Sequence aware genotyping improves the accuracy of molecular markers associated with cassava mosaic disease resistance loci

Cassava ( Manihot esculenta ) is a critical food crop for sub-Saharan Africa. Cassava mosaic disease (CMD) caused by cassava geminiviruses, can severely reduce crop yield. Improved host resistance presents the most viable strategy for CMD management, but long breeding cycles constitute a major stumbling block. To ameliorate this challenge, contemporary CMD resistance breeding is highly reliant on marker-assisted selection for the rapid identification of CMD resistance loci in new germplasm. High rates of false discovery (> 30%) limit the efficiency of CMD resistance loci associated molecular markers. Marker-locus recombination and genetic background epistasis are known to exacerbate false discovery, but the contribution of size homoplasy remains understudied. Further, markers loci have been identified in intronic regions of quantitative trail locus (QTL) genes, but the direct impact of marker sequence polymorphism on CMD response phenotype remains undetermined. In this study, sequencing of marker amplicons derived from CMD resistant, tolerant, and susceptible germplasm, revealed the frequent occurrence of size homoplasy associated ambiguities in marker screening. Single nucleotide polymorphisms (SNPs) in marker amplicons were identified which correlated with CMD response phenotype. Elimination of susceptibility associated marker amplicons based on these SNPs reduced false discovery rates by between 15–22%, offering a substantial improvement in CMD resistance breeding efficiency.