information nucleus flocks between 2008 and 2011 (n = 3224). Correlations were also estimated between autopsy categories and the production parameters Yearling greasy-fleece weight and Yearling weight, and the potential survival indicator traits: Lamb ease, Thorax circumference and Crown–rump length. All autopsy trait heritability estimates were low (range 0.01–0.04). For all traits, a higher proportion of the variance was partitioned into the maternal permanent environment than the direct effects (range 0.01–0.12), suggesting that selection based on lamb autopsy results would impart little advantage over the lamb survival trait itself in improving lamb survival. Genetic correlations between Lamb ease and all autopsy traits were positive, indicating that birth trauma is related to all causes of lamb deaths and that Lamb ease may be a useful selection criterion in seedstock flocks to reduce overall mortality. There were also positive genetic correlations between Thorax circumference after adjusting for birthweight and two classes of dystocia, as well as a positive correlation between Thorax circumference and incidences of Starvation mismothering, implying that Thorax circumference may be a useful indirect field measurement to reduce death from these causes. Of concern were the antagonistic genetic correlations estimated between Yearling greasy-fleece weight and a composite trait of All Dystocia classes plus Starvation mismothering (0.27 ± 0.15), implying that selection for increased fleece weight could be having a detrimental effect on overall lamb survival.

Exploring Genetic Basis of GVHD by Whole-Genome Association Studies in a Large Series from the Japan Marrow Donation Program (JMDP).

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 3232-3232
Author(s):  
Yasuhito Nannya ◽  
Makoto Onizuka ◽  
Koichi Kashiwase ◽  
Masashi Sanada ◽  
Yoshiki Akatsuka ◽  
...  
Keyword(s):  
Large Scale ◽  
Genetic Basis ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Whole Genome ◽  
Minor Histocompatibility Antigens ◽  
Therapeutic Benefits ◽  
Gvhd Prophylaxis ◽  
Genome Association ◽  
Whole Genome Association

Abstract Allogeneic stem cell transplantation (allo-HSCT) has been established as one of the most effective therapeutic options for hematopoietic malignancies. Its major therapeutic benefits are obtained from allo-immunity directed against patients’ tumor cells (graft-versus-tumor effects, GVT). However, the same kind of allo-immune reactions can also be directed to normal host tissues resulting in graft-versus-host disease (GVHD) and subsequently offset the potential benefit from GVT. Because both reactions are initiated by donor T-cells that recognize minor histocompatibility antigens (mHA) that are incompatible between donor and recipient, the knowledge of these mHA is of particular importance to develop a new measure to prevent GVHD while harnessing the antitumor potential of allo-HSCT. On the other hand, the incompatibility of mHAs, as well as other predispositions to development of GVHD, is basically determined genetically, and thus, are plausible targets of genetic association studies, which have recently been enabled with the advent of large-scale genotyping technology. In the current study, we explored genetic basis of GVHD by whole genome association studies, in which relevant SNPs to GVHD development were explored by genotyping a large cohort of GVHD-positive and negative transplantations performed through the Japan Marrow Donor Program (JMDP). Among 7,800 transplants genotyped for HLA types, we selected 1856 transplants (3712 donors/recipients) for large scale genotyping of more than 500,000 SNPs using Affymetrix® GeneChip® 500K arrays, according to the following criteria: HLA A, B, C, DR, DQ loci were completely matched at the DNA level Short term MTX (stMTX) + CyA or stMTX + FK506 was employed as GVHD prophylaxis, and Genome DNA from both donor and recipient and record of clinical course was available. Based on the genotyping data, possible association was tested for each SNP in donors and recipients with regard to the development of GVHD. Association of genotype incompatibilities was also investigated for major HLA subtypes to identify the mHA loci that are relevant to GVHD pathogenesis. In the intermediate analysis, a number of candidate polymorphisms in donors and recipients have been identified together with possible mHA loci.

