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Table 4 Results of the genetic analyses performed on the WOSR (A) or DH (B) populations for [a] the genotypic estimates extracted from the multi-environment model (\( {\boldsymbol{P}}_{\boldsymbol{i}\boldsymbol{jklm}} = \boldsymbol{\mu} +\underline {{\boldsymbol{G}}_{\boldsymbol{i}}} + {\boldsymbol{N}}_{\boldsymbol{j}} + \underline {{\boldsymbol{T}}_{\boldsymbol{l}}}+\underline {{\boldsymbol{T}}_{\boldsymbol{l}}\left({\boldsymbol{R}}_{\boldsymbol{k}}\right)} + \underline {{\boldsymbol{G}}_{\boldsymbol{i}}\times {\boldsymbol{N}}_{\boldsymbol{j}}}+\underline {{\boldsymbol{G}}_{\boldsymbol{i}} \times {\boldsymbol{T}}_{\boldsymbol{l}}} + \underline {{\boldsymbol{G}}_{\boldsymbol{i}}\times {\boldsymbol{N}}_{\boldsymbol{j}}\times {\boldsymbol{T}}_{\boldsymbol{l}}} + \underline {{\boldsymbol{e}}_{\boldsymbol{i}\boldsymbol{jklm}}} \) (model 1)) and [b] the ecovalence values calculated using the G × N or G × T model (\( {\boldsymbol{W}}_{\boldsymbol{i}} = {\displaystyle \sum_{\boldsymbol{i}}}\left({\boldsymbol{Y}}_{\boldsymbol{i}\boldsymbol{j}}-{\boldsymbol{Y}}_{\boldsymbol{i}.}-{\boldsymbol{Y}}_{.\boldsymbol{j}}+{\boldsymbol{Y}}_{..}\ \right)2 \) (model 8))

From: Genetic basis of nitrogen use efficiency and yield stability across environments in winter rapeseed

A (WOSR populations)
Model (a) Trait LG Marker (b) Position (cM) (c) Position (bp) (d) MAF (e) FDR (f) R2 (g) CI (cM) (h) CI (bp) (i) Favorable allele (j) Additivity (k)
G [a] SY A1 Bn-A01-p1000115 3.0 617,658 0.18 0.08 0.13 1.73 234,187 T 0.25
Bn-A01-p5480514 36.4 5,042,546 0.43 0.10 0.13 1.50 158,442 G 0.18
Bn-A01-p20990218 65.3 17,795,523 0.21 0.10 0.12 0.30 370,421 C 0.23
Bn-A01-p24697185 74.6 20,465,114 0.40 0.10 0.12 5.70 184,781 G 0.20
A3 Bn-A03-p766322 1.1 634,722 0.39 0.14 0.11 4.70 400,479 A 0.20
Bn-C3-p15411996 64.8 9,973,043 0.10 0.13 0.12 72.10 315,568 T 0.27
A4 Bn-A04-p11510797 22.1 12,567,132 0.10 0.02 0.21 0.65 323,361 A 0.39
A5 Bn-A05-p4108818 32.1 3,986,210 0.32 0.15 0.11 6.00 608,673 A 0.20
Bn-A05-p6897871 48.8 6,348,806 0.07 0.03 0.17 7.10 1,584,822 A 0.40
Bn-A05-p23166612 99.8 21,325,804 0.19 0.02 0.18 6.15 2,427,395 C 0.30
A8 Bn-A08-p14156050 17.9 11,851,743 0.42 0.15 0.11 2.30 390,921 C 0.19
Bn-A08-p16125811 28.2 13,582,310 0.06 0.15 0.11 3.35 370,297 G 0.31
A9 Bn-A09-p3024539 20 2,944,505 0.49 0.02 0.22 32.53 5,529,615 T 0.28
Bn-A08-p9226756 65.5 14,301,186 0.09 0.15 0.11 0.00 1,533,647 T 0.29
A10 Bn-A10-p9052583 13.5 10,444,212 0.10 0.12 0.12 6.80 1,679,566 A 0.29
C1 Bn-C1-p5199797 31.5 5,036,240 0.31 0.09 0.13 0.00 410,741 A 0.21
Bn-C1-p37170472 77.4 34,962,509 0.17 0.09 0.13 0.00 1,141,921 A 0.23
C2 Bn-C2-p50647994 125.4 44,768,073 0.40 0.06 0.15 39.00 5,044,117 C 0.22
C5 Bn-C5-p45854218 117.0 42,566,107 0.29 0.07 0.14 1.50 230,043 A 0.20
C6 Bn-C6-p19300068 42.9 18,948,227 0.12 0.06 0.14 8.20 1,201,949 G 0.30
