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Article|08 Jul 2023|OPEN
Genomic basis of selective breeding from the closest wild relative of large-fruited tomato
Junwei Yang1 ,† , Yun Liu1 ,† , Bin Liang1 , Qinqin Yang1 , Xuecheng Li1 , Jiacai Chen1 , Hongwei Li1 , Yaqing Lyu2 and Tao Lin,1 ,
1State Key Laborary of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China
2Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
*Corresponding author. E-mail:
Both authors contributed equally to the study.

Horticulture Research 10,
Article number: uhad142 (2023)
Views: 117

Received: 04 Mar 2023
Revised: 31 Jul 2023
Published online: 08 Jul 2023


The long and intricate domestication history of the tomato (Solanum 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 are 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 (FW), as well as the major haplotypes of fw2.2/cell number regulator (CNR), fw3.2/SlKLUH, and fw11.3/cell size regulator (CSR) in cultivars. Furthermore, 18 loci were found to be significantly associated with FW and six fruit-related agronomic traits in genome-wide association studies. By examining population differentiation, we identified the causative variation underlying 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 the 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.