Red Dirt Thinking on Power, Pedagogy and Paradigms: Reframing the Dialogue in Remote Education

2013 ◽  
Vol 42 (2) ◽  
pp. 111-122 ◽  
Author(s):  
Sam Osborne ◽  
John Guenther
Keyword(s):  
Large Scale ◽  
Ways Of Knowing ◽  
Strong Sense ◽  
Research Centre ◽  
Cooperative Research ◽  
Remote Education ◽  
Academic Level ◽  
Starting Point ◽  
Indigenous Educators ◽  
Red Dirt

Recent debates in Australia, largely led by Aboriginal and Torres Strait Island academics over the past 5 or so years, have focused on the need for non-Indigenous educators to understand how their practices not only demonstrate lack of understanding of Indigenous ways of knowing, being and doing, but even deny their presence. This debate has serious implications for the non-Indigenous remote educator who wishes to support remote students to achieve ‘success’ through their education. The debates on the one hand advocate the decolonising of knowledge, pedagogy and research methods in order to promote more just or equal approaches to research and education, while other voices continue to advocate the pursuit of mainstream dominant Western ‘outcomes’ as the preferred goal for Indigenous students across Australia. This dilemma frames the context for this study. The Remote Education Systems Project, in the Cooperative Research Centre for Remote Economic Participation, seeks to explore these and other questions as part of the broader research agenda being undertaken. This project is particularly focused on large-scale questions such as: ‘What is a remote education for and what would ‘success’ look like in the remote education context?’ We are approaching these research questions from community standpoints and perspectives as a critical starting point for these types of debates and discussions. In doing so, our findings indicate that remote Aboriginal community members have a strong sense of western education and its power to equip young people with critical skills, knowledge and understandings for the future, but also a strong sense of retaining of their ‘own’ knowledge, skills and understanding. This presents a complex challenge for educators who are new to this knowledge interface. Here, we offer the concept of ‘Red Dirt Thinking’ as a new way to position ourselves and engage in situated dialogue about what remote schooling might be if it took into account power issues around Indigenous knowledges in the current policy context. This article questions whether remote communities, schools and systems have, in fact, taken account of the knowledge/power debates that have taken place at an academic level and considers how remote education might consider the implications of stepping outside the ‘Western–Indigenous binary’. It seeks to propose new paradigms that non-Indigenous educators may need to engage in order to de-limit the repositioning of power-laden knowledge and pedagogies offered in remote classrooms.

Genetic parameters for faecal worm egg count at different ages in Australian sheep under natural challenge

2019 ◽  
Vol 59 (7) ◽  
pp. 1201 ◽  
Author(s):  
L. Li ◽  
D. J. Brown ◽  
A. A. Swan ◽  
J. H. J. van der Werf
Keyword(s):  
Genetic Correlations ◽  
Random Regression ◽  
Research Centre ◽  
Steady Increase ◽  
Cooperative Research ◽  
Multiple Trait ◽  
Full Data ◽  
Different Ages ◽  
Australian Sheep ◽  
Univariate Analyses

The data used in the present study consisted of 24535 worm egg count records on sheep observed from 63 to 560 days of age under conditions of the natural challenge of trichostrongylid species. Records were extracted from the Information Nucleus Flock database of the Australia Sheep Cooperative Research Centre program from 2007 to 2011. Records were observed at various ages and subdivided into weaning (W, ~3 months), post-weaning (P, ~4 months), yearling (Y, ~12 months) and hogget (H, ~18 months) age stages and were used to investigate genetic variation at different age stages in univariate analyses and estimate genetic correlations between age stages in multi-trait analyses. The full data were also analysed by random regression models to study how heritability and genetic correlations varied with age. Heritability estimates from univariate analyses were 0.20 ± 0.05, 0.15 ± 0.02, 0.36 ± 0.09, 0.22 ± 0.06 for W, P, Y and H age stages respectively. A similar trend of heritability over ages was found from random regression analyses, which decreased from 0.16 at 90 days to 0.09 at 120 days, following a steady increase to 0.32 at ~410 days, and then decreased afterwards to 0.24 at 520 days. Strong genetic correlations (>0.8) were found between W and P age stages, along with Y and H age stages. Sire by flock interaction effects were significant, and accounted for the reduced estimates of heritability and increased genetic correlations between age stages. The results indicated that a multiple-trait approach is required for genetic evaluation of worm egg count when measurements are at different ages, and the accuracy of evaluations would benefit from recording at least two separate age stages.

