Assembly of a training population (TP) is an important component of effective genomic selection‐based breeding programs. In this study, we examined the power of diverse germplasm assembled from two cassava (Manihot esculenta Crantz) breeding programs in Tanzania at different breeding stages to predict traits and discover quantitative trait loci (QTL). This is the first genomic selection and genome‐wide association study (GWAS) on Tanzanian cassava data. We detected QTL associated with cassava mosaic disease (CMD) resistance on chromosomes 12 and 16; QTL conferring resistance to cassava brown streak disease (CBSD) on chromosomes 9 and 11; and QTL on chromosomes 2, 3, 8, and 10 associated with resistance to CBSD for root necrosis. We detected a QTL on chromosome 4 and two QTL on chromosome 12 conferring dual resistance to CMD and CBSD. The use of clones in the same stage to construct TPs provided higher trait prediction accuracy than TPs with a mixture of clones from multiple breeding stages. Moreover, clones in the early breeding stage provided more reliable trait prediction accuracy and are better candidates for constructing a TP. Although larger TP sizes have been associated with improved accuracy, in this study, adding clones from Kibaha to those from Ukiriguru and vice versa did not improve the prediction accuracy of either population. Including the Ugandan TP in either population did not improve trait prediction accuracy. This study applied genomic prediction to understand the implications of constructing TP from clones at different breeding stages pooled from different locations on trait accuracy.

https://dx.doi.org/10.1002/csc2.20003

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Ismail Rabbihttps://orcid.org/0000-0001-9966-2941

Chiedozie Egesihttps://orcid.org/0000-0002-9063-2727

Jean-Luc Janninkhttps://orcid.org/0000-0003-4849-628X

https://dx.doi.org/10.1002/csc2.20003

Biotech and Plant Breeding

Agronomy; Cassava; Disease Control; Food Security; Genetic Improvement; Plant Breeding; Plant Diseases; Plant Genetic Resources; Plant Production

Cassava; Breeding; African Cassava Mosaic Virus; Food Security; Germplasm; Genomics

Africa; East Africa

Tanzania; Uganda

Eastern Africa Hub

Crop Science