Figure 6.

Diagram of proposed two-stream GS breeding program. Stream 1 (yellow boxes) consists of pre-breeding, in which favorable alleles from exotic germplasm are introduced into adapted germplasm. Exotic parents are crossed with elite germplasm to develop Breeding Population 1. Selection of individuals from Breeding Population 1 is performed using a combination of GS + de novo GWAS models (GS+), in which the exotic QTL are fit as fixed effects, and phenotype. The training population GS would be a subset of breeding population 1, that is, a fraction of breeding population 1 would be both genotyped and phenotyped, while the rest of breeding population 1 would be genotyped only. Adapted materials from Breeding Population 1 are crossed into Breeding Population 2 (Stream 2, blue boxes) where they are further refined using GS + de novo GWAS models, where the fixed effects would include valuable QTL identified based on GWAS performed in Breeding Population 2, the exotic QTL from Stream 1, or any other large effect QTL a breeder might normally target for trait improvement. Output from Stream 2 can be advanced toward variety release or fed back into Stream 1 to serve as parents for further crossing and population development.