Program Leader
Professor Julius van der Werf
University of New England
Tel: 02 6773 2092
Email - julius.vanderwerf@une.edu.au
To find more information about the Information Nucleus click here.
To read about the program scroll down below 'Latest Updates'.
In March we completed the second batch of 50k chips with Geneseek, consisting of remainder samples from the 2008-2010 drop and around 400 samples from the 2011 drop (total 2900 from INF progeny buffy coats), pilot project 2 samples (~750) and industry sires (~250). The number of Information Nucleus (INF) progeny remaining to be genotyped is ~2000 and we need to do a few hundred more industry sires. For these we need a new service contract with Geneseek (~250k).
The additional genotypes will need to be analysed to obtain increased accuracies of genomic prediction. In this quarter we obtained the first estimates for NLW, with results looking pretty good (genomic prediction accuracy ~.25-.30 for merino and Border Leicester. The delivery of results in the pilot project 2 is being achieved in a timely manner (for Sheep Genetics registered samples the average is 38 days, longer delays occur for non-SG registered samples). We have also started to do some validation of research breeding values from pilot project 1, as those sires now have some progeny. Correlations of GEBV and current ASBV are substantial and as expected. A potential issue to be resolved in the procedure is in the accounting for genetic groups: this needs to be consistent between GEBVs and ASBVs, i.e. both predictions need to consist of a between group component (representing bloodline, breed etc) and a within breed deviation.
We have obtained results from phase 2 of the validation of parentage testing. The first phase was ‘in silico’ based on the INF database. This validation was based on samples from real flocks, and genotypes were obtained on a sequonom platform (which will be the platform for cheap parentage testing). Genotyping results look good and we concluded that we need in first instance ~150 SNPS (3 panels for a parentage test. This will also include 3 SNPs to predict poll/horn. The next step is to negotiate price and condition for a larger pilot project (20,000 samples) that will include samples from commercial flocks, breeders and INF flocks.
We have started to investigate options for cheaper genotyping, such that breeders can more easily afford genotyping for the purpose of genomic selection. Samples genotyped from a 10k test could often be imputed to 50k data, allowing enough SNP density for genomic prediction. Options are to run a 10k SNP chip (cost ~$70 via Geneseek) or a test for 10k SNPs obtained via Genotyping by Sequencing (DPIVic). The latter is a new technology that seems very promising and we also explore this with a Canberra based company (possibly delivering 100k SNPs for $50). It was decided that we take out time to properly develop and test these options in the next financial year, not to confuse the market place too much and for 2012 keep offering a 50k test (possibly subsidised in a ‘pilot project 3 framework). Together with a parentage/horn-poll test there will be enough excitement and activity at this front later this year.
Work on phenotypic analysis is progressing, but slowly. The team is attempting to at least complete some of the across trait correlations before the end of the financial year.
During the last quarter, there has been additional genotyping data added to the database. This significant quantity of new information and the commencement of the second Genomics Pilot Project provided the justification to re-analyse all of the genomic association data. The results have sparked a lot of interest. The accuracies with which a wide range of important traits can now be predicted, based on genomic information, has proven beyond doubt that the genomics technology will be of lasting value for the Australian sheep industry. The results of the improved predictions are already flowing through to industry.
The first recipients of the upgraded information were breeders with rams entered in the Pilot Project. The next groups to receive new information were breeders with rams that had been used in the Information Nucleus and participants in the first Genomics Pilot Project. A valuable aspect of the genomic approach is ability to update and expand predictions for all animals for which genotypes are available. The prediction of horn/poll was also released as part of this new analysis.
Information Nucleus Operations
A review of reproductive performance in the ewe progeny identified a number of problems leading to low fertility. There appear to be a number of factors contributing to low lamibing percentages including the complication of measuring age at puberty and some ewes below target weight at first joining. A series of measures have been put in place to overcome these problems.
All arrangements are now in place for the 2012 AI program. Approximately 6,000 ewes have been allocated across two sites (UNE/Kirby and the Katanning/DAFWA sites). Moving to two sites and increasing the number of ewes per site provides a more cost-effective model for data collection and reflects the transition to a post-CRC model for the Information Nucleus program.
Genomics
Ongoing genotyping has provided a few thousand extra genotypes and these are being used to increase accuracy of genomic breeding values. Most of the time, accuracies are increasing with more data, which is encouraging. Some traits require further work, e.g. shear force tenderness and a couple of new carcass traits seem to have low accuracies, which could be related to quality of phenotypes, especially in the first year. Data on reproductive traits is still limited and will be enhanced with genotyping of industry sires with high ASBV accuracies.
All INF DNA and blood samples are now stored in duplicate in different freezers in Armidale and a lab inventory software/database is linked up to the CRC INF database.
The Genomics Pilot Project 2 project is now running and first samples have been received and genotyped. Close to 800 samples are expected before November. Genomic breeding values will be delivered quite promptly via AGBU. Another workshop with ram breeders has analysed the (costs and) benefits of genomic testing and the breeders are generally very positive about the prospects.
Information Nucleus Version 2
Following the CRC’s Third Year Review in February 2011 which strongly recommended industry continuation of the INF, the CRC has examined various designs for an Information Nucleus Version 2 (INF2). The resultant design is similar to the current INF, but with the number of sites reduced from 8 down to 2 sites – Kirby in northern NSW and Katanning in WA. The focus will initially be on the major breeds (Merino, Border Leicester, White Suffolk and Poll Dorset) due to the large numbers needed to be measured from each breed to deliver meaningful genomic predictions. Also more progeny will be needed for Merino due to their diversity. Strategies are being explored to determine the feasibility of genomic predictions for smaller breeds.
