Leveraging low-cost short-read sequencing: revolutionizing complex trait genetics

The genetics of complex traits has been fundamentally transformed by the dramatic reduction in short-read sequencing costs, leading to a dramatic reversal in the relative costs of genotyping versus phenotyping. We explore this new scientific landscape by examining key experimental strategies that leverage inexpensive sequencing, including low-coverage whole-genome sequencing with imputation (lcWGS + I) for genotyping large cohorts. Although somewhat limited in outbred populations, lcWGS + I can be extremely effective in multiparent populations and in founder-unknown closed colonies, where imputation accuracy can exceed 98%. We further explore pooled-sequencing approaches for dissecting complex traits, such as Evolve and Resequence for tracking adaptive changes in allele frequency over several generations, and extreme quantitative trait loci mapping that identifies loci by contrasting pooled samples from phenotypic extremes. We show that extreme quantitative trait loci mapping in multiparent populations, by testing for shifts in founder haplotype frequencies across small genomic windows, can be extremely powerful and cost-effective. Finally, we discuss methods where sequencing reads serve as the phenotype itself. DNA barcoding enables massive-scale fitness assays, while the "*-seq" toolkit (e.g. RNA-seq, ATAC-seq) allows for mapping molecular quantitative trait loci, though this introduces a significant multiple testing burden. Systems leveraging certain breeding designs in concert with low cost sequencing can greatly accelerate progress toward a mechanistic understanding of the genotype-phenotype relationship.