SNP Detection for QTL Mapping in Ducks

QTL detection in ducks is limited by the scarcity in genetic markers. As a typical example, a first genome scan in the INRA GENECAN backcross design could only be done with 91 microsatelllite markers, covering 778 cM in 16 linkage groups, whereas the duck karyotype is composed of 40 pairs of chromosomes, including the Z and W gonosomes. The GENECAN design is composed of 7 half-sib families, so we sequenced each of the 7 F1 sires (one per lane of an Illumina HiSeq), to detect SNP markers. Using reads with a mapping quality > 30, 11 million SNP were detected. In the absence of genome maps in duck, the chicken was chosen to guide the choice of markers along chromosomes. Amongst the 10 million duck SNP mapped on the chicken genome, 500 000 (5%) are heterozygote in at least 6 of the 7 sires and 350 000 (3.5%) in all 7 sires. The choice of a final set of markers was done using three criteria: (1) maximization on the informativity in the sires; (2) no other SNP in the vincinity that could affect genotyping quality; (3) optimization of the genome coverage in cM, taking into account the differences in recombination tares between macrochromosomes and microchromosomes.