Beef CRC Genomics Database Annotation

Summary

The Beef Cooperative Research Centre (CRC) was established in July 1993 and has completed three, seven-year CRC terms. Research undertaken in CRC II and III generated a significant amount of data, including substantial DNA information, for which there was no link to datasets of cattle performance.

The aim of this project was to establish a ‘Beef CRC genomics database’ and provide a link between the data and cattle performance traits to improve beef production in Australia.

As a result of this project, there is more streamlined access to Beef CRC research data, which ensures the genetic information can inform future research.

Objectives

The key objective of this project was to include DNA sample identifications within the performance database, along with descriptive information of the DNA to enable the pre-existing database to become the Beef CRC Genomics database.

Key findings

• As a result of this project, researchers now have better access to genomic data from the Beef CRC DNA projects, and are provided more documentation for access and use of the Beef CRC performance data.
• Explanation of the key DNA information within the database has been updated and improved, along with publication lists to ensure experimental designs behind the data collection can be accounted for.
• Maintenance requirements and budgets have been provided for continued operation of the database and Livestock Library.

Benefits to industry

It would beneficial to the industry to have a national database of DNA research data, to ensure resources are maintained and researchers get the most from their data. This project has provided recommendations for the incorporation of data recording and database design in future research proposals have been provided.

Future research

• MLA should consider the potential benefits of having a fully accessible national database for DNA research data storage and documentation.
• This national database should ideally include as much detail of experimental design and data definition as possible, and outline the points to the value of a national data design protocol.

Related resources

• Burrow H (2006) Links between the genetics of beef quality and components of herd profitability in northern Australia. MLA final report.
• Burns B, Corbet N, McGowan M, Holroyd R (2014) Male indicator traits to improve female reproductive performance. MLA final report.
• Johnston D, Grant T, Prayaga K, Walkley J (2013) Early predictors of lifetime female reproductive performance. MLA final report.
• Beef CRC database

Publications resulting from this project

• Boe-Hansen, GB, Rego, JP, Crisp, JM, Moura, AA, Nouwens, AS, Li, Y, Venus, B, Burns, BM, McGowan, MR (2015) Seminal plasma proteins and their relationship with percentage of morphologically normal sperm in 2-year-old Brahman (Bos indicus) bulls. Anim Reprod Sci 162, 20-30.
• Fortes, MR, Kemper, K, Sasazaki, S, Reverter, A, Pryce, JE, Barendse, W, Bunch, R, McCulloch, R, Harrison, B, Bolormaa, S, Zhang, YD, Hawken, RJ, Goddard, ME, Lehnert, SA (2013) Evidence for pleiotropism and recent selection in the PLAG1 region in Australian Beef cattle. Anim Genet 44, 636-47.
• Reverter, A, Fortes, MR (2013) Association weight matrix: a network-based approach towards functional genome-wide association studies. Methods Mol Biol 1019, 437-47.
• Fortes, MR, Deatley, KL, Lehnert, SA, Burns, BM, Reverter, A, Hawken, RJ, Boe-Hansen, G, Moore, SS, Thomas, MG (2013) Genomic regions associated with fertility traits in male and female cattle: advances from microsatellites to high-density chips and beyond. Anim Reprod Sci 141, 1-19.
• Burns B. M., Corbet N. J., Corbet D. H., Crisp J. M., Venus B. K., Johnston D. J., Li Y., McGowan M. R., Holroyd R. G. (2012) Male traits and herd reproductive capability in tropical beef cattle. 1. Experimental design and animal measures. Animal Production Science 53, 87-100. https://doi.org/10.1071/AN12162
• Corbet N. J., Burns B. M., Johnston D. J., Wolcott M. L., Corbet D. H., Venus B. K., Li Y., McGowan M. R., Holroyd R. G. (2012) Male traits and herd reproductive capability in tropical beef cattle. 2. Genetic parameters of bull traits. Animal Production Science 53, 101-113. https://doi.org/10.1071/AN12163
• Fortes, MR, Li, Y, Collis, E, Zhang, Y, Hawken, RJ (2013) The IGF1 pathway genes and their association with age of puberty in cattle. Anim Genet 44, 91-5.
• Fortes, MRS, Reverter, A, Hawken, RJ, Bolormaa, S, Lehnert, SA (2012) Candidate Genes Associated with Testicular Development, Sperm Quality, and Hormone Levels of Inhibin, Luteinizing Hormone, and Insulin-Like Growth Factor 1 in Brahman Bulls1. Biology of Reproduction 87.
• Fortes, MR, Holroyd, RG, Reverter, A, Venus, BK, Satake, N, Boe-Hansen, GB (2012) The integrity of sperm chromatin in young tropical composite bulls. Theriogenology 78, 326-33, 333.e1-4.