Will benchtop sequencers resolve the sequencing trade-off in plant genetics?

Abstract

An important experimental design consideration in plant genetics is the trade-off between number of individuals and number of loci that can be genotyped (Davey et al., 2011). For any given study, an investigator must choose how they partition research effort and resources, with the generation of many loci usually coming at the expense of many individuals, and vice versa. For example, for parentage and paternity analysis it is usually more important to sample many individuals (e.g., Andrew et al., 2013), while for comparative genome evolution the emphasis is firmly placed on recovering more loci (Figure 1). This trade-off still exits despite the plummeting costs of sequence data, with researchers having to decide the number of individuals feasible for a given sequencing strategy, and how the libraries will be multiplexed across lanes of a next generation sequencing (NGS) platform (Shen et al., 2011).