Fig. 3.

Framework for LAI of cultivated C. canephora. ELAI was performed for each individual chromosome and involved three main steps. Step 1: analyzing the genetic structure of the ancestral group, by performing sNMF on the reference set and tested set. Step 2: simulating source populations based on sNMF-estimated ancestral genotypic frequencies. Step 3: running ELAI on the tested individuals using two marker sets, that is whole-chromosome SNPs and evenly distributed SNPs. Step 4: merging the ancestry dosages inferred in the two SNP sets to determine the final consensus inference of the target chromosome.