A linkage disequilibrium study in a layer chicken population
Résumé
Knowledge of the linkage disequilibrium (LD) pattern is useful for QTL detection by genome-wide association study and for subsequent causal polymorphisms identification. The LD extent is also one of the parameters which affect the genomic evaluation accuracy and, consequently, the genetic gain in selection. Recently, the availability of the high density 600 K Affymetrix® Axiom® HD SNP genotyping array allows to asses a higher resolution of the LD structure and extent in chicken genome. In this study, we analyzed genotypes of 438 males for a set of 284 643 SNP from this high density chip to characterize the LD pattern in a brown layer population. LD was measured by the average r2 value at a given physical distance. Genome wide, the mean value of r2 observed in pair-wise distances of <25 Kb is 0.5 and it decreased to 0.32 at a distance of 120 to 200 kb. Across autosomal chromosomes, it varied between 0.38 and 0.60 at a distance <25kb and between 0.16 and 0.44 at a distance of 120 to 200 kb. Most differences appeared between macrochromosomes, intermediates, microchromosomes and Z sexual chromosome. Average r2 values were higher for larger chromosomes than for intermediates and microchrosomes. Chromosome Z had the highest average r2 equal to 0.75 and 0.54 at distances <25 Kb and between 120 to 200 kb.
In conclusion, the density of usable marker in this study guarantees sufficient LD at small distances and is sufficient to achieve reasonable resolution and accuracy in QTL detection by genome-wide association study and genomic selection. Moreover, this study shed light on high LD for Z sexual chromosome. Finally, this knowledge will be useful for the design of a low density genotyping array.