Pacific Oyster Genomics

November 25th, 2019

The CSIRO Applied Breeding team provides the genetics expertise and advice to support a family-based Pacific oyster breeding program run by Australian Seafood Industries (ASI). Through the know-how of lead geneticist, Dr Peter Kube, the program has been extremely successful in breeding animals with increased resistance to a viral disease that threatened the entire Australian industry.
Genomic selection is a new breeding method that is rapidly becoming the standard approach for animal breeding. Genomic selection can be used to improve the accuracy of breeding values and the rate of genetic gain. This method is not currently being used in operational shellfish breeding, however, CSIRO and ASI are seeking to evaluate this method for the Australian Pacific oyster breeding program.
A first step is to have a suitable DNA genotyping tool available, while no such tool has been available for the Australian Pacific oyster population. This changed when an international team lead by Dr Ross Houston at the Roslin Institute developed a‘SNP chip’ capable of collecting genetic data from tens of thousands of locations throughout the oyster genome. Seeing the potential for the local breeding program, the CSIRO team formed a research collaboration with Dr Houston and together they tested the new SNP chip on samples from the ASI breeding population. The team was pleased to find that 18,000 (67%) of the DNA markers on the chip were informative in the ASI animals, opening the possibility to begin a genomic selection study.
The data allowed estimates of genetic diversity to be performed. This showed the ASI population carries comparable levels to breeding populations from New Zealand, France and the British Isles. The data also revealed that the Australian population appears genetically separate from the other populations evaluated in the experiment (refer to the Figure below). Importantly, the team found the genetic data provided high resolution information about the precise degree of relatedness between animals. This represents promising news for the team as they make plans to transition the Pacific oyster breeding program to genomics selection.
A detailed explanation of the research, along with the associated conclusions can be found here