*2.5. Linkage Map Construction*

The F1 individuals were genotyped based on marker polymorphisms. The marker-segregation data were analyzed with JOINMAP Version 4.1 by treating the segregation data of the markers as a "cross pollination" (CP) population. The significance of each allele was tested by JoinMap, which further filters for independence of segregation using logarithm of odds (LOD) scores [30]. The significance was determined at a LOD threshold of 5.0 and 8.0. SNP markers, which were heterozygous in only one of the parents (testcross markers), were scored either lm × ll or nn × np depending on the parent, and heterozygous markers in both parents with two alleles (intercross markers) were scored as hk × hk. The segregation patterns lm × ll and hk × hk were used for the maternal map construction, while the patterns nn x np and hk × hk were used for the paternal map according to the two-way pseudo-testcross mapping strategy [31]. Chi-square tests were performed to test for deviation from the expected Mendelian segregation ratio for each marker. The testcross markers were tested against a Mendelian segregation ratio of 1:1 using a chi-square test ( *P* < 0.05), while those intercross markers were tested against a 1:2:1 ratio ( *P* < 0.05). SNP markers with more than 30% missing data were removed from the analysis. After linkage groups (LGs) were computed, their number was assigned according to the chromosome number of the mapped marker. The regression algorithm and Kosambi [32] mapping function were used in the marker distance calculation, expressed in centiMorgans (cM). Maps were viewed using MapChart 2.3 [33].
