KASP SNP genotyping assays (LGC Genomics, Teddington, Middlesex, UK) were developed for candidate SNPs discovered in comparison of the reference based assembly of the parents and used to genotype the original DH population. The parent genome alignments were used to design primer sequences for the KASP assays. A genetic linkage map was constructed which incorporated the molecular markers using JoinMap3 (Van Ooijen and Voorrips 2001 ) with a threshold recombination frequency of < 0.25 and a minimum logarithm of the odds ratio (LOD) score of 6 for creating linkage groups. Genetic distances were calculated using the Kosambi function (Kosambi 1944 ). Average genome-wide recombination rates for the A and C genomes were estimated by dividing the length of a particular genome’s physical map (bp) by that of its genetic map (cM).
Genome-wide QTL scans were performed using Haley-Knott Regression (Haley and Knott 1992 (link)) in R/qtl with 1 cM steps. QTL were selected using a step-wise model selection approach (Manichaikul et al. 2009 (link)) based on significance thresholds made from 1000 permutations (Churchill and Doerge 1994 (link)).
Genome-wide QTL scans were performed using Haley-Knott Regression (Haley and Knott 1992 (link)) in R/qtl with 1 cM steps. QTL were selected using a step-wise model selection approach (Manichaikul et al. 2009 (link)) based on significance thresholds made from 1000 permutations (Churchill and Doerge 1994 (link)).