A large deletion within the clock gene
            <i>LNK2</i>
            contributed to the spread of tomato cultivation from Central America to Europe

Mora-Garcı́a, Santiago; Yanovsky, Marcelo J.

doi:10.1073/pnas.1808194115

Cited by 1 publication

(1 citation statement)

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“…Further functional characterization of these variants may enable a better understanding of the genetic basis of phenotypic divergence between domesticated tomatoes and their wild relatives. Previous studies have identified several SVs responsible for phenotypic variation, including a 1.4-kb deletion in the CSR gene resulting in increased fruit weight 28 , a 7.1-kb deletion in the LNK2 locus responsible for a light-conditional clock deceleration 29 , an 85-bp deletion in the promoter of ENO that regulates floral meristem activity 30 and a CNV affecting NSGT associated with biosynthesis of a fruit flavor volatile guaiacol 12 . These SVs were all accurately detected in this study (Supplementary Figs.…”

Section: Extensive Variation Among Wild and Cultivated Tomatoesmentioning

confidence: 99%

Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species

Wang

et al. 2023

Nat Genet

120

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Effective utilization of wild relatives is key to overcoming challenges in genetic improvement of cultivated tomato, which has a narrow genetic basis; however, current efforts to decipher high-quality genomes for tomato wild species are insufficient. Here, we report chromosome-scale tomato genomes from nine wild species and two cultivated accessions, representative of Solanum section Lycopersicon, the tomato clade. Together with two previously released genomes, we elucidate the phylogeny of Lycopersicon and construct a section-wide gene repertoire. We reveal the landscape of structural variants and provide entry to the genomic diversity among tomato wild relatives, enabling the discovery of a wild tomato gene with the potential to increase yields of modern cultivated tomatoes. Construction of a graph-based genome enables structural-variant-based genome-wide association studies, identifying numerous signals associated with tomato flavor-related traits and fruit metabolites. The tomato super-pangenome resources will expedite biological studies and breeding of this globally important crop.

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Section: Extensive Variation Among Wild and Cultivated Tomatoesmentioning

confidence: 99%