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Table 3 Favored alleles and genetic effects of 76 SNP loci significantly (P < 3.06 × 10− 4) associated with six phenotypic traits

From: Association of yield-related traits in founder genotypes and derivatives of common wheat (Triticum aestivum L.)

Trait SNP Name Chr. Position Favored allele Freq. (%) Allele effect
09TA 09YL 09YZ 10TA 10YL 10YZ BLUP
PH wsnp_Ra_c16846_25598885 3A 54.99 GG 93.56 −1.50*       
  wsnp_Ex_c13802_21639096 3A 56.74 TT 93.56    −1.57*     
  wsnp_BF292596A_Ta_1_1 3A 119.09 CC 74.29       −1.49*  
  wsnp_JD_c8158_9193784 3B 69.01 CC 82.52 −2.69*       
  wsnp_CAP8_c4989_2410261 3B 97.05 CC 94.37      −1.10*   
  wsnp_CAP8_c1419_836050 3B 97.26 GG 94.37     −1.24*    
  wsnp_Ex_c33463_41948471 3B 97.72 GG 94.37      −1.21*   
  wsnp_Ex_c12048_19288999 5B 71.11 TT 85.78 −4.93** −1.68* − 1.87*    −1.53* − 1.36*
  wsnp_Ku_c99567_87349060 5B 163.25 CC 90.73   −8.82** −6.91**    −5.90**  
  wsnp_Ex_c34597_42879693 6A 180.19 TT 79.02   −6.88** −6.07**     
  wsnp_Ra_rep_c69821_67403173 6B 82.68 TT 43.28     −3.06*    
  wsnp_Ex_c15458_23737002 7B 65.56 GG 61.43 −3.46**    −3.32*    
SL wsnp_JD_c6974_8084752 3B 95.50 GG 93.49 0.80*       
  wsnp_CAP8_c4989_2410261 3B 97.05 CC 94.37     1.05*    
  wsnp_CAP8_c1419_836050 3B 97.26 GG 94.37      1.10**   1.09**
  wsnp_Ex_c33463_41948471 3B 97.72 GG 94.37    0.76*     
  wsnp_Ex_c1563_2987002 4A 136.22 GG 93.95      0.64*   0.72*
  wsnp_Ex_c28092_37240192 4A 140.47 GG 95.10     0.58*    
  wsnp_Ex_rep_c67779_66463916 4A 141.36 CC 94.84   0.40* 0.37*   0.49*   0.62*
  wsnp_Ex_c2266_4247520 4A 141.80 AA 94.81      0.38*   0.49*
  wsnp_Ex_c12_21212 4A 143.00 TT 94.84    0.49*     
  wsnp_Ex_c3463_6348659 4A 144.11 GG 94.81     0.48* 0.45* 0.60*  
  wsnp_Ex_c13942_21820758 5A 102.41 GG 91.63        0.89*
  wsnp_Ex_c49211_53875575 5A 108.64 GG 60.47 0.32** 0.42** 0.30** 0.27** 0.62** 0.52**  
  wsnp_Ex_c10127_16635328 5A 108.92 TT 64.19 0.18*       
  wsnp_Ex_c19647_28632894 5A 123.92 GG 53.49       0.48*  
  wsnp_Ex_c1630_3105100 5B 161.77 AA 94.81      1.34**   
  wsnp_Ex_c2459_4591695 5B 212.53 AA 94.88      0.97**   0.68**
  wsnp_Ex_c8510_14306239 6A 175.39 AA 94.39      1.02**   0.74**
  wsnp_Ex_c46061_51675853 7B 25.00 GG 19.34       0.89*  
  wsnp_Ex_rep_c101269_86664147 7B 132.23 AA 23.27   0.57**     0.78**  
SNPS wsnp_BM140362B_Ta_1_1 1B 76.37 AA 93.84     1.08*    
  wsnp_Ku_rep_c68484_67499824 3A 99.60 TT 66.67    0.46*     
  wsnp_Ex_rep_c67136_65617520 4B 108.15 CC 87.25    0.73*     
  wsnp_Ku_c21275_31007309 5A 85.17 CC 36.28   0.45*      
