Low pass genome sequencing along with genotype imputation has been shown as a cost-effective alternative to genotyping arrays for trait mapping in the agriculture field. While research has shown the feasibility of driving down the sequencing depth to 1x or 0.5x, coverage uniformity throughout the genome and low coverage of important trait sites usually makes it challenging to increase sample numbers in each sequencing run to further drive down sequencing depth. To resolve this, additional target capture library preparations to enrich the interest sites can provide valuable information when combined with low pass sequencing. However, these additional library preparation processes are usually costly and complex. Recently, we explored the application of a probe-specific flow cell to enable low pass sequencing and selected enrichment simultaneously, using a standard whole genome sequencing library.
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