Mutations in EID1 and LNK2 caused light-conditional clock deceleration during tomato domestication

Niels A. Müller, Lei Zhang, Maarten Koornneef*, José M. Jiménez-Gómez

*Corresponding author for this work

    Research output: Contribution to journalArticleAcademicpeer-review

    7 Citations (Scopus)

    Abstract

    Circadian period and phase of cultivated tomato (Solanum lycopersicum) were changed during domestication, likely adapting the species to its new agricultural environments. Whereas the delayed circadian phase is mainly caused by allelic variation of EID1, the genetic basis of the long circadian period has remained elusive. Here we show that a partial deletion of the clock gene LNK2 is responsible for the period lengthening in cultivated tomatoes. We use resequencing data to phylogenetically classify hundreds of tomato accessions and investigate the evolution of the eid1 and lnk2 mutations along successive domestication steps. We reveal signatures of selection across the genomic region of LNK2 and different patterns of fixation of the mutant alleles. Strikingly, LNK2 and EID1 are both involved in light input to the circadian clock, indicating that domestication specifically targeted this input pathway. In line with this, we show that the clock deceleration in the cultivated tomato is light-dependent and requires the phytochrome B1 photoreceptor. Such conditional variation in circadian rhythms may be key for latitudinal adaptation in a variety of species, including crop plants and livestock.

    Original languageEnglish
    Pages (from-to)7135-7140
    JournalProceedings of the National Academy of Sciences of the United States of America
    Volume115
    Issue number27
    DOIs
    Publication statusPublished - 3 Jul 2018

    Fingerprint

    domestication
    tomatoes
    mutation
    circadian rhythm
    Solanum lycopersicum
    phytochrome
    photoreceptors
    marker-assisted selection
    livestock
    alleles
    mutants
    genetic variation
    crops
    genes

    Keywords

    • Circadian rhythms
    • Domestication
    • Light signaling
    • Phytochrome
    • Tomato

    Cite this

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    title = "Mutations in EID1 and LNK2 caused light-conditional clock deceleration during tomato domestication",
    abstract = "Circadian period and phase of cultivated tomato (Solanum lycopersicum) were changed during domestication, likely adapting the species to its new agricultural environments. Whereas the delayed circadian phase is mainly caused by allelic variation of EID1, the genetic basis of the long circadian period has remained elusive. Here we show that a partial deletion of the clock gene LNK2 is responsible for the period lengthening in cultivated tomatoes. We use resequencing data to phylogenetically classify hundreds of tomato accessions and investigate the evolution of the eid1 and lnk2 mutations along successive domestication steps. We reveal signatures of selection across the genomic region of LNK2 and different patterns of fixation of the mutant alleles. Strikingly, LNK2 and EID1 are both involved in light input to the circadian clock, indicating that domestication specifically targeted this input pathway. In line with this, we show that the clock deceleration in the cultivated tomato is light-dependent and requires the phytochrome B1 photoreceptor. Such conditional variation in circadian rhythms may be key for latitudinal adaptation in a variety of species, including crop plants and livestock.",
    keywords = "Circadian rhythms, Domestication, Light signaling, Phytochrome, Tomato",
    author = "M{\"u}ller, {Niels A.} and Lei Zhang and Maarten Koornneef and Jim{\'e}nez-G{\'o}mez, {Jos{\'e} M.}",
    year = "2018",
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    language = "English",
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    pages = "7135--7140",
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    Mutations in EID1 and LNK2 caused light-conditional clock deceleration during tomato domestication. / Müller, Niels A.; Zhang, Lei; Koornneef, Maarten; Jiménez-Gómez, José M.

    In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 115, No. 27, 03.07.2018, p. 7135-7140.

    Research output: Contribution to journalArticleAcademicpeer-review

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    T1 - Mutations in EID1 and LNK2 caused light-conditional clock deceleration during tomato domestication

    AU - Müller, Niels A.

    AU - Zhang, Lei

    AU - Koornneef, Maarten

    AU - Jiménez-Gómez, José M.

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    N2 - Circadian period and phase of cultivated tomato (Solanum lycopersicum) were changed during domestication, likely adapting the species to its new agricultural environments. Whereas the delayed circadian phase is mainly caused by allelic variation of EID1, the genetic basis of the long circadian period has remained elusive. Here we show that a partial deletion of the clock gene LNK2 is responsible for the period lengthening in cultivated tomatoes. We use resequencing data to phylogenetically classify hundreds of tomato accessions and investigate the evolution of the eid1 and lnk2 mutations along successive domestication steps. We reveal signatures of selection across the genomic region of LNK2 and different patterns of fixation of the mutant alleles. Strikingly, LNK2 and EID1 are both involved in light input to the circadian clock, indicating that domestication specifically targeted this input pathway. In line with this, we show that the clock deceleration in the cultivated tomato is light-dependent and requires the phytochrome B1 photoreceptor. Such conditional variation in circadian rhythms may be key for latitudinal adaptation in a variety of species, including crop plants and livestock.

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