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Table 5 Location, significance and effect of QTLs detected for phenology, berry size and seed content

From: Berry and phenology-related traits in grapevine (Vitis viniferaL.): From Quantitative Trait Loci to underlying genes

Trait QTL position LOD LOD threshold % var KW sig
  LG Map Peak (cM) Nearest marker cM Interval   α = 0.20 α = 0.05   
FT 1 Ia 54.7 VVIS21 44.7 43.1–66.6 2.3, 3.2, 4.3 2.0 2.8 6.3, 11.7, 8.6 1, 1, 2
   Ib 88.2 mCTGeACC1   83.0–88.9 2.1, 4.7, 3.1 2.0 2.8 6.3, 11.5, 6.5 0, 3, 3
  1 Ca 54.4 VVIS21 44.4 44.3–65.0 2.3, 3.8, 4.6 2.2 3.2 7.8, 13.9, 9.1 1, 1, 2
   Cb 87.5 mCTGeACC1   82.8-b -, 4.8, 3.1 2.2 3.2 -, 11.7, 6.6 -, 3, 3
  1 BPa 35.4 VVIS21 25.4 24.3–46.4 2.3, 3.1, 4.2 2.1 3.0 6.2, 11.4, 8.4 1, 1, 2
   BPb 67.3 mCTGeACC1   62.2–68.0 2.1, 4.7, 3.1 2.1 3.0 6.3, 11.5, 6.6 0, 3, 3
  2 I 35.0 VVIB23   31.9–36.5 3.4, 3.5, 8.2 2.0 2.9 9.1, 7.3, 16.1 3, 4, 7
  2 C 62.6 VVIB23   59.5–64.0 3.3, 3.6, 8.4 2.2 2.9 9.0, 7.7, 16.4 3, 4, 7
  2 BP 60.2 VVIB23   55.1–61.5 3.4, 3.5, 8.1 2.0 2.9 9.2, 7.4, 16.1 3, 4, 7
  6 I 5.0 VVIN31 t t-9.5 4.1, 7.4, 6.8 1.8 2.6 13.8, 20.5, 15.5 3, 7, 5
  6 C 5.0 VVIN31 t t-9.5 3.9, 7.2, 6.8 1.9 2.7 13.4, 19.9, 15.4 3, 7, 5
  6 BP 5.0 VVIN31 t t-9.2 4.1, 7.4, 6.9 1.9 2.8 13.9, 20.8, 15.6 3, 7, 5
VT 2 I 30.1 VVIO55   27.0–31.9 3.5, 3.0, 5.6 2.3 3.5 6.6, 5.9, 12.6 0, 3, 1
  2 C 55.0 VMC2C10.1   52.0–55.2 3.5, 2.9, 5.6 2.6 4.0 6.6, 5.8, 12.6 0, 1, 1
  2 BP 52.5 VMC2C10.1   48.1–53.4 3.5, 2.9, 5.6 2.0 2.7 6.6, 5.8, 12.6 0, 1, 1
  6 I 17.6 VMC4G6   13.4–18.0 4.6, 4.9, - 1.6 2.4 9.0, 9.8, - 3, 4, -
  6 C 17.6 VMC4G6   13.5–17.9 4.8, 4.9, - 1.8 2.6 9.3, 9.9, - 3, 4, -
  6 BP 17.4 VMC4G6   13.4–17.7 4.8, 4.9, - 1.9 2.7 9.3, 9.9, - 3, 4, -
  16 I 17.8 VMC1E11   15.6–20.6 13.7, 9.7, 11.3 1.8 2.5 31.6, 21.1, 29.1 7, 7, 7
  16 C 16.9 VMC1E11 18.0 15.2–20.5 15.1, 9.6, 11.9 1.9 2.7 38.0, 24.1, 45.4 7, 7, 7
  16 BP 17.8 VMC1E11   14.3–17.8 14.0, 9.7, 11.5 1.5 2.2 32.1, 21.2, 29.1 7, 7, 7
VP 2 I 19.0 mCTGeACC2   3.6–20.2 13.6, 15.4, 7.0 2.1 3.9 41.8, 38.0, 44.2 7, 7, 7
  2 C 40.9 colour   40.2–45.9 14.0, 16.4, - 3.0 4.4 40.0, 39.8, - 7, 7, -
  2 BP 40.5 colour   39.8–44.4 13.9, 16.4, 4.3 2.0 2.7 38.9, 39.6, 15.8 7, 7, 7
R 6 I 19.6 VMC4H5   18.4–20.8 4.1, 3.5, - 1.7 2.5 17.2, 10.2, - 5, 2, -
  6 C 19.7 VMC4H5   18.5–21.0 4.1, 3.5, - 1.9 2.7 17.2, 10.2, - 5, 2, -
