Towards a Methylation Chip and the Way Forward for Genotyping

Recent years have seen impressive progress in the ability to improve the rate of genetic gain through the use of SNP chips. However, the expression of a gene is not solely defined by the DNA sequence, and it is becoming clear that simply knowing nucleotide changes does not provide the full picture for predicting downstream animal production. Over the last decade, the importance of epigenetics (including DNA methylation) in regulating gene expression and phenotype has become apparent, even though mechanisms of action remain elusive. Here we report our progress on the development of an Illumina Infinium Methylation chip for sheep.

In addition, to developing a suite of array based genotyping tools, AgResearch has also invested in genotyping by sequencing (GBS) methods. High-throughput GBS methodology produces SNP genotypes that are supported by varying depth of sequence reads, dependent on the number of samples and proportion of the genome assayed within a lane of sequencing.  A recently-developed algorithm produces bias free genomic relationship matrices, based on allele read depths, which can be interrogated to estimate: breed composition, pedigree, traceability, inbreeding and co-ancestry as well as be included directly in existing mixed models to estimate breeding values. The GBS pipeline is cost competitive compared to array based technologies and offers the potential to eliminate ascertainment bias. Its disadvantage is the requirement for high quality DNA, however, this can be overcome by appropriate sample collection, storage and extraction methods at minimal cost.