Reducing false discovery rate for cassava mosaic disease resistance associated molecular markers.

Breeding for cassava mosaic disease (CMD), an economically important disease caused by cassava geminiviruses, remains reliant on three canonical resistance loci, CMD1, CMD2 and CMD3. A high false discovery rate (FDR~20%) has been observed for the molecular markers associated with these loci, which reduces breeding efficiency. Elimination of size homoplasy induced genotyping errors provides a potential method for FDR reduction without marker replacement. While instances of size homoplasy between susceptibility and resistance associated marker alleles/amplicons have been noted for CMD resistance markers, the contribution of size homoplasy to marker FDR remains understudied. This study sought to investigate the prevalence of size homoplasy induced error in CMD marker screening.