Abstract
BackgroundUnlike 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.ResultsIn 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.ConclusionsWe 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.
Highlights
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.)
A 1 Mb region at the top of chromosome 18 is homozygous in Ugni Blanc and the fleshless berry mutant The flb mutation was localised by Fernandez et al [21] at the top of chromosome 18, above the markers VMC2A3 and VMC8B5 on the consensus map of a progeny of Chardonnay by Ugni Blanc mutant
The flb locus was mapped indirectly relative to VMC2A3 that segregated in Chardonnay and not in Ugni Blanc mutant
Summary
Little is known about the genetic and molecular control of fleshy fruit development of perennial fruit trees like grapevine (Vitis vinifera L.). The physiological mechanisms involved have been related to the control of (i) the cell number in the pericarp, as for the fw2.2 locus [9,2,10], (ii) the locule number [2,11], (iii) the late endo-reduplication in pericarp cells [12,10] and (iv) the cell wall plasticity in relation to the cell expansion [10] All these advances in tomato are useful to assist the study of similar trait in other crops with fleshy fruits, less amenable to genetic studies, such as perennial fruit trees. The degree of transferability of knowledge from tomato to non-Solanaceae species remains an open question
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