QTL mapping in autotetraploids using SNP dosage information

• DOI: 10.1007/s00122-014-2347-2
• Publication Date: 2014-07-01T00:22:21Z
• Authors: Christine A. Hackett; John E. Bradshaw; Glenn J. Bryan
• Keywords: Family-based QTL mapping; SNP genotyping; Association mapping

Dense linkage maps derived by analysing SNP dosage in autotetraploids provide detailed information about the location of, and genetic model at, quantitative trait loci. Recent developments sequencing genotyping technologies enable researchers to generate high-density single nucleotide polymorphism (SNP) genotype data for mapping studies. For polyploid species, genotypes are informative allele dosage, Hackett et al. (PLoS ONE 8:e63939, 2013) presented theory how can be used map construction locus (QTL) an F1 population autotetraploid species. Here, QTL using is explored simulated phenotypic traits of moderate heritability possibly non-additive effects. Different strategies compared, looking at additive more complicated models, fitting as a step or iteratively re-weighted modelling. We recommend without iterative re-weighting, then exploring models means estimated most likely position. apply this strategy re-analyse high from potato 190 individuals: flower colour, maturity, height resistance late blight (Phytophthora infestans (Mont.) de Bary) cyst nematode (Globodera pallida), 3839 SNPs. The approximate confidence intervals locations have been improved map, each has revealed. several reported QTLs, candidate SNPs identified, propose genes. conclude that marker density loci large effects, but larger populations needed detect smaller QTLs.