title: Patterns of sequence polymorphism in the fleshless berry locus in cultivated and wild Vitis vinifera accessions.
abstract: BACKGROUND
  Unlike in tomato, little is known about the genetic and molecular control of fleshy fruit development of perennial fruit trees like grapevine (Vitis vinifera L.). Here we present the study of the sequence polymorphism in a 1 Mb grapevine genome region at the top of chromosome 18 carrying the fleshless berry mutation (flb) in order, first to identify SNP markers closely linked to the gene and second to search for possible signatures of domestication.
  
  
  RESULTS
  In total, 62 regions (17 SSR, 3 SNP, 1 CAPS and 41 re-sequenced gene fragments) were scanned for polymorphism along a 3.4 Mb interval (85,127-3,506,060 bp) at the top of the chromosome 18, in both V. vinifera cv. Chardonnay and a genotype carrying the flb mutation, V. vinifera cv. Ugni Blanc mutant. A nearly complete homozygosity in Ugni Blanc (wild and mutant forms) and an expected high level of heterozygosity in Chardonnay were revealed. Experiments using qPCR and BAC FISH confirmed the observed homozygosity. Under the assumption that flb could be one of the genes involved into the domestication syndrome of grapevine, we sequenced 69 gene fragments, spread over the flb region, representing 48,874 bp in a highly diverse set of cultivated and wild V. vinifera genotypes, to identify possible signatures of domestication in the cultivated V. vinifera compartment. We identified eight gene fragments presenting a significant deviation from neutrality of the Tajima's D parameter in the cultivated pool. One of these also showed higher nucleotide diversity in the wild compartments than in the cultivated compartments. In addition, SNPs significantly associated to berry weight variation were identified in the flb region.
  
  
  CONCLUSIONS
  We observed the occurrence of a large homozygous region in a non-repetitive region of the grapevine otherwise highly-heterozygous genome and propose a hypothesis for its formation. We demonstrated the feasibility to apply BAC FISH on the very small grapevine chromosomes and provided a specific probe for the identification of chromosome 18 on a cytogenetic map. We evidenced genes showing putative signatures of selection and SNPs significantly associated with berry weight variation in the flb region. In addition, we provided to the community 554 SNPs at the top of chromosome 18 for the development of a genotyping chip for future fine mapping of the flb gene in a F2 population when available.
authors.affiliation: Unité mixte de Recherche en Génomique Végétale (URGV), INRA UEVE ERL CNRS, 2 rue Gaston Crémieux, 91 057 Evry cedex, France. houel@evry.inra.fr
authors.forename: Cléa
authors.initials: C
authors.lastname: Houel
authors.forename: Rémi
authors.initials: R
authors.lastname: Bounon
authors.forename: Jamila
authors.initials: J
authors.lastname: Chaïb
authors.forename: Cécile
authors.initials: C
authors.lastname: Guichard
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Péros
authors.forename: Roberto
authors.initials: R
authors.lastname: Bacilieri
authors.forename: Alexis
authors.initials: A
authors.lastname: Dereeper
authors.forename: Aurélie
authors.initials: A
authors.lastname: Canaguier
authors.forename: Thierry
authors.initials: T
authors.lastname: Lacombe
authors.forename: Amidou
authors.initials: A
authors.lastname: N'Diaye
authors.forename: Marie-Christine
authors.initials: MC
authors.lastname: Le Paslier
authors.forename: Marie-Stéphanie
authors.initials: MS
authors.lastname: Vernerey
authors.forename: Olivier
authors.initials: O
authors.lastname: Coriton
authors.forename: Dominique
authors.initials: D
authors.lastname: Brunel
authors.forename: Patrice
authors.initials: P
authors.lastname: This
authors.forename: Laurent
authors.initials: L
authors.lastname: Torregrosa
authors.forename: Anne-Françoise
authors.initials: AF
authors.lastname: Adam-Blondon
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics*; D056426:Genetic Loci / Q000235:genetics; D014644:Genetic Variation; D005838:Genotype; D017404:In Situ Hybridization, Fluorescence; D015810:Linkage Disequilibrium; D018895:Microsatellite Repeats / Q000235:genetics; D009154:Mutation; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide; D013045:Species Specificity; D026801:Synteny; D027843:Vitis / Q000145:classification / Q000235:genetics*