In an initial study, promising results regarding the prediction of genetic variance in cassava crosses convinced us to pursue genomic mate selection in practice. In that study, we used a high-quality validated pedigree-based and a custom pedigree-informed phasing pipeline with a custom genetic map for the analyses.
In this workflowr project, I am integrating cross-variance predictions into our current genomics-enabled breeding pipeline leveraging all available data. I conduct additional tests to assess whether current Beagle imputed-and-phased data and a basic pedigree-validation step are sufficient. I also further develop functions to make automating all the steps in the process easier.
This project should for the template for genomic mate selection in NextGen Cassava.
We will immediately implement in summer 2021 with IITA GS C5.