Chutimanitsakun et al. BMC Genomics 2011, 12:4 http://www.biomedcentral.com/1471-2164/12/4 Table 3 Summary of QTL based on RAD-only map constructed with 436 RAD and nine morphological loci Trait, QTL number Chrom. QTL peak 2-LOD Morphological and/or cloned LOD Additive R2* LOD MIM and QTL interaction position confidence genes within 2 LOD conf. interval effect threshold R2** interval H2 Final leaf number 1 2 3 4 Plant height 1 2 3 4 Spike number 1 2 3 1 × 2 Spike length 1 2 3 4 5 1 × 2 Floret number 1 2 3 4 5 Grain number 1 2 3 1 × 2 2 × 3 Hundred grain weight 1 2 3 Gain yield 1 2 1H 4H 5H 7H 1H 2H 3H 6H 2H 5H 6H 1H 2H 3H 5H 6H 1H 2H 3H 4H 6H 1H 2H 2H 2H 6H 7H 1H 2H 175 123 154 27 144 122 57 112 57 9 91 175 122 20 105 106 175 57 39 123 103 169 56 122 57 66 104 175 122 (170-175) (120-123) (148-156) (133-158) (119-128) (51-73) (103-121) (50-64) (2-24) (85-98) (158-175) (120-127) (7-34) (157-1175) (54-61) (30-45) (117-123) (66-120) (162-174) (53-62) (116-130) (54-62) (56-70) (86-130) (170-175) (112-131) VRN-H2 VRN-H1 ZEO1 VRS1 ZEO1 VRS1 VRS1 ZEO1 VRS1 ZEO1 6.2 2.9 2.8 2.7 11.4 3.8 3.6 6.5 -6.5 31.0 -21.7 5.6 6.0 5.7 5.9 -0.9 0.6 -0.6 0.6 3.6 -1.8 1.2 -1.5 4.9 -0.5 42.9 -3.1 5.1 -0.5 2.4 -0.2 2.7 0.3 0.4 7.5 -5.3 38.6 -21.4 3.2 -3.2 3.1 3.2 4.8 3.9 3.8 -5.0 18.7 -12.4 10.3 -7.2 2.9 3.3 19.8 3.5 3.9 3.5 6.2 0.5 -0.1 0.2 -2.8 -3.7 0.18 0.08 0.07 0.07 0.06 0.64 0.05 0.05 0.40 0.06 0.05 0.06 0.00 0.82 0.04 0.01 0.02 0.04 0.05 0.77 0.02 0.02 0.03 0.01 0.47 0.18 0.04 0.05 0.54 0.04 0.05 0.11 0.19 2.8 2.8 2.7 2.9 2.8 3.0 2.8 2.8 Page 8 of 13 0.41 0.87 0.78 0.94 0.56 0.63 0.92 0.98 0.89 0.97 0.75 0.92 0.66 0.78 0.30 0.49 *Proportion of phenotypic the variance explained by individual QTL **R2 of the multi-locus model that includes QTL and their significant interactions calculated with MIM The QTLs in italic and underlined showed a trend in the full map but did not reach the LOD threshold. resources and have useful applications in molecular breeding. Ongoing optimization of the RAD marker system will foster more sophisticated analysis in future studies. Selection of nucleases that generate more markers will allow higher density linkage maps to be constructed, while improvements in sequencing chemistries and frag- ment preparation protocols will permit longer read lengths for comparative genome analysis. Additionally, sequenced RAD markers arrayed in genetic maps would