est destinée au dépôt

Multilocus SNPs analysis allows phylogenetic assignation of DNA fragments to decipher the interspecific mosaic genome structure of cultivated citrus

Franck Curk, Gema Ancillo, Andres Garcia-Lor, Luro François, Luis Navarro,

Patrick Ollitrault

To cite this version:

Franck Curk, Gema Ancillo, Andres Garcia-Lor, Luro François, Luis Navarro, et al.. Multilocus SNPs analysis allows phylogenetic assignation of DNA fragments to decipher the interspecific mosaic genome structure of cultivated citrus. Plante genome evolution, Sep 2011, Amsterdam, Netherlands. 2011.

hal-02746454

Comment citer ce document : Curk, F., Ancillo, G., Garcia-Lor, A., Luro, F., Navarro, L., Ollitrault, P. ( 2011). Multilocus SNPs analysis allows phylogenetic assignation of DNA fragments to decipher the interspecific mosaic genome structure of cultivated citrus. Presented at Plante genome evolution, Amsterdam, NLD (2011-09-04 -2011-09-06).

Multilocus SNPs Analysis Allows Phylogenetic Assignation of DNA Fragments to Decipher the Interspecific Mosaic Genome Structure of Cultivated Citrus

Curk F. (1,2) , Ancillo G. (2) , Garcia-Lor A. (2) , Luro F. (1) , Navarro L. (2) and Ollitrault P. (3,2) ( Moreover we checked the potential of parallel pyrosequencing (454 Roche) for direct multilocus haplotyping of heterozygous genotypes. Amplified fragments from 7 genes in 8 genotypes of Citrus were obtained by using an original new method based on universal primers (Figure 2).

C. clementina (clementine) was used as model for secondary species. Each haplotype sequence of Clementine was univocally assigned to one of the haplotype clusters of the basic taxa.

As an example, we can see with the Figure 5 (NJ tree of the locus 5.5) that both haplotypes belong to the Mandarin group. For each gene an ACP was performed from SNP data to analyze the genetic organization (e.g. Figure 3).

It was assumed that intermediary position between two species cluster corresponded to interspecific heterozygosity

For each amplified fragment, the polymorphism was enough for multilocus differentiation of the basic species and assignation of a phylogenetic origin for the secondary species. A preliminary reconstitution of phylogenetic structure of the chromosome 3 is proposed for clementine, sweet orange, sour-orange, grapefruit, lime and lemon (figure 4). However only haplotype analysis would allow definitive assignment. A Parallel pyrosequencing (454 Roche) for multilocus haplotyping of heterozygous genotypes has been done…

  Figure 1: Origin of the Modern Cultivars of Citrus

Figure 2 :

 2 Figure 2: Fragment Amplification Using Universal M13 Primers

Figure

  Figure 5: Neighbor Joining Tree of Locus 5.5 Haplotypes

Figure 6 :

 6 Figure 6: Neighbor Joining Tree of Locus 9.2 Haplotypes

Figure

  Figure 3: ACP, Phylogenetic Assignation of the Sequenced Fragments of the Locus 5.5