Bn-C6-p8469110 65.9 28,380,973 0.37 0.15 0.11 9.50 5,946,818 C 0.21
C7 Bn-C7-p32630456 41.0 32,902,306 0.22 0.02 0.21 0.70 3,328,120 T 0.31
Bn-C7-p37740616 57.8 34,843,632 0.22 0.02 0.20 3.68 1,113,132 A 0.32
C8 Bn-C8-p21614432 31.8 20,898,335 0.28 0.11 0.12 6.40 545,619 G 0.21
C9 Bn-C9-p2006237 16.3 872,443 0.49 0.03 0.17 12.80 3,275,350 G 0.26
O A5 Bn-A02-p26656981 103.2 22,149,643 0.20 0.12 0.21 2.86 976,652 G 0.84
A9 Bn-A09-p1989556 15.6 1,964,619 0.33 0.12 0.27 12.60 2,168,340 A 0.84
Bn-A09-p6950255 50.4 5,891,565 0.37 0.12 0.24 0.55 329,763 A 0.74
C1 Bn-C1-p5199797 31.5 5,036,240 0.31 0.12 0.23 3.14 1,808,094 A 0.78
C7 Bn-C7-p36749441 53.6 33,959,826 0.20 0.12 0.23 10.22 3,157,954 A 0.93
Bn-C7-p38504198 59.9 35,328,335 0.32 0.14 0.20 2.75 651,737 T 0.73
O/Pr A9 Bn-A09-p3051349 20.3 2,971,796 0.46 0.13 0.24 4.80 745,210 G 0.13
G × N [b] O A5 Bn-A02-p26656981 103.2 22,149,643 0.20 0.12 0.21 2.86 976,653 G 0.32
A9 Bn-A09-p1989556 15.6 1,964,619 0.33 0.12 0.27 12.60 2,168,341 A 0.32
Bn-A09-p6950255 50.4 5,891,565 0.37 0.12 0.24 0.55 329,762 A 0.28
C1 Bn-C1-p5195180 31.5 5,031,632 0.31 0.12 0.23 3.14 1,771,001 T 0.30
C7 Bn-C7-p35762591 51.0 33,046,261 0.20 0.12 0.23 10.22 3,825,530 G 0.35
G × T [b] SY A1 Bn-A01-p3005793 22.7 2,717,050 0.12 0.15 0.20 25.00 467,612 T 1.42
Bn-A01-p19929280 62.9 16,718,048 0.07 0.15 0.19 1.20 953,751 G 1.67
Bn-A01-p23321507 70.1 19,192,316 0.06 0.06 0.31 5.40 2,053,778 C 2.38
A3 Bn-A03-p3795299 31.7 3,348,503 0.07 0.15 0.20 1.00 142,079 A 1.69
Bn-A03-p19897251 108 18,786,539 0.08 0.15 0.20 1.80 309,561 A 1.71
A4 Bn-A04-p8348806 11.2 9,654,868 0.06 0.06 0.30 0.30 290,373 T 2.52
A7 Bn-A07-p10750190 27.6 11,956,021 0.08 0.15 0.23 13.35 2,016,127 A 1.80
  Bn-A07-p13485722 45.2 15,490,316 0.07 0.09 0.26 0.90 179,009 T 1.95
C6 Bn-C6-p10394225 64.7 26,530,886 0.07 0.15 0.21 3.00 2,341,718 C 1.73
Bn-C6-p4142963 74.6 32,815,121 0.13 0.15 0.19 5.58 855,273 A 1.30
O A3 Bn-A03-p3857752 32.2 3,414,578 0.12 0.03 0.36 1.50 243,919 C 407.71
Bn-A03-p19897251 108 18,786,539 0.08 0.00 0.56 8.20 1,991,427 A 646.30
A5 Bn-A05-p5372015 39.9 5,159,907 0.06 0.05 0.32 9.80 1,033,840 T 527.86
Bn-A05-p23876386 104.6 22,847,000 0.17 0.13 0.28 2.60 397,014 T 333.29
A8 Bn-A08-p10270998 5.3 8,220,334 0.06 0.06 0.31 14.40 7,267,401 A 518.40
Bn-A08-p14375712 20.3 12,062,255 0.07 0.15 0.27 0.90 299,176 G 435.05
C4 Bn-C4-p1583238 7.5 1,269,444 0.12 0.04 0.34 0.00 543 G 406.32
Bn-C4-p9031482 47.8 8,359,826 0.06 0.05 0.32 3.30 643,168 C 527.86
Pr A3 Bn-A03-p3862928 32.2 3,422,213 0.10 0.06 0.34 1.40 73,710 C 96.42
Bn-A03-p11364656 68.3 10,465,900 0.07 0.11 0.27 0.60 120,617 G 99.10
Bn-A03-p19897251 108 18,786,539 0.08 0.02 0.45 6.10 1,665,096 A 126.30
O/Pr A1 Bn-A01-p1409723 6.7 1,006,909 0.07 0.10 0.29 1.24 148,550 A 2.21
Bn-A01-p3378332 24.8 3,044,540 0.10 0.15 0.25 0.00 131,684 A 1.84
A3 Bn-A03-p3851195 32.2 3,406,943 0.12 0.08 0.31 2.00 212,147 T 1.85
