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Breeding in the CGIAR Research Program on Roots, Tubers and Bananas (RTB) targets highly diverse biotic and abiotic constraints, whilst meeting complex end-user quality preferences to improve livelihoods of beneficiaries in developing countries. Achieving breeding targets and increasing the rate of genetic gains for these vegetatively propagated crops, with long breeding cycles, and genomes with high heterozygosity and different ploidy levels, is challenging. Cheaper sequencing opens possibilities to apply genomics tools for complex traits, such as yield, climate resilience, and quality traits. Therefore, across the RTB program, genomic resources and approaches, including sequenced draft genomes, SNP discovery, quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS), are at different stages of development and implementation. For some crops, marker-assisted selection (MAS) is being implemented, and GS has passed the proof-of-concept stage. Depending on the traits being selected for using prediction models, breeding schemes will most likely have to incorporate both GS and phenotyping for other traits into the workflows leading to varietal development.