1 Preamble

This manual aims at providing a training on the implementation of genomics-enabled decision support for NextGen Cassava Breeding Project and its community of practice partnerships.

Associated with this manual we will provide a codebase and standard operating procedures for a reproducible BreedBase-integrated workflow.

Two major sections are currently planned:

  1. Genomic (Mate) Selection Workflow Example: Using an example dataset from Cassavabase, work hands-on, with demos, over the full workflow. Provide skeleton for each pipeline segment: purpose, SOP, checklist, template, necessary inputs, KPI and outputs.

  2. Data wrangling and reproducibility: Intro and hands-on with the computing and data environment / manipulation side of things. Learning resources/links. No excel! R, Tidyverse, functions, loops, bash / command line, genomic data manipulation programs.

Collectively these two components will support learning Genomic prediction and selection: in practice.

Genomic prediction and selection: in theory

Students also may further need/want to learn the statistical and quantitative genetic theory. An additional section is planned that, at a minimum will provide guidance and access to reading and other learning resources. For starters, (Lynch and Walsh 1998; Falconer and FALCONER 2003; Isik et al. 2017; Bernardo 2020)!