Patterns of sequence polymorphism in the fleshless berry locus in cultivated and wild Vitis vinifera accessions

<p>Abstract</p> <p>Background</p> <p>Unlike in tomato, little is known about the genetic and molecular control of fleshy fruit development of perennial fruit trees like grapevine (<it>Vitis vinifera </it>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 <it>fleshless berry </it>mutation (<it>flb</it>) in order, first to identify SNP markers closely linked to the gene and second to search for possible signatures of domestication.</p> <p>Results</p> <p>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 <it>V. vinifera cv</it>. Chardonnay and a genotype carrying the <it>flb </it>mutation, <it>V. vinifera cv</it>. 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 <it>flb </it>could be one of the genes involved into the domestication syndrome of grapevine, we sequenced 69 gene fragments, spread over the <it>flb </it>region, representing 48,874 bp in a highly diverse set of cultivated and wild <it>V. vinifera </it>genotypes, to identify possible signatures of domestication in the cultivated <it>V. vinifera </it>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 <it>flb </it>region.</p> <p>Conclusions</p> <p>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 <it>flb </it>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 <it>flb </it>gene in a F2 population when available.</p

High throughput SNPs discovery in grapevine, poplar and tomato

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Association genetics in relation with berry size variation in grapevine (Vitis vinifera)

International audienceBerry size is an important trait both for yield (table grapes) and in relation to quality (wine grapes). The final size of an organ is dependent on cell number, cell size and/or number of carpel. Indeed it has been shown that cell number is a major determinant of fruit size variability in Solanaceae and Prunus, whereas a preliminary study on a small sample of grapevine genotypes suggested that the variability of berry size resulted from cell volume enlargement. At present only few genes involved in fruit size variation have been identified, mainly in Solanaceae and none in grapevine. Our aims are: (1) to check, in a large sample of grapevine genotypes, the relative importance of cell volume enlargement, number of cell and carpel in berry size variation, (2) to develop association genetics approaches with candidate genes for berry size and (3) to study the DNA polymorphism along the region carrying the fleshless berry locus (flb) in order to detect possible selection pressures in cultivated varieties. The flb locus was identified in a grapevine natural mutant which present berries with a size reduced by 20 times and circular seeds similar to wild grapevine berries. The ovaries and the berries of 3 subpopulations of cultivated Vitis vinifera genotypes (279), which represent the genetic and phenotypic variability of berry size, have been phenotyped. Preliminary results on a small sample of individual (27) suggested that the final berry size was determined at early stage of berry development. The ovarian size just before fertilization was variable and proportional to the final berry size. However the ovarian cell number or size seemed to explain the final berry size differently according to sub-populations. Several mechanisms and probably several genes would be involved in the variation of the berry size in these sub-populations. These data are currently under validation on the whole set of 279 individuals. In parallel, 44 candidate genes, orthologous to genes known to be involved in flower or fruit development and/or co-localizing with berry size QTLs (Quantitative Trait Locus) and/or expressed during grapevine berry development, have been partially or totally sequenced in 47 genotypes which reflect all the genetic diversity of grapevine. Several thousands of SNPs (Single Nucleotide Polymorphims) have been identified. A subset of these SNPs will be used for genotyping the 3 sub-populations using the SNPlex technology, in order to detect a possible correlation between genotypic and phenotypic variation. Finally, in order to test the hypothesis that flb is one of the genes selected during grapevine domestication, 69 gene fragments along flb locus (1Mbp) were sequenced in a sample of wild and cultivated Vitis vinifera. Our results revealed a small zone showing more polymorphism in wild genotypes than in cultivated genotypes and a large zone of 171Kb showing either more polymorphism in cultivated genotypes than in wild genotypes. These intervals will be studied more in details using two approaches: gene expression studies and an improvement of the genotype sampling for the DNA polymorphism studies