  6 BP 19.6 VMC4H5   18.3–20.8 4.1, 3.5, - 1.9 2.7 17.2, 10.2, - 5, 2, -
F-V 2 I 24.0 VMC5G7 24.2 20.4–24.8 7.7, 6.4, 5.7 2.5 3.9 18.7, 14.0, 12.6 6, 6, 4
  2 C 51.2 VMC5G7 51.4 47.1–51.8 7.7, 6.4, 5.8 2.8 4.1 18.4, 13.8, 12.7 6, 6, 4
  2 BP 45.5 VMC5G7 48.9 40.4–49.4 8.0, 6.5, 5.8 1.9 2.8 21.4, 15.6, 12.7 6, 6, 4
  6 I 17.6 VMC4G6   13.3–18.0 3.9, 4.0, - 1.7 2.5 8.5, 8.2, - 1, 1, -
  6 C 17.6 VMC4G6   13.3–18.0 3.9, 4.0, - 1.8 2.6 8.5, 8.2, - 1, 1, -
  6 BP 17.4 VMC4G6   13.3–17.8 3.9, 4.0, - 1.9 2.6 8.5, 8.2, - 1, 1, -
  16 I 17.8 VMC1E11   15.8–19.1 7.9, 7.3, 11.4 1.8 2.6 18.7, 15.5, 27.8 7, 7, 7
  16 C 18.0 VMC1E11   15.8–19.3 8.7, 7.2, 11.8 1.9 2.6 23.0, 15.4, 37.2 7, 7, 7
  16 BP 17.8 VMC1E11   15.0–17.8 7.9, 7.2, 11.4 1.4 2.2 18.7, 15.4, 27.8 7, 7, 7
F-R 6 I 19.6 VMC4H5   18.3–21.0 3.6, 3.1, - 1.7 2.6 15.3, 9.1, - 4, 2, -
  6 C 19.7 VMC4H5   18.3–21.2 3.6, 3.1, - 1.8 2.5 15.3, 9.1, - 4, 2, -
  6 BP 19.6 VMC4H5   18.1–21.0 3.6, 3.1, - 1.9 2.6 15.3, 9.1, - 4, 2, -
V-R 2 I 35.0 VVIB23#   29.9–35.7 3.3, 6.6, 6.0 2.0 3.0 15.4, 18.0, 20.7 2, 7, 7
  2 C 62.6 VVIB23#   57.3–63.3 3.4, 6.5, 5.9 2.2 3.1 14.6, 17.8, 19.9 2, 7, 7
  2 BP 60.2 VVIB23#   55.1–60.8 3.7, 6.6, 6.2 2.0 2.8 15.9, 18.1, 21.7 2, 7, 7
  12* I 18.7 VMC2H4 23.8 7.8–29.5 3.2, -, 2.6 2.0 2.8 16.7, -, 10.4 3, -, 1
  12* C 21.9 VMC2H4   21.4–28.5 3.3, -, 2.8 1.9 2.7 13.5, -, 9.0 3, -, 3
  12* BP 18.8 PHEA-sscp   16.3–19.2 3.5, -, 2.5 1.9 2.6 16.8, -, 9.1 0, -,0
MBW 1 C 18.9 mCACeATC4   t-19.5 3.2, 2.6, 5.4 2.2 3.1 10.7, 4.7, 17.5 1, 2, 4
  1 BP t mCACeATC4   t-0.9 -, 2.4, 3.7 2.0 2.8 -, 4.6, 9.1 -, 2, 4
  12 C 29.8 mCTGeAAG5   22.8–29.8 3.4, 3.2, 3.9 1.9 2.8 8.4, 5.6, 8.8 2, 2, 6
  12 BP 28.5 mCTGeAAG5   20.6–28.6 2.4, 3.2, 3.7 1.9 2.8 5.1, 5.7, 8.0 1, 2, 6
  18 C 81.9 SdI   74.5–81.9 14.2, 19.4, 11.5 2.5 3.3 41.7, 43.1, 32.6 7, 7, 7
  18 BP 17.4 SdI   13.8–17.4 11.8, 18.3, 9.9 1.9 2.6 29.6, 40.8, 27.2 7, 7, 7
MSN 2 I 35.0 VVIB23   31.6–35.6 6.2, 8.5, - 1.9 2.6 19.6, 22.9, - 7, 7, -
  2 C 62.6 VVIB23   60.8–63.0 6.3, 8.5, - 2.1 2.9 19.9, 22.9, - 7, 7, -
  2 BP 60.2 VVIB23   58.7–60.7 6.3, 8.5, - 2.0 2.7 19.8, 22.9, - 7, 7, -
% SDM 18 BP 17.4 SdI   13.1–17.5 65.9, 61.7, 59.2 2.1 3.6 90.0, 86.5, 91.4 7, 7, 7
MSFW 6* BP 42.3 mCACeACA4   39.4–48.3 3.4, -, 4.2 1.9 2.7 5.3, -, 13.2 0, -, 4
  6 C 47.2 mCTCeACA1   37.4–48.3 4.3, 2.1, 5.8 1.8 2.5 11.3, 3.5, 21.4 1, 1, 4
