A minimum LOD score of 4.0 and a maximum recombination frequency of 0.35 were used to group the microsatellite markers into potential linkage groups.
Marker coding and the genetic map (in cM Kosambi) from the DSP × 90 2131 RIL population were established with a minimum LOD score threshold of 3.0 and a maximum recombination frequency of 0.4, as described in [ 46].
A minimum independence logarithm of odds (LOD) score of 11 and a maximum recombination frequency of 0.4 was used to define linkage groups in all map calculations mentioned here on.
Second, for each linkage group, markers were ordered using the regression algorithm with the minimum LOD score of 1.0 and maximum recombination frequency of 0.35.
Genetic linkage analyses were performed using the "group" commands of CarthaGene software [ 71], with a minimum LOD score threshold of 3.0 and a recombination frequency < 0.3.
The genetic linkage map was constructed using the JoinMap 4.0 software (http://www.kyazma.nl/index.php/mc.JoinMap) with the threshold for goodness-of-fit of ≦ 5, a recombination frequency of < 0.4 and minimum logarithm of odds (LOD) score of 2.0.
The frequency of recombination within the Pvama1 population is relatively high compared to the predicted frequency within the Pfama1 population (10 minimum recombination events within 73 Pvama1 sequences vs. 3 in 30 Pfama1 sequences; Table 3), yet both of these are low compared to estimates from other regions.
Of the remaining 833 segregating markers (641 SNPs and 192 SSRs), 829 were incorporated into 19 major linkage groups using a minimum logarithm of odds (LOD) score of 11 and maximum recombination frequency of 0.4.
Marker data were assigned to LG using a minimum logarithm of odds ratio (LOD) score of 6.0, and a recombination frequency value of 0.3.
Homologous recombination frequency is significantly increased in the vicinity of a DNA double-strand break.