Bn-A03-p11364656 68.3 10,475,189 0.07 0.12 0.28 0.90 223,645 G 2.16
Bn-A03-p19897251 108 18,786,539 0.08 0.00 0.55 8.20 1,991,427 A 3.03
A7 Bn-A07-p16965943 67.1 18,885,532 0.06 0.07 0.35 2.00 190,634 T 2.71
B: (DH populations)
Model(l) Population Trait LG Marker (m) Position (cM) (n) Position (bp) (o) LOD (p) R2 (q) CI (cM) (r) CI (bp) (s) Favorable allele (t) Additivity (u)
G [a] AM-DH DTF A1 Bn-A01-p821328 0.9 449,990 10.48 0.19 1.8 157,286 Aviso 1.67
A2 Bn-A02-p10621504 31.6 7,486,332 10.73 0.20 2 1,268,217 Aviso 1.34
C2 Bn-C2-p2374956 22 - 12.51 0.24 4.5 2,829,279 Aviso 1.38
C6 Bn-C6-p4847689 54 32,036,565 12.08 0.23 7.4 4,825,658 Montego 1.58
SY A5 BS005820 30.7 3,536,588 7.2 0.21 5.8 577,487 Montego 0.92
C3 Bn-C3-p1719357 8.2 1,592,799 5.72 0.16 5.1 749,919 Aviso 0.84
SN A1 Bn-A01-p2884934 22.4 2,388,770 4.76 0.15 19.6 2,415,980 Montego 1513.74
A5 BS006984 44.4 8,910,408 4.43 0.14 39.8 17,132,188 Montego 1794.32
TSW C3 BS010983 136.7 51,428,020 3.57 0.11 20 7,091,270 Aviso 0.05
C4 BS009060 0 834,581 3.66 0.11 22.4 11,856,417 Aviso 0.07
C5 Bn-C5-p41401139 66.3 38,568,003 4.15 0.12 10 3,714,187 Montego 0.06
DK-DH DTF A2 BS006299 44 375,658 12.87 0.28 7.4 3,335,785 Express 1.67
A10 BS010793 50 2,137,761 6.59 0.12 3.8 651,272 Express 1.18
C6 Bn-C6-p8468434 63.7 28,381,646 16.92 0.41 1.6 82,072 Tenor 2.32
TSW A5 BS038657 83.7 - 3.57 0.12 18 1,623,621 Express 0.05
A6 Bn-A06-p3184395 37.1 3,059,935 4.98 0.17 11 591,264 Tenor 0.06
C2 Bn-C2-p7577094 12 - 5.1 0.17 10 8,848,115 Tenor 0.07
O/Pr C2 Bn-Scaffold00285-p518297 42.9 39,511,111 3.45 0.17 15.7 7,299,924 Express 0.01
Pr C2 Bn-Scaffold00285-p518297 42.9 39,511,111 4.07 0.20 24 7,170,032 Tenor 0.11
G × N [b] AM-DH SN A1 Bn-A01-p2841043 22.4 2,350,106 4.93 0.16 15.6 936,796 Montego 9.0.105
A5 Bn-A05-p15236669 45.3 11,713,855 4.79 0.16 39.8 8,839,936 Montego 8.8.105
TSW A1 Bn-A01-p2841043 22.4 2,350,106 3.89 0.07 11.8 1,358,912 Aviso 0.01
A4 BS009059 0 834,628 8.2 0.17 8.9 5,557,003 Aviso 0.01
A7 Bn-A07-p10635069 21.7 11,816,784 3.83 0.07 14.3 2,286,113 Aviso 0.01
A9 Bn-A09-p32257776 109.2 30,105,456 5.09 0.10 10 36,978 Montego 0.01
C3 Bn-C3-p55422785 136.7 51,342,596 5.82 0.11 5.1 1,520,491 Aviso 0.01
C5 Bn-C5-p41401139 66.3 38,568,003 5.91 0.12 4 1,265,089 Montego 0.01
O C1 Bn-C1-p7004482 44.6 6,770,122 3.56 0.14 22 4,433,568 Montego 0.35
Pr A1 BS010224 69.5 19,925,267 3.49 0.14 48 18,210,785 Aviso 0.28
O/Pr A2 Bn-A02-p26398002 74.4 24,112,871 3.66 0.13 16 1,091,767 Montego 1.82.10−3
C3 Bn-C3-p579321 1 520,340 3.81 0.14 2.8 441,719 Aviso 1.90.10−3
DK-DH DTF A2 Bn-A02-p9506103 43.7 6,320,247 14.1 0.30 4 2,927,770 Express 14.1
A10 BS010815 44.9 15,547,512 5.63 0.09 8 651,272 Express 5.63
C6 Bn-C6-p8468434 63.7 28,381,646 17.41 0.41 1.3 790,491 Express 17.41
TSW A5 Bn-A05-p21375514 83.7 19,544,037 4.14 0.14 20 1,334,758 Express 4.14
A6 Bn-A06-p3184395 37.1 3,059,935 4.57 0.16 9.7 162,861 Express 4.57
C2 Bn-Scaffold01089-p23965 11.5 6,472,037 4.47 0.15 12.3 2,436,439 Express 4.47
