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France: Postdoctoral Positions in Fine Mapping of Linkage Disequilibrium (LD) in Grapevine (Vitis Vinifera) at INRA Montpellier

Association genetics is expected to significantly enhance our knowledge of the genetic basis of complex traits of agronomical interest, particularly for perennial species such as grapevine, for which QTL results are still very few and progeny studies are heavy.

Thanks to the recombinations already accumulated in genetic resources, it is possible to test for the association between the phenotypic variability of traits and the polymorphism of either candidate genes or markers spread all over the genome, depending on the extent and structure of LD (Thornsberry et al 2001, Werner et al 2005, Zhang et al 2005, Breseghello et Sorrells 2006). Detailed knowledge of LD is required before association genetic studies can be performed.

Data on LD in V. vinifera are still scarce. Our group obtained a first estimation of LD within a core-collection, for SSR markers at the scale of a few cM in 5 genome regions (Barnaud et al 2006). Preliminary association genetics studies are under way in our group on the same core-collection to test for candidate genes for berry composition in flavonoïds (Fournier-Level 2006, This et al 2007, L. Lecunff comm. pers.). These first results show that LD between SSRs extends over 15 cM, whereas it is not significant between SNPs of adjacent regions within genes. Moreover, we will build a SNPs/indels diversity map (SNPGrapMap project), by sequencing 2000 fragments of 1.5 kb distributed over the whole genome for 48 plants. Lastly, our group showed that V. vinifera diversity is structured in 7 ancestral populations of cultivated plants and 1 ancestral population of wild plants (subsp. silvestris) from France and Italie (Di Vecchi Staraz 2007). Differences in the amount of recombination are expected between these populations, and therefore also for LD extent : low LD extent in silvestris (Barnaud 2003), Atlantic population genetically close to silvestris, strong familial structure for Chasselas and Muscat populations.

The objective of the post-doc is to answer the following questions in order to optimize association genetics analyses in grapevine : is LD structured in blocks as in the human genome ? What marker type and density should be used for association tests ? Is it possible to find populations with contrasted LD extent ? For this goal, we propose to finely characterize LD between SSRs and SNPs in specific genomic regions, within 2 populations expected to differ for LD extent.

After choosing the 2 populations, defining samples of about 100 plants per population, and choosing 2 genomic regions of about 200 kb each including QTLs for traits of interest, about 50 SSRs and 50 SNPs will be selected among the polymorphic markers yielded by the SNPGrapMap project, to be densely distributed within each region. SSRs and SNPs will be genotyped in multiplex on a capillary automatic sequencer. Haplotypes will be reconstructed, and the structure of genotypic and haplotypic LD estimated by different statistical methods already used in our group (softwares Phase, Structure, Tassel, GDA, …).

Latest publications of the scientific supervisor :

  1. Barnaud A, Lacombe T, Doligez A (2006) Linkage disequilibrium in cultivated grapevine, Vitis vinifera L. Theoretical and Applied Genetics 112:708-716
  2. Doligez A, Adam-Blondon AF, Cipriani G, Di Gaspero G, Laucou V, Merdinoglu D, Meredith CP, Riaz S, Roux C, This P (2006) An integrated SSR map of grapevine based on five mapping populations. Theoretical and Applied Genetics 113:369-382
  3. Doligez A, Audiot E, Baumes R, This P (2006) QTLs for muscat flavor and monoterpenic odorant content in grapevine (Vitis vinifera L.). Molecular Breeding 18:109-125
  4. Fernandez L, Doligez A, Lopez G, Thomas MR, Bouquet A, Torregrosa L (2006) Somatic chimerism, genetic inheritance, and mapping of the fleshless berry (flb) mutation in grapevine (Vitis vinifera L.). Genome 49:721-728
  5. Riaz S, Doligez A, Henry RJ, Walker MA (2007) Grape. In: Genome mapping and molecular breeding in plants, vol. 4 Fruits and Nuts (Kole C ed.), Springer-Verlag, Berlin Heidelberg, pp 63-101

Administrative details :
Please visit the website.



Ref: P-GAP-3

INRA Montpellier, France
UMR DIA-PC (1097) (head: S Hamon, serge.hamon@mpl.ird.fr)
Equipe Génétique Vigne (head: P This, patrice.this@supagro.inra.fr)

Scientific supervisor and contact for the post-doc position:
A Doligez, agnes.doligez@supagro.inra.fr
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