The Effects of Restriction-Enzyme Choice on Properties of Genotyping-by-Sequencing Libraries: A Study in Cassava (Manihot esculenta)

Abstract

Compared with other reduced-representation sequencing methods, library construction for genotyping-by-sequencing (GBS) is simpler and less expensive. However, elimination of size-selection steps results in libraries of more variable fragment size than with other reduced-representation methods, affecting several aspects of the data. To test the effect of restriction enzyme choice on library quality, the authors made GBS libraries with PstI (6-cutter), PstI/TaqI (4-cutter), or ApeKI (4.5-cutter) from the same set of DNAs from a cassava biparental population. This work is part of the “Next Generation Cassava Breeding Project” which is supported by the UK Department for International Development, in partnership with the Bill & Melinda Gates Foundation