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1. Effect of migrations and breeding on the organization of maize genetic diversity

1.1   Molecular polymorphism in maize germplasm

New technologies of genotyping and sequencing offer new opportunities for genetic studies. We contribute to the development of new methods and tools such as:

  • the first 50k SNP chip (collaborative project, Ganal et al., 2011, Plos one). We used this chip to genotype of around 1200 maize lines, 250 landraces and 230 Highly Recombinant Inbred Lines.
  • the discovery of new polymorphisms such as SNPs or indels or more complex ones as CNVs in collaboration with ABI and GEAR teams. To discover these new polymorphisms, we achieved deep reseqencing of 5 inbred lines including the French reference line Fv2 (projects Amaizing and CNV-maize) and of 120 lines at a lower depth (projects Amaizing, http://www.amaizing.fr/, and Cornfed).

 

1.2   Consequences of evolution and breeding on the organization of genetic diversity

We aim at deciphering how evolution and modern breeding shaped the genetic diversity.

  • Following our previous studies on traditional maize varieties in Europe (Tenaillon & Charcosset, 2011, C R Biol), we extended our research to Asia and Africa within an international cooperation (Generation Challenge Program). More than 800 landraces were genotyped to evaluate the contribution of American maize genetic groups to the world diversity, hybridization areas were pointed out (Mir et al., 2013, Theor Appl Genet).
  • We showed the emergence of new genetic groups resulting from recent breeding (Truntzler et al., 2011, Theor Appl Genet).

 

1.3   Modelling of linkage desequilibrium

We have been studying the range and variability of linkage disequilibrium (LD) along the genome in different panels and evaluated the impact of genetic structure on LD.

  • In a panel of 375 lines, the average LD has been found to be quite broad (197 kb for a R2 of 0.1) and to be amplified by the genetic structure of the population (Bouchet et al., 2013, Plos One). Population structure and kinship must therefore be taken into account in the different models of association mapping (Veyrieras et al., 2007b, Crop Sci, Mezmouk et al., 2011, Theor Appl Genet)
  • We evaluated several tools for haplotype reconstruction and imputation. Our results show that lines can share large IBD regions (coll. B. Servin et B. Mangin, INRA Toulouse). We use this information on local identity to develop models for GWAS and QTL detection in multiparental context (see below).