  wsnp_RFL_Contig3939_4369467 5A 94.73 CC 88.37   1.08**      
  wsnp_Ex_c7713_13153321 6B 127.53 CC 89.47 1.48**       
KNPS wsnp_JD_c6974_8084752 3B 95.50 GG 93.49     2.79*    
  wsnp_Ex_c6129_10723019 3B 97.26 CC 91.59    2.71**    2.50**  
  wsnp_Ku_c29102_39008953 3B 123.29 AA 74.04 3.18** 3.84**      3.45**
  wsnp_Ku_c31407_41142340 3B 125.61 AA 76.64      1.23*   
  wsnp_Ex_c11837_18996495 3B 126.24 GG 77.25   3.97**      3.27**
  wsnp_Ex_c12781_20280445 3B 126.61 GG 76.64      3.25** 3.27**  
  wsnp_Ex_c13154_20784674 3B 127.87 CC 76.92 3.59** 4.18**      3.73**
  wsnp_Ex_c13154_20785032 3B 127.87 AA 76.56 3.44**       3.55**
  wsnp_Ex_c13953_21831752 4A 13.89 CC 81.43    4.27** 3.45**    
  wsnp_Ex_c16551_25060833 5A 190.95 CC 19.53 2.01*       
  wsnp_Ex_c1630_3105100 5B 161.77 AA 94.81     2.49*    
  wsnp_Ex_c1302_2489542 5B 184.33 TT 89.37       2.62*  
  wsnp_Ku_c56917_60245833 5B 185.06 CC 89.47       2.74*  
  wsnp_Ku_c19037_28455905 7B 57.38 GG 80.90    0.88*     
KWPS wsnp_Ex_rep_c106111_90308719 1A 12.73 TT 6.10   0.11*      0.10*
  wsnp_Ex_c1130_2166731 1D 54.49 GG 6.05        0.20*
  wsnp_Ex_rep_c69919_68881108 3A 117.88 AA 70.48     0.03*    
  wsnp_Ex_rep_c104327_89077792 3A 118.07 AA 70.48    0.03*     
  wsnp_Ra_c19079_28210937 3A 123.35 AA 47.85   0.02*      
  wsnp_Ex_c12341_19693570 3A 127.51 CC 57.21 0.14**    0.20**   0.21**  
  wsnp_Ku_c29102_39008953 3B 123.29 CC 25.96    0.10*     
  wsnp_Ex_c13154_20785032 3B 127.87 GG 23.44 0.11*       
  wsnp_Ex_rep_c67136_65617520 4B 108.15 CC 87.25    0.05*     
  wsnp_JD_rep_c49046_33288885 5A 116.00 CC 92.56    0.31**     0.15**
  wsnp_Ku_c14275_22535693 5A 116.57 AA 90.70     0.15*    
  wsnp_Ku_c14275_22535576 5A 116.83 TT 90.70       0.17*  
  wsnp_Ex_c43578_49857984 5A 130.98 TT 72.56   0.20**      0.20**
  wsnp_Ex_rep_c101757_87064771 5A 133.01 CC 97.21    0.18*     
  wsnp_Ex_rep_c101757_87065169 5A 133.17 CC 90.70 0.18*       
  wsnp_Ex_c57667_59284398 5B 125.89 CC 56.59 0.07*       
  wsnp_Ex_c1050_2009301 6A 45.73 TT 85.10     0.19*    
  wsnp_Ex_c19467_28423197 6B 50.70 AA 7.62 0.26*       
  wsnp_Ex_c65899_64135487 7D 1.12 AA 95.12   0.01*      
TKW wsnp_Ex_c3685_6723631 2A 9.91 GG 34.11        1.07*
  wsnp_BE406351A_Ta_2_2 2A 112.62 TT 66.03 0.83*       
  wsnp_RFL_Contig2914_2757372 2B 211.84 AA 61.46      1.19*   
  wsnp_Ku_rep_c69511_68887456 3A 59.73 TT 55.77 1.41** 1.01** 1.48**     1.33**
  wsnp_CAP12_c4769_2174195 4B 106.45 CC 89.76     1.26*    
  wsnp_BF291478B_Ta_2_1 6B 80.00 CC 84.21 1.18*       
  1. *indicates significant at P < 0.05 **indicates significant at P < 0.01