Genome assembly of nine wild species and two domesticated accessions of tomato generated a super-pangenome for the tomato clade. Comparative analyses revealed the landscape of structural variations in wild and cultivated tomatoes and led to the discovery of a wild tomato gene that has the potential for yield increase in modern breeding.
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References
Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485, 635–641 (2012). This paper reports the genome sequence of domesticated tomato and a draft sequence for its closest wild relative.
Szymański, J. et al. Analysis of wild tomato introgression lines elucidates the genetic basis of transcriptome and metabolome variation underlying fruit traits and pathogen. response. Nat. Genet. 52, 1111–1121 (2020). This paper identifies genes and loci associated with fruit quality traits and pathogen response by using wild tomato introgression (backcrossed) lines.
Zamir, D. Improving plant breeding with exotic genetic libraries. Nat. Rev. Genet. 2, 983–989 (2001). An opinion article that recommends the utilization of wild species introgression lines to improve the agricultural performance of modern crop varieties.
Khan, A. W. et al. Super-pangenome by integrating the wild side of a species for accelerated crop improvement. Trends Plant Sci. 25, 148–158 (2020). This opinion article indicates the need for super-pangenomes that include wild species and their application for crop improvement.
Gao, L. et al. The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nat. Genet. 51, 1044–1051 (2019). This paper reports a tomato pan-genome, constructed from genome sequences of 725 tomato accessions, that captures 4,873 genes absent from the reference genome and identifies a rare TomLoxC allele regulating fruit flavor.
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This is a summary of: Li, N. et al. Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species. Nat. Genet. https://doi.org/10.1038/s41588-023-01340-y (2023).
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Tomato super-pangenome highlights the potential use of wild relatives in tomato breeding. Nat Genet 55, 744–745 (2023). https://doi.org/10.1038/s41588-023-01341-x
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DOI: https://doi.org/10.1038/s41588-023-01341-x
