Table 5

Single-locus QTLs detected for popping traits using multiple-QTL model mapping for individual environment analysis
Trait Environment QTL (position)a Linkage group Closest marker (position)b LOD scorec LOD thresholdd R2e Af
    Popping dimension index (PDI)
LD09 PDI3PP (68.1-74.5) 3 IAC24 (71.0) 2.7 2.6 7.5 1.92
PDI5PP (32.8-38.4) 5 BMc321 (37.8) 4.3 13.4 2.61
SD09 PDI1PP (55.6-59.3) 1b E32M60-147 (58.2) 3.0 2.8 7.7 1.57
PDI3PP (62.8-66.3) 3 BMd1 (63.7) 4.4 12.6 1.97
LD10 PDI3PP (58.7-65.8) 3 PVEST042 (60.0) 3.1 2.6 8.2 1.93
PDI7PP (33.4-37.8) 7 BMc294 (36.6) 4.7 12.9 −2.44
SD10 PDI3PP (62.1-65.9) 3 BMd1 (63.7) 4.7 2.7 9.2 1.46
PDI6PP (1.8-5.5) 6 E40M60-91 (5.0) 8.9 18.7 2.15
LD11 PDI5PP (35.9-40.4) 5 BM138 (39.8) 3.0 2.8 7.7 2.07
PDI7PP (22.9-37.6) 7 BMc294 (36.6) 5.1 13.3 −2.72
    Expansion coefficient (EC)
LD09 EC5PP (41.3-46.1) 5 BM175 (46.1) 3.6 2.6 9.8 6.18
EC7PP (30.1-37.7) 7 BMc294 (36.6) 2.7 7.3 −5.25
SD09 Not significant 2.1
LD10 EC7PP (30.5-37.9) 7 BMc294 (36.6) 3.5 2.4 10.7 −6.62
SD10 EC3PP (67.2-76.8) 3 IAC24 (71.0) 5.9 2.6 12.0 5.69
EC6PP (1.2-5.4) 6 E40M60-91 (5.0) 7.6 15.9 6.75
LD11 EC5PP (39.1-43.3) 5 BM138 (39.8) 4.2 2.8 9.8 6.82
EC7PP (32.7-41.6) 7 BMc294 (36.6) 5.9 14.2 −8.18
    Percentage of unpopped seeds (PUS)
LD09 PUS5PP (38.3-46.1) 5 BM175 (46.1) 3.9 2.9 12.3 −9.14
SD09 PUS3PP (66.9-74.6) 3 PvM152a (67.6) 3.3 2.9 8.9 −9.11
PUS9PP (42.3-46.1) 9 E31M51-59 (27.5) 3.4 10.1 9.78
LD10 PUS6PP (3.1-6.4) 6 E40M60-91 (5.0) 3.2 2.9 9.7 −8.63
PUS7PP (22.7-38.4) 7 BM185 (24.2) 3.0 8.9 7.81
SD10 PUS3PP (67.1-70.6) 3 PvM152a (67.6) 4.5 2.8 8.8 −8.26
PUS6PP (1.6-6.2) 6 BMc238 (2.3) 7.7 16.5 −11.36
LD11 PUS1.2 PP (35.9-39.1) 1b E43M38-138 (36.4) 3.3 2.8 6.3 −7.23
PUS5PP (38.1-40.2) 5 BM138 (39.8) 4.6 8.7 −8.33
PUS7PP (26.9-39.3) 7 BMc294 (36.6) 5.2 9.9 9.29
PUS10PP (6.2-7.1) 10 BMb414 (7.0) 3.4 6.3 −6.79

Those QTLs identified in 2 or more environments are marked in bold.

a QTL name (according to Miklas and Porch 2010) and its estimated map position (in Kosambi cM).

b Nearest marker to peak of the detected QTL and its map position (in Kosambi cM).

c LOD score detected for the nearest marker.

d LOD thresholds score determined by permutation test for each trait in each environment (P = 0.05).

e Percentage of the total phenotypic variation explained by the QTL.

f Estimated additive effect. Positive values indicate allele arising from PHA1037 and negative values indicate allele arising from PMB0225.

Yuste-Lisbona et al.

Yuste-Lisbona et al. BMC Plant Biology 2012 12:136   doi:10.1186/1471-2229-12-136

Open Data