Genotyping-By-Sequencing Applications in Biology

Genotyping-by-Sequencing (GBS) is a method used to develop rapid and cost-effective high-density genetic marker data for diverse applications in biology. We have developed the infrastructure and skill base required to apply (high throughput) GBS for different purposes across a wide range of species. Thus far, we have optimised GBS in 25 different species encompassing plants, mammals, shellfish, fish, birds, and insects. The methodology has been scaled from small sample sizes (< 100) for diversity studies, up to many thousands in animal and plant breeding programmes where GBS underpins genomic selection. GBS is also being extended into environmental metagenomics, population genetics and conservation genetics studies. Continuous improvements in wet-lab methods have enabled increased quality and quantity of data generated. Furthermore, data analysis has been enhanced through improved bioinformatic pipelines tailored to each species, including a novel statistical method (KGD) designed specifically for utilising GBS data to develop genomic relationship matrices (Dodds et al., BMC Genomics 16:1047, 2015). Components of the data analysis pipeline are available in a public Github repository (https://github.com/Agresearch). Many studies are in collaboration with universities & research organisations, as well as commercial entities, both nationally and internationally.