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Table 2 Location of QTL and magnitude of QTL effects

From: A genome scan for quantitative trait loci affecting growth-related traits in an F1 family of Asian seabass (Lates calcarifer)

Trait QTL name LG Nearest marker LOD LOD threshold PVE (%) Phenotype means
      Genome-wide Linkage-group-wide   m1f1 m1f2 m2f1 m2f2 Significance
Body weight (g) qBW2-a 2 Lca287 5.25* 4.5 3.4 28.8 27.0 23.3 39.1 27.0 †‡
  qBW2-b 2 Lca371 4.62* 4.5 3.4 6.4 25.7 29.0 28.9 34.0 †‡
  qBW3 3 Lca154 5.33* 4.5 2.3 8.8 30.7 26.6 34.6 26.4
  qBW12 12 Lca178 3.34 4.5 3.0 18.7 23.4 34.2 25.5 34.1
  qBW16 16 LcaE22 1.96 4.5 1.7 2.5 28.5 26.9 30.9 31.3
  qBW20 20 Lca234 3.16 4.5 3.0 3.8 32.8 26.4 29.6 29.7 ‡§
Total length (mm) qTL1 1 Lca148 4.65 6.1 4.4 8.8 134.8 111.7 106.8 135.8 §
  qTL2-a 2 Lca287 6.59* 6.1 5.4 58.9 119.7 104.2 138.5 131.5 †‡
  qTL2-b 2 Lca371 5.45 6.1 5.4 7.6 117.1 123.2 122.9 130.9 †‡
  qTL3 3 Lca154 5.08 6.1 2.3 8.3 125.9 119.1 131.0 119.4
  qTL12 12 Lca178 3.26 6.1 3.3 22.6 113.8 131.6 116.7 131.4
  qTL16 16 LcaE22 2.06 6.1 1.7 2.6 121.5 120.3 126.5 126.2
Standard length (mm) qSL1 1 Lca148 4.65 6.1 4.5 8.3 111.4 92.3 88.3 112.3 §
  qSL2-a 2 Lca287 6.30* 6.1 5.4 59.7 98.3 86.1 114.7 108.9 †‡
  qSL2-b 2 Lca371 5.05 6.1 5.4 7.2 99.4 100.9 99.0 108.4 †‡
  qSL3 3 Lca154 5.16 6.1 2.3 8.4 104.1 98.3 108.4 98.7
  qSL12 12 Lca178 3.32 6.1 3.2 21.9 93.7 109.2 97.0 108.1
  qSL16 16 LcaE22 2.19 6.1 1.7 2.7 100.4 99.3 104.7 104.3
KTL qKTL6-a 6 Lca409 2.76 4.6 2.6 8.1 1.51 1.50 1.43 1.50 †‡
  qKTL6-b 6 Lca223 3.99 4.6 2.6 10.7 1.46 1.45 1.49 1.55
  qKTL7 7 Lca436 3.55 4.6 2.3 4.3 1.50 1.52 1.46 1.46
  qKTL11-a 11 Lca315 2.48 4.6 2.4 6.7 1.46 1.45 1.52 1.51
  qKTL11-b 11 Lca058 2.43 4.6 2.4 5.9 1.51 1.51 1.45 1.45
  qKTL12 12 Lca115 2.87 4.6 2.8 18.3 1.50 1.44 1.44 1.55 †‡
  qKTL16 16 LcaE22 1.99 4.6 1.7 2.5 1.51 1.48 1.46 1.48
  qKTL21 21 Lca349 3.78 4.6 2.3 4.9 1.53 1.47 1.47 1.46
KSL qKSL6-a 6 Lca409 2.38 6.1 2.4 8 2.67 2.66 2.53 2.67 †‡
  qKSL6-b 6 Lca223 3.22 6.1 2.4 3.8 2.59 2.60 2.64 2.70
  qKSL7 7 Lca436 3.88 6.1 2.8 4.6 2.68 2.67 2.58 2.58
  qKSL16 16 LcaE22 2.29 6.1 1.7 2.9 2.67 2.63 2.57 2.63
  qKSL21-a 21 Lca349 3.26 6.1 2.4 4.2 2.69 2.65 2.58 2.59
  qKSL21-b 21 Lca421 3.24 6.1 2.4 6 2.63 2.71 2.56 2.61 †‡
  1. For each QTL detected, the linkage group maximum LOD score, and percentage of the phenotypic variance explained (PVE) are indicated. The genome-wide LOD significance thresholds are 4.5 body weight, and 6.1 for total length and body length. Mean phenotypic values of each trait were also calculated for those progeny with the alternate alleles at the most closely linked microsatellite markers, inherited from the male parent (m1 or m2), alleles inherited from the female parent (f1 or f2). *: Significant QTL; †: Significant effect within male alleles, ‡: Significant effect within female alleles; and § Significant interaction between alleles from male and female.