Pr C2 Bn-Scaffold00285-p518297 42.9 39,511,111 4.35 0.21 15.6 7,299,924 Express 4.35
O/Pr A6 Bn-A06-p18634396 85 19,998,443 4.61 0.14 15.3 1,358,110 Express 1.88.10−5
A8 Bn-A08-p14799839 21.3 12,362,293 3.77 0.11 10 999,231 Tenor 1.93.10−5
C2 Bn-C3-p24936161 39.5 36,232,623 6.23 0.20 7 1,632,362 Express 2.18.10−5
G × T [b] AM-DH DTF A1 Bn-A01-p1150857 5.2 754,478 7.55 0.13 7 537,061 Aviso 55
A2 Bn-A02-p7892272 31.6 4,878,455 10.63 0.20 3.6 2,645,488 Aviso 59.93
C2 Bn-C2-p2054626 19 246,359 10.27 0.19 6.8 202,734 Aviso 49.08
C6 Bn-C6-p8905311 47.2 27,985,250 9.79 0.18 7.3 298,022 Montego 48.73
SN A1 Bn-A01-p2069488 13.3 1,561,728 4.74 0.19 19.2 1,921,336 Montego 2.34.108
Pr A1 Bn-A01-p2538180 17.3 2,035,020 3.12 0.11 16.8 1,601,066 Aviso 2.6
A9 Bn-C9-p17562068 54.4 9,942,680 4.49 0.16 15.4 17,290,961 Aviso 3.28
DK-DH DTF A2 Bn-A02-p9506103 43.7 6,320,247 13.09 0.29 4.2 2,152,190 Express 13.09
  A10 A10_BS010815 44.9 15,547,512 5.14 0.09 7.8 651,272 Express 41.43
  C6 Bn-C6-p8468434 63.7 28,381,646 16.43 0.40 1.3 790,491 Tenor 84.49
TSW C2 Bn-C2-p17324647 19.1 13,977,345 4.92 0.24 11.5 16,386,686 Tenor 0.34
Pr C2 Bn-Scaffold00285-p518297 42.9 39,511,111 4.01 0.20 15.6 7,299,924 Tenor 6.7
O/Pr C2 Bn-Scaffold00285-p518297 42.9 39,511,111 3.26 0.16 13.9 6,363,073 Express 0.24
  1. (a) For the model considered in [a], genotypic estimates were extracted from multi-environment model (1), and for the model considered in [b], ecovalence values were calculated using G × N or G × T model (8)
  2. (b) SNP at the most significant position of the QTL
  3. (c) Genetic position of the most significant marker on the WOSR map (in cM)
  4. (d) Physical position of the most significant marker within the physical sequence of B. napus (in bp)
  5. (e) Minor allele frequency
  6. (f) False discovery rate
  7. (g) Phenotypic variance explained by the most significant SNP
  8. (h) Confidence interval of the QTL on the WOSR genetic map (in cM)
  9. (1) Confidence interval of the QTL within the genomic sequence (in bp)
  10. (j) Favorable allele at the most significant SNP
  11. (k) Allelic effect of the favorable allele at the most significant position
  12. (l) Model considered (as in Table 4A)
  13. (m) SNP at the most significant position of the QTL
  14. (n) Genetic position of the most significant marker on the WOSR map (in cM)
  15. (o) Physical position of the most significant marker within the physical sequence of B. napus (in bp)
  16. (p) Log of likelihood of the genetic model for the tested QTL
  17. (q) Phenotypic variance explained by the most significant SNP
  18. (r) Confidence interval of the QTL on the WOSR genetic map (in cM)
  19. (s) Confidence interval of the QTL within the genomic sequence (in bp)
  20. (t) Favorable allele at the most significant SNP
  21. (u) Allelic effect of the favorable allele at the most significant position