Genomic basis of selective breeding from the closest wild relative of large-fruited tomato

Abstract

The long and intricate domestication history of the tomato (S. lycopersicum) includes selection sweeps that have not been fully explored, and these sweeps show significant evolutionary trajectories of domestication traits. Using three distinct selection strategies, we represented comprehensive selected sweeps from 53 Solanum pimpinellifolium (PIM) and 166 S. lycopersicum (BIG) accessions, which is defined as pseudo-domestication in this study. We identified 390 potential selection sweeps, some of which had a significant impact on fruit-related traits and were crucial to the pseudo-domestication process. During tomato pseudo-domestication, we discovered a minor-effect allele of the SlLEA gene related to fruit weight, as well as the major haplotypes of fw2.2/CNR (Cell Number Regulator), fw3.2/SlKLUH, fw11.3/CSR (Cell Size Regulator) in cultivars. Furthermore, 18 loci were found to be significantly associated with fruit weight and six fruit-related agronomic traits in genome-wide association studies. By examining population differentiation, we identified the causative variation underline the divergence of fruit flavonoids across the large-fruited tomatoes, and validated BRI1-EMS-SUPPRESSOR 1.2 (SlBES1.2), a gene that may affect flavonoid content by modulating MYB12 expression profile. Our results provide new research routes for the genetic basis of fruit traits and excellent genomic resources for tomato genomics-assisted breeding.