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Table 3 Summary of QTL based on RAD-only map constructed with 436 RAD and nine morphological loci.

From: Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley

Trait, QTL number and QTL interaction Chrom. QTL peak position 2-LOD confidence interval Morphological and/or cloned genes within 2 LOD conf. interval LOD Additive effect R2* LOD threshold MIM R2** H2
Final leaf number        2.8 0.41 0.87
1 1H 175 (170-175)   6.2 -0.9 0.18    
2 4H 123 (120-123) VRN-H2 2.9 0.6 0.08    
3 5H 154 (148-156) VRN-H1 2.8 -0.6 0.07    
4 7H 27    2.7 0.6 0.07    
Plant height        2.8 0.78 0.94
1 1H 144 (133-158)   6.5 -6.5 0.06    
2 2H 122 (119-128) ZEO1 31.0 -21.7 0.64    
3 3H 57 (51-73)   5.6 6.0 0.05    
4 6H 112 (103-121)   5.7 5.9 0.05    
Spike number        2.7 0.56 0.63
1 2H 57 (50-64) VRS1 11.4 3.6 0.40    
2 5H 9 (2-24)   3.8 -1.8 0.06    
3 6H 91 (85-98)   3.6 1.2 0.05    
1 × 2       -1.5 0.06    
Spike length        2.9 0.92 0.98
1 1H 175 (158-175)   4.9 -0.5 0.00    
2 2H 122 (120-127) ZEO1 42.9 -3.1 0.82    
3 3H 20 (7-34)   5.1 -0.5 0.04    
4 5H 105    2.4 -0.2 0.01    
5 6H 106    2.7 0.3 0.02    
1 × 2       0.4 0.04    
Floret number        2.8 0.89 0.97
1 1H 175 (157-1175)   7.5 -5.3 0.05    
2 2H 57 (54-61) VRS1 38.6 -21.4 0.77    
3 3H 39 (30-45)   3.2 -3.2 0.02    
4 4H 123 (117-123)   3.1 3.2 0.02    
5 6H 103 (66-120)   4.8 3.9 0.03    
Grain number        3.0 0.75 0.92
1 1H 169 (162-174)   3.8 -5.0 0.01    
2 2H 56 (53-62) VRS1 18.7 -12.4 0.47    
3 2H 122 (116-130) ZEO1 10.3 -7.2 0.18    
1 × 2       2.9 0.04    
2 × 3       3.3 0.05    
Hundred grain weight       2.8 0.66 0.78
1 2H 57 (54-62) VRS1 19.8 0.5 0.54    
2 6H 66 (56-70)   3.5 -0.1 0.04    
3 7H 104 (86-130)   3.9 0.2 0.05    
Gain yield        2.8 0.30 0.49
1 1H 175 (170-175)   3.5 -2.8 0.11    
2 2H 122 (112-131) ZEO1 6.2 -3.7 0.19    
  1. *Proportion of phenotypic the variance explained by individual QTL
  2. **R2 of the multi-locus model that includes QTL and their significant interactions calculated with MIM
  3. The QTLs in italic and underlined showed a trend in the full map but did not reach the LOD threshold.