Fig. 2

Differentiation and genomic regions under selection among the PIM, CER and BIG groups detected using the EigenGWAS method. A–D Candidate domestication (217; top 5%, −log₁₀ P value ≥ 2.98) (A) and improvement (280; top 5%, −log₁₀ P value ≥ 4.19) sweeps (B) using EigenGWAS. The orange and green bars above the chromosomes represent the domestication and improvement sweeps identified using the nucleotide diversity (𝜋) method. Candidate genes or quantitative trait loci (QTL) previously reported or identified are marked with different colors. Genes or QTLs marked in red are those detected by the EigenGWAS and 𝜋 methods. Genes or QTLs marked in black are within or surrounding the EigenGWAS peaks. The intersection and union of domestication genes (C) and improvement genes (D) were identified by EigenGWAS and 𝜋 method. E–J Local Manhattan plots for single marker GWAS signals (black dots) and 100-kb sliding window GWAS signals (green triangles) of methyl salicylate (E), neorickiioside B (F), and esculeoside A (I). Genomic distribution of 𝜋 of the PIM (green), CER (orange), and BIG (blue) groups for S-adenosyl-L-methionine: salicylic acid carboxyl methyltransferase (SlSAMT) in chromosome 9 during domestication (G), GLYCOALKALOID METABOLISM 9 (GAME9) in chromosome 1 (H), and GORKY (Solyc03g120570) in chromosome 3 (J) during improvement. K Schematic representation of the core steroidal glycoalkaloid (SGA) metabolic pathway from cholesterol to esculeoside A. Genes in orange and green colors are the domestication and improvement genes, respectively