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Plant Physiol. 2018 Jul;177(3):1234-1253. doi: 10.1104/pp.18.00259. Epub 2018 May 31.

The Major Origin of Seedless Grapes Is Associated with a Missense Mutation in the MADS-Box Gene VviAGL11.

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Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logrono, Spain.
Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-Centro de Investigación Forestal, INIA-UPM, 28040 Madrid, Spain.
Institut National de la Recherche Agronomique, Centre de Ressources Biologiques de la Vigne, Domaine de Vassal, 34340 Marseillan-Plage, France.
AGAP, Universite Montpellier, CIRAD, Institut National de la Recherche Agronomique, Montpellier SupAgro, 34060 Montpellier, France.
Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario, Sociedad Murciana de Investigación y Tecnología de Uva de Mesa, 30150 La Alberca, Spain.
Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logrono, Spain


Seedlessness is greatly prized by consumers of fresh grapes. While stenospermocarpic seed abortion determined by the SEED DEVELOPMENT INHIBITOR (SDI) locus is the usual source of seedlessness in commercial grapevine (Vitis vinifera) cultivars, the underlying sdi mutation remains unknown. Here, we undertook an integrative approach to identify the causal mutation. Quantitative genetics and fine-mapping in two 'Crimson Seedless'-derived F1 mapping populations confirmed the major effect of the SDI locus and delimited the sdi mutation to a 323-kb region on chromosome 18. RNA-sequencing comparing seed traces of seedless and seeds of seeded F1 individuals identified processes triggered during sdi-determined seed abortion, including the activation of salicylic acid-dependent autoimmunity. The RNA-sequencing data set was investigated for candidate genes, and while no evidence for causal cis-acting regulatory mutations was detected, deleterious nucleotide changes in coding sequences of the seedless haplotype were predicted in two genes within the sdi fine-mapping interval. Targeted resequencing of the two genes in a collection of 124 grapevine cultivars showed that only the point variation causing the arginine-197-to-leucine substitution in the seed morphogenesis regulator gene AGAMOUS-LIKE11 (VviAGL11) was fully linked with stenospermocarpy. The concurrent postzygotic variation identified for this missense polymorphism and seedlessness phenotype in seeded somatic variants of the original stenospermocarpic cultivar supports a causal effect. We postulate that seed abortion caused by this amino acid substitution in VviAGL11 is the major cause of seedlessness in cultivated grapevine. This information can be exploited to boost seedless grape breeding.

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