title: Haplotype diversity of VvTFL1A gene and association with cluster traits in grapevine (V. vinifera).
abstract: BACKGROUND
  Interaction between TERMINAL FLOWER 1 (TFL1) and LEAFY (LFY) seem to determine the inflorescence architecture in Arabidopsis. In a parallel way, overexpression of VvTFL1A, a grapevine TFL1 homolog, causes delayed flowering and production of a ramose cluster in the reiterated reproductive meristem (RRM) somatic variant of cultivar Carignan. To analyze the possible contribution of this gene to cluster phenotypic variation in a diversity panel of cultivated grapevine (Vitis vinifera L. subsp. vinifera) its nucleotide diversity was characterized and association analyses among detected sequence polymorphisms and phenology and cluster traits was carried out.
  
  
  RESULTS
  A total of 3.6 kb of the VvTFL1A gene, including its promoter, was sequenced in a core collection of 140 individuals designed to maximize phenotypic variation at agronomical relevant traits. Nucleotide variation for VvTFL1A within this collection was higher in the promoter and intron sequences than in the exon regions; where few polymorphisms were located in agreement with a high conservation of coding sequence. Characterization of the VvTFL1A haplotype network identified three major haplogroups, consistent with the geographic origins and the use of the cultivars that could correspond to three major ancestral alleles or evolutionary branches, based on the existence of mutations in linkage disequilibrium. Genetic association studies with cluster traits revealed the presence of major INDEL polymorphisms, explaining 16%, 13% and 25% of flowering time, cluster width and berry weight, respectively, and also structuring the three haplogroups.
  
  
  CONCLUSIONS
  At least three major VvTFL1A haplogroups are present in cultivated grapevines, which are defined by the presence of three main polymorphism LD blocks and associated to characteristic phenotypic values for flowering time, cluster width and berry size. Phenotypic differences between haplogroups are consistent with differences observed between Eastern and Western grapevine cultivars and could result from the use of different genetic pools in the domestication process as well as different selection pressures on the development of table and wine cultivars, respectively. Altogether, these results are coherent with previous classifications of grapevine phenotypic diversity mainly based on cluster and berry morphotypes as well as with recent results on the structure of genetic diversity in cultivated grapevine.
authors.forename: Lucie
authors.initials: L
authors.lastname: Fernandez
authors.forename: Loïc
authors.initials: L
authors.lastname: Le Cunff
authors.forename: Javier
authors.initials: J
authors.lastname: Tello
authors.forename: Thierry
authors.initials: T
authors.lastname: Lacombe
authors.forename: Jean Michel
authors.initials: JM
authors.lastname: Boursiquot
authors.forename: Alexandre
authors.initials: A
authors.lastname: Fournier-Level
authors.forename: Gema
authors.initials: G
authors.lastname: Bravo
authors.forename: Sandrine
authors.initials: S
authors.lastname: Lalet
authors.forename: Laurent
authors.initials: L
authors.lastname: Torregrosa
authors.forename: Patrice
authors.initials: P
authors.lastname: This
authors.forename: José Miguel
authors.initials: JM
authors.lastname: Martinez-Zapater
mesh_terms: D035263:Flowering Tops / Q000502:physiology*; D017343:Genes, Plant; D006239:Haplotypes; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA; D027843:Vitis / Q000235:genetics*
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