Abstract 2597: Centralized and Study-specific Phenotyping in a Large-scale Stroke Genetics Study: An Analysis from the NINDS Stroke Genetics Network (SiGN)

Stroke ◽  
2012 ◽  
Vol 43 (suppl_1) ◽  
Author(s):  
Bradford B Worrall ◽  
Alejandro Rabinstein ◽  
Dale M Gamble ◽  
Kevin M Barrett ◽  
Shaneela Malik ◽  
...  
Keyword(s):  
Ischemic Stroke ◽  
Large Scale ◽  
Association Studies ◽  
Web Based ◽  
Stroke Treatment ◽  
Automated Algorithm ◽  
Genome Association ◽  
Whole Genome Association ◽  
Toast Classification ◽  
User Friendly

Background: The Stroke Genetics Network (SiGN) funded by the NINDS aims to identify genetic risk factors in ischemic stroke using whole-genome association studies (GWAS). High quality phenotyping is crucial to successful application of GWAS. As a heterogenous disorder, stroke poses specific challenges. The Trial of Org 10172 in Acute Stroke Treatment (TOAST) classification is a broadly used, but its validity is challenged especially when performed by multiple investigators with differing interpretations of the system. The Causative Classification System for Ischemic Stroke (CCS) system is a new, web-based, and computerized algorithm that integrates clinical, diagnostic, and etiologic stroke characteristics in an evidence-based manner ( ccs.mgh.harvard.edu ) to generate subtypes. Methods: In planning the SiGN proposal, a sample of 20 coded charts were collected from a subset of participating studies to assess feasibility of central adjudication and comparability to study-specific TOAST. Two central adjudicators reviewed all records and generated TOAST and CCS subtypes. These were compared to study-specific TOAST subtype and the CCS phenotype generated for SiGN by local trained adjudicators. CCS data is now available for 7134 included cases using both a 5 and a 7 category system as defined in the table . Results: All 4 phenotypes were available for 115 ischemic stroke cases from 6 studies in SiGN. Basic demographics were 54% women, 63% white, and median age between 65-74. Table 1 provides the agreement between the various subtypes. Table 2 describes the types of disagreement. Conclusions: Central adjudication with only two adjudicators and curated medical records yielded more consistent subtyping independent of phenotyping system. The agreement for TOAST was higher than published rates by independent groups (∼0.50). In contrast, the agreement for CCS was lower than previously published (0.85-0.95). Site adjudicators' familiarity with TOAST and inexperience with CCS may contribute. Although CCS is an automated algorithm and has a number of user friendly features, our findings suggest that formal training and certification process before starting to use CCS may be worthwhile to achieve optimal benefit from the system.

scholarly journals Prospects and pitfalls in whole genome association studies

2005 ◽  
Vol 360 (1460) ◽  
pp. 1589-1595 ◽  
Author(s):  
Robert W Lawrence ◽  
David M Evans ◽  
Lon R Cardon
Keyword(s):  
Genetic Variation ◽  
Genetic Markers ◽  
Complex Traits ◽  
Large Scale ◽  
Association Studies ◽  
Whole Genome ◽  
Common Genetic Variation ◽  
Close Attention ◽  
Genome Association ◽  
Whole Genome Association

Recent large-scale studies of common genetic variation throughout the human genome are making it feasible to conduct whole genome studies of genotype–phenotype associations. Such studies have the potential to uncover novel contributors to common complex traits and thus lead to insights into the aetiology of multifactorial phenotypes. Despite this promise, it is important to recognize that the availability of genetic markers and the ability to assay them at realistic cost does not guarantee success of this approach. There are a number of practical issues that require close attention, some forms of allelic architecture are not readily amenable to the association approach with even the most rigorous design, and doubtless new hurdles will emerge as the studies begin. Here we discuss the promise and current challenges of the whole genome approach, and raise some issues to consider in interpreting the results of the first whole genome studies.