Information Nucleus data analysis
Work on phenotypic analysis is progressing, with more attention now directed to analysis of parasites and reproduction. The parasite data is challenging, with various ages measured, different worms types etc, and correlations of sire ranking between sites seem to be lower than expected (e.g. based on industry data).
Design and Analysis
Analysis of the accuracy of genomic predictions across breeds and of individuals unrelated to the reference population have been undertaken, required for input into the design of the next version of the Information Nucleus Flock (INF2) to follow the work of the Sheep CRC. Results show that genomic predictions across Australian sheep breeds have low accuracy. Prediction within breed can be high for animals related to the reference population, but even unrelated animals can have an acceptable accuracy provide there are many records of the breed in the reference population. Consequently a design of INF2 has been proposed. Two scientific papers have been drafted and a discussion paper has been prepared.
Further progress has been made with extracting DNA samples of INF progeny with most of the animals from the 2007-2009 drops now extracted and a start was made with animals from the 2010 drop. 2000 genotypes have been added to the database, and another 1000 are planned this month which will complete the number planned for the financial year.
The Genomics Pilot Project 2 is underway with DNA samples to be collected via blood cards. 1000 young sires are planned to be sampled in July from Terminals, Maternals and Merinos.
INF Operations
The Dorper site near Narrogin in WA continues with sires for the second mating identified (10 Dorper and 3 link) and semen assembled for the 2011 AI mating.
Information management
A letter and the latest RBVs were sent out in mid March to all Genomics Pilot Project 1 participants.
A commercial Laboratory Information Management system (FreezerPro) has been implemented for tracking of DNA samples from the INF and Genomics Pilot Project 2. All DNA samples have now been relocated to the new freezers in Armidale.
Design and Analysis
Further progress has been made with extracting DNA samples of INF progeny with most of the animals from the 2007-2009 drops now extracted and a start was made with animals from the 2010 drop. Extractions have been done at UNE (2000 samples) and at the animal genetics lab of UQ in Gatton (1500 samples). Data on genotypes has been returned and there is now a more efficient pipeline to QA and store genotype data with AGBU. ~4200 INF progeny have been genotyped since October 2010, with ~800 to follow this FY. Some animals that failed in first instance in the Genomics Pilot Project have also been re-genotyped. Further results have been sent out in the Pilot Project, e.g. carcass traits for 155 terminals as well as further results for 82 merinos (staple strength, birth weight, and wrinkle) and 16 maternal sires. Freezers have purchased and good progress is being made with a solid documentation system for storing DNA samples.
In the last quarter we will start a whole new series of association analysis with hopefully higher accuracies for genomic breeding values across the board. In first week of April we have a genomics workshop in Armidale to discuss the further ways for data analysis, the design of INF2 as a reference population for future genomic selection, and further collaboration with the International Sheep Genomics Consortium to ensure that developments of high density SNPs and sequencing projects are carried out with sufficient Australian stake holding (e.g. using Australian genetic resources).
Various papers have been written by the group for AAABG and the Livestock Genomics Conference in Melbourne 2-5 May 2011.
Operations
The Dorper site near Narrogin on the property of Adrian Veitch continues with assistance being provided by DAFWA staff from the Katanning INF site. Sires for the second mating have been identified (10 Dorper and 3 link) and semen assembled for the 2011 AI mating.
Information Management
Genotyping data are in the new genotyping database and a letter with the latest Research Breeding Values were sent out in mid March to all Genomic Pilot Project participants.
A commercial Laboratory Information Management system (FreezerPro) has been ordered and will be available in Q4 for tracking of DNA samples from the INF and Genomics Pilot Project Stage 2.
The Information Nucleus Program integrates sophisticated genetic design and analysis with comprehensive measurement of biological and production parameters. It will allow breeders and commercial producers to quickly exploit information on breeding values for new traits potentially supported by information on animals’ genomes to achieve more rapid genetic improvement in their flocks and across the whole sheep industry. The Information Nucleus will also provide the base for core research activities in other CRC programs and enhance the application of results by industry.
The Information Nucleus will test progeny of key young industry sires for an extensive range of traits in differing environments. This information will be added to the Sheep Genetics (SG) database to enhance the accuracy of Australian Sheep Breeding Values (ASBVs) used by industry. The Program will also analyse and use genotypic information on IN progeny and industry sires to estimate and test SNP panels as predictors of breeding value. Genetic information will be generated about new and novel traits and traits that are difficult or expensive to measure on-farm that may be related to wool and meat quality, disease resistance and reproductive fitness. The Information Nucleus will also be the focus of management, wool and meat research being undertaken in the other CRC research programs.
The Information Nucleus will provide progeny test data to Sheep Genetics (SG) that will flow immediately into routine SG genetic evaluations to enhance the accuracy of the ASBVs for immediate delivery to industry. SG has the breeder networks and proven ability to source all of the semen required for the Information Nucleus. Molecular ASBVs will be developed and tested based on data from the Information Nucleus, the previous Sheep Genomics project and industry sires and jointly with phenotypic IN data. This should lead to increased accuracy of selection of young males combined with existing quantitative ASBVs for various traits to improve the rate of response to selection in industry. The result is a potential increase in value of genetic gain of 20-30%, with considerable more gain for some hard-to-measure traits that currently are difficult to improve.
SG’s program for adoption of ASBV involves extensive marketing and training in the seedstock sector and with commercial breeders. This includes information workshops, one-on-one instruction and promotion via industry events and publications. Additionally, a pilot project has been designed to engage breeders in genotyping young breeding animals and use resulting information for breeding decisions. Extension and training activities will be coordinated with Project 5.2 (Industry Training). Strategies and supportive software will be developed to assist them in making optimal genotyping and selection decisions. These programs build pull-through demand for the provision of ASBV by the stud breeders and ensure demand for the products of the CRC Information Nucleus that add value to commercial production.