  10 I 43.3 mCTAeAAG10   39.0–53.0 2.6, 3.3, - 2.0 2.7 9.4, 10.0, - 0, 0, -
  10 C 47.2 mCTAeAAG10#   46.9–55.6 4.4, 6.4, '- 2.3 3.0 36.3, 13.4, - 2, 0, -
  10 BP 50.0 mCTGeATT18 50.6 44.8–55.7 2.9, 4.2, 2.2 2.0 2.7 7.7, 12.1, 9.8 2, 3, 0
  13 I 62.6 mCATeATG9# b 42.5–b 3.5, 3.9, - 1.9 2.7 14.6, 14.2, - 1, 3, -
  13 C b mCATeATG9#   52.0–b 3.8, 4.4, - 2.3 3.0 8.8, 15.7, - 0, 3, -
  13 BP 25.5 VMC3D12#   25.1–29.8 3.3, 3.4, - 1.7 2.4 7.2, 7.8, - 1, 2, -
  15 I 5.8 mCACeACA10#   5.5–13.5 2.1, 2.6, 3.5 1.9 2.6 7.5, 6.7, 13.0 0, 0, 5
  18 C 80.1 SdI 81.9 65.0–82.0 10.7, 5.5, 6.4 2.4 3.2 27.5, 15.8, 25.7 7, 4, 6
  18 BP 17.4 SdI   8.7–17.7 10.3, 3.9, 5.9 1.9 2.7 26.3, 13.8, 24.8 7, 4, 6
MSDW 2* I 35.0 VVIB23   29.8–36.7 3.3, -, 2.9 1.8 2.6 10.5, -, 10.8 6, -, 2
  2* C 62.6 VVIB23   60.4–63.2 8.9, -, 2.3 2.2 8.0 4.6, -, 3.7 6, -, 2
  15 I 5.8 mCACaACA10#   5.2–12.3 -, 2.9, 2.2 1.8 2.6 -, 10.8, 8.2 -, 0, 2
  15 C 5.7 mCACeACA10#   5.5–9.4 -, 2.2, 3.2 1.8 2.8 -, 3.1, 5.4 -, 0, 2
  18 C 80.1 SdI 81.9 72.0–81.4 55.5, 27.5, 19.8 2.2 3.4 73.8, 57.1, 49.3 7, 7, 7
  18 BP 15.0 SdI 17.4 12.9–17.4 54.5, 25.6, 19.0 2.0 2.8 75.0, 62.1, 49.4 7, 7, 7
  1. LG = linkage group; Map = map in which the QTL was identified (I for Italia, C for consensus, BP for Big Perlon); Peak = QTL position as estimated by the cM distance of the local LOD maximum from the top of the linkage group, with 't' for top and 'b' for bottom of linkage group; Nearest marker = marker nearest to the QTL position; Interval = 1-LOD confidence interval of QTL position in cM; # = LOD peak position and confidence interval were not exactly the same in different years; LOD = LOD value at QTL position; LOD threshold = chromosome wide LOD threshold for type I error rates of 20% and 5%; %var = proportion of the total phenotypic variance explained by the QTL; KW = Kruskal-Wallis significance level, given by the P value (1 = 0.1, 2 = 0.05, 3 = 0.01; 4 = 0.005; 5 = 0.001; 6 = 0.0005; 7 = 0.0001). Complete data are referred to 2003 (2002 in case of QTL lack in 2003, as indicated by an asterisk), yearly details (year 2002, 2003 and 2004 are respectively in first, second and third position) are given for LOD scores, percentage of explained variance and Kruskal-Wallis significance, which represent the most variable data
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