Long-term realized genetic gain and population dynamics under genomic selection in Brazilian cassava germplasm

Abstract

Genomic selection has become an important strategy in cassava breeding, enabling faster selection cycles and sustained genetic progress. Despite its widespread adoption, long-term evaluations integrating predictive performance, realized genetic gain, and genetic diversity remain scarce, particularly in clonally propagated crops. We present a comprehensive assessment of genomic selection outcomes in the Brazilian cassava breeding program across four recurrent selection cycles (C0 to C3) implemented between 2011 and 2024, using historical phenotypic and genomic data from 210 multi-environment trials. Predictive ability of genomic best linear unbiased prediction models ranged from low to moderate, depending on the traits genetic architecture and heritability. Prediction accuracies were highest in early cycles (C0 and C1) and showed modest declines in later cycles (C2 and C3). Root yield, shoot yield, plant height, starch content, and dry matter content exhibited stable predictive performance across cycles, with a gradual reduction in RMSE, indicating improved model calibration as training populations expanded. Regression analyses of genomic estimated breeding values revealed significant realized genetic gains for most yield-related traits. In contrast, dry matter content and starch content exhibited small, non-significant negative trends, consistent with known unfavorable genetic correlations with yield. Targeted reductions in plant architecture scores reflected deliberate selection for ideotypes suited to mechanized production systems. At the same time, analyses of genetic diversity revealed a slight decrease in observed heterozygosity, with higher values in the most advanced selection cycle. These results provide an integrated framework for monitoring predictive performance, realized genetic gain, and population genetic dynamics under long-term genomic selection. Collectively, they offer valuable insights into balancing short-term genetic improvement with long-term sustainability and support the development of strategies to optimize selection decisions, breeding planning, and population management in Brazilian cassava breeding programs.