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

Abstract

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.

Acknowledgements

This study was supported by the National Natural Science Foundation of China (32072571), the 111 Project (B17043), and the Construction of Beijing Science and Technology Innovation and Service Capacity in Top Subjects (CEFF-PXM2019_014207_000032).

Author contributions

T.L. designed the research, and J.-W.Y. analyzed all the data and conducted experiments. Y.L. performed qRT-PCR experiments. B.L. performed dual-luciferase experiments. Q.-Q.Y., H.-W.L., and J.-C.C. provided technical support. J.-W.Y. and T.L. wrote the manuscript. All authors have discussed the results and the manuscript.

Data Availability

Raw sequence data reported in this study have been deposited in the NCBI Sequence Read Archive under the accession number SRP045767. The RNA-seq data have been deposited under an NCBI BioProject accession PRJNA396272. The complete phenotype data set is also available in ref. 15.

Conflict of Interests

The authors declare no competing interests.

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