Sequencing: the powerhouse of genomic studies
DNA sequencing, especially of the whole genome, has emerged as one of the most useful tools for understanding genomes and genetic variation amongst and between species. Whole genome sequencing is used for generating high-quality reference genomes to serve as a benchmark for comparisons to identify genetic variants from SNPs, to indels, to large structural variants. Sequencing is used for QTL mapping efforts to tie genetic variation to specific traits targeted by breeding programs. Sequencing has also been used to identify and develop the markers to be used for genotyping tools like microarray.
There’s no question that sequencing is a powerhouse of utility for genetics in breeding. However, does it meet the requirements to become a routine tool for genomic selection in breeding programs?
As sequencing technology has matured, it’s become a fast and easy data type to get your hands on. The instrumentation itself can be a little costly, but it is pretty straightforward to access a service provider or set up a sequencing machine in your own facility to capture the 30X coverage that is the gold standard of whole genome sequencing for variant detection projects.
Unfortunately, even though costs have been steadily declining over the past decade or more, sequencing to 30X coverage for every individual in a population is still prohibitively expensive. What this means is that high-coverage sequencing, while extremely useful, is still falling short of the requirements to be used as a routine breeding tool.