Genetic relationships between internal parasite resistance and production traits in Merino sheep

2017 ◽  
Vol 57 (2) ◽  
pp. 209 ◽  
Author(s):  
D. J. Brown ◽  
N. M. Fogarty
Keyword(s):  
Genetic Parameters ◽  
Genetic Correlations ◽  
Production Traits ◽  
Parasite Resistance ◽  
Breeding Programs ◽  
Sheep Breeding ◽  
Breeding Values ◽  
Merino Sheep ◽  
Internal Parasite ◽  
Australian Sheep

Breeding Merino sheep that are resistant to internal parasites alleviates the high costs associated with treatment of worm infestation and loss of production, as well as mitigating the development of anthelmintic resistance among the major worm species. Faecal worm egg count ((cube root transformation), wec) can be used in sheep as a measure of internal parasite resistance. Accurate estimates of genetic parameters for wec are required for calculation of Australian Sheep Breeding Values and inclusion of worm resistance in sheep breeding programs. This study provides updated estimates of heritability for wec and its genetic correlations with production traits. Data were analysed from a wide range of Australian and New Zealand Merino sheep in the MERINOSELECT database, which included 141 flocks with 801 flock years and up to 217 137 animals with wec recorded in at least one of four ages (W = weaning, P = post weaning, Y = yearling, H = hogget). The heritability estimates ranged from 0.16 ± 0.01 for Ywec to 0.29 ± 0.01 for Wwec, with generally high genetic correlations between the ages. Bivariate analyses estimated genetic correlations between wec at the various ages and growth, carcass quality, reproduction and wool production traits at various ages. These genetic correlations were generally small or close to zero, albeit with some significantly different from zero. The moderate heritability for wec (0.2–0.3) and its high phenotypic variation (coefficient of variation >30%) shows that relatively rapid selection response for worm resistance could be achieved. Inclusion of wec in sheep breeding programs to increase worm resistance would be expected to have little if any impact on other important production traits. These genetic parameters have been incorporated into MERINOSELECT by Sheep Genetics to provide Australian Sheep Breeding Values for wec and appropriate indices for wool and meat production. There is evidence that genotype × environment interactions may be important in some environments by reducing the accuracy of Australian Sheep Breeding Values for wec. Hence it may be prudent for breeders to implement strategies that manage the risk of any impact of genotype × environment on their breeding program.

scholarly journals CRC breeding program design, measurements and database: methods that underpin CRC research results

2001 ◽  
Vol 41 (7) ◽  
pp. 943 ◽  
Author(s):  
W. Upton ◽  
H. M. Burrow ◽  
A. Dundon ◽  
D. L. Robinson ◽  
E. B. Farrell
Keyword(s):  
Large Scale ◽  
Research Centre ◽  
Progeny Testing ◽  
Cooperative Research ◽  
Beef Quality ◽  
Beef Industry ◽  
Processing Technologies ◽  
Factors Affecting ◽  
Beef Processing ◽  
Design Generation

The Cooperative Research Centre (CRC) for the Cattle and Beef Industry (Meat Quality) developed an integrated research program to address the major production and processing factors affecting beef quality. Underpinning the integrated program were 2 large-scale progeny testing programs that were used to develop genetic, nutritional, management and beef processing technologies to overcome deficiencies in beef quality. This paper describes the experimental design, generation of experimental cattle and the collection and storage of data derived from these straightbreeding and crossbreeding progeny testing programs.

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