Trait, QTL number and QTL interaction Final leaf number 1 2 3 4 Plant height 1 2 3 4 Spike number 1 2 3 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 Grain 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 158 118 157 29 131 156 51 100 99 43 80 158 156 20 138 95 156 99 36 120 91 151 99 156 99 60 103 157 160 (154-158) (117-120) (154-161) (26-36) (120-136) (155-158) (43-60) (74-104) (95-102) (152-158) (155-159) (13-23) (137-144) (93-100) (150-158) (97-101) (112-127) (73-103) (142-156) (99-101) (150-163) (97-101) (54-61) (96-111) (153-158) (150-165) VRN-H2 VRN-H1 ZEO1 VRS1 ZEO1 VRS1 VRN-H2 VRS1 ZEO1 VRS1 ZEO1 6.9 4.6 3.5 3.6 -0.9 0.7 -0.7 0.7 7.1 -6.7 32.1 -22.8 6.1 6.3 6.0 5.7 13.3 3.5 2.4 -1.3 2.7 1.3 6.7 -0.5 45.8 -3.0 5.0 -0.5 3.8 -0.3 4.5 0.4 0.5 9.4 -5.8 40.3 -21.6 2.9 -2.9 3.6 3.3 4.6 3.7 3.9 -4.9 20.1 -12.3 10.4 -7.3 2.9 3.4 19.9 0.5 3.5 -0.1 4.2 0.2 4.4 8.1 -2.9 -4,1 0.17 0.10 0.09 0.08 0.06 0.67 0.05 0.05 0.38 0.05 0.06 0.00 0.81 0.04 0.02 0.02 0.05 0.06 0.79 0.01 0.02 0.02 0.01 0.46 0.18 0.04 0.05 0.53 0.04 0.05 0.11 0.23 3.0 3.1 2.9 3.1 3.0 3.0 2.9 3.1 Chutimanitsakun et al. BMC Genomics 2011, 12:4 http://www.biomedcentral.com/1471-2164/12/4 Table 2 Summary of QTL based on a skeleton map derived from the 2846 loci data set Chrom. QTL peak 2-LOD position confidence interval Morphological and/or cloned genes within 2 LOD conf. interval LOD Additive R2* LOD MIM effect threshold R2** H2 ***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 italics and underlined showed a trend in the RAD-only map but did not reach the LOD threshold. criteria i) a small number of singletons ii) consistency with non-RAD marker order iii) segregation distortion between maps in equivalent positions iv) comparable genome coverage and v) comparable map lengths. Construction of this linkage map could serve as a bridge to allow identification of loci associated with traits of interest, thus facilitating gene discovery and manipula- tion. The consistency of QTL results between RAD and RAD + prior marker maps confirms that sequenced RAD markers will be useful for developing genetic maps and QTL tagging. Therefore, sequenced RAD markers can contribute to the enrichment of molecular marker Page 7 of 13 0.47 0.87 0.82 0.94 0.50 0.63 0.93 0.98 0.87 0.97 0.74 0.92 0.66 0.78 0.29 0.49