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. 2021 Mar 18;10(3):572. doi: 10.3390/plants10030572

Table 1.

Single nucleotide polymorphisms (SNPs) significantly associated with stripe rust disease severity identified in the Manhattan plots. The “Chr” and “Position” columns correspond to the chromosome and position of the particular SNP in the reference sequence assembly in base pairs (bp). The “p-value” is the significance level from the Manhattan plots in Figure 5. “MAF” is the minor allele frequency at that SNP. The “R2 of Model without SNP” is the value of the coefficient of determination (R2) if the SNP were not present. The “R2 of Model with SNP” is the R2 value with that SNP included and indicates the effect of the quantitative trait loci (QTL). “Effect” is the effect of that allele on stripe rust disease severity.

Loc/Year SNP Chr Position (bp) p-Value MAF R2 of Model without SNP R2 of Model with SNP Effect
Pull17 S3B_5601689 3B 5601689 4.92E-06 0.4897 0.0293 0.1417 −14.4141
S3B_6309966 3B 6309966 1.14E-06 0.4948 0.0293 0.1578 −15.5142
S3B_6309968 3B 6309968 1.44E-06 0.4948 0.0293 0.1552 15.2734
S3B_6309973 3B 6309973 3.97E-06 0.4923 0.0293 0.1441 −14.7001
S3D_4068757 3D 4068757 4.67E-06 0.4923 0.0293 0.1423 −14.5157
S3D_4068759 3D 4068759 1.37E-06 0.4948 0.0293 0.1558 15.3027
S3D_4068764 3D 4068764 3.37E-06 0.5000 0.0293 0.1459 −14.7276
SUN_234960006 UN 234960006 6.41E-06 0.4871 0.0293 0.1389 14.0261
SUN_242439365 UN 242439365 1.40E-06 0.4974 0.0293 0.1556 15.3145
SUN_242439370 UN 242439370 1.64E-06 0.4923 0.0293 0.1538 −15.2480
SUN_242439372 UN 242439372 1.44E-06 0.4948 0.0293 0.1552 15.2734
SUN_242452400 UN 242452400 1.44E-06 0.4948 0.0293 0.1552 15.2734
SUN_242452405 UN 242452405 1.85E-06 0.4923 0.0293 0.1525 −15.0780
SUN_242452407 UN 242452407 1.44E-06 0.4948 0.0293 0.1552 15.2734
SUN_34103779 UN 34103779 4.82E-06 0.4871 0.0293 0.1420 −14.1982
SUN_36153637 UN 36153637 1.18E-06 0.4923 0.0293 0.1575 15.2504
Pull18 S3B_10644041 3B 10644041 6.31E-06 0.4948 0.0454 0.1533 −3.6371
S3B_5601689 3B 5601689 9.62E-08 0.4897 0.0454 0.1993 −4.5888
S3B_6309966 3B 6309966 3.01E-08 0.4948 0.0454 0.2124 −4.8326
S3B_6309968 3B 6309968 3.53E-08 0.4948 0.0454 0.2106 4.7814
S3B_6309973 3B 6309973 5.02E-07 0.4923 0.0454 0.1808 −4.3634
S3D_4068757 3D 4068757 9.81E-08 0.4923 0.0454 0.1990 −4.6159
S3D_4068759 3D 4068759 3.80E-08 0.4948 0.0454 0.2098 4.7628
S3D_4068764 3D 4068764 8.89E-08 0.5000 0.0454 0.2001 −4.6256
S3D_909572 3D 909572 3.03E-07 0.4871 0.0454 0.1864 4.4075
SUN_234960006 UN 234960006 3.19E-07 0.4871 0.0454 0.1858 4.3198
SUN_242439365 UN 242439365 2.82E-08 0.4974 0.0454 0.2132 4.8227
SUN_242439370 UN 242439370 4.26E-08 0.4923 0.0454 0.2085 −4.7693
SUN_242439372 UN 242439372 3.53E-08 0.4948 0.0454 0.2106 4.7814
SUN_242452400 UN 242452400 3.53E-08 0.4948 0.0454 0.2106 4.7814
SUN_242452405 UN 242452405 4.94E-08 0.4923 0.0454 0.2068 −4.7150
SUN_242452407 UN 242452407 3.53E-08 0.4948 0.0454 0.2106 4.7814
SUN_34103779 UN 34103779 2.57E-07 0.4871 0.0454 0.1883 −4.3396
SUN_36153637 UN 36153637 4.08E-08 0.4923 0.0454 0.2090 4.6933
MV17 S3B_5601689 3B 5601689 1.83E-06 0.4897 0.0399 0.1618 −13.6630
S3B_6309966 3B 6309966 6.72E-08 0.4948 0.0399 0.1987 −15.7371
S3B_6309968 3B 6309968 9.41E-08 0.4948 0.0399 0.1948 15.4645
S3B_6309973 3B 6309973 2.71E-07 0.4923 0.0399 0.1829 −14.9769
S3D_4068757 3D 4068757 1.64E-07 0.4923 0.0399 0.1886 −15.1775
S3D_4068759 3D 4068759 9.68E-08 0.4948 0.0399 0.1945 15.4336
S3D_4068764 3D 4068764 1.25E-07 0.5000 0.0399 0.1917 −15.3139
S3D_909572 3D 909572 9.27E-06 0.4871 0.0399 0.1443 12.6911
SUN_234960006 UN 234960006 4.29E-06 0.4871 0.0399 0.1526 12.9439
SUN_242439365 UN 242439365 1.24E-07 0.4974 0.0399 0.1918 15.3257
SUN_242439370 UN 242439370 1.26E-07 0.4923 0.0399 0.1915 −15.3581
SUN_242439372 UN 242439372 9.41E-08 0.4948 0.0399 0.1948 15.4645
SUN_242452400 UN 242452400 9.41E-08 0.4948 0.0399 0.1948 15.4645
SUN_242452405 UN 242452405 1.11E-07 0.4923 0.0399 0.1929 −15.3378
SUN_242452407 UN 242452407 9.41E-08 0.4948 0.0399 0.1948 15.4645
SUN_34103779 UN 34103779 7.49E-06 0.4871 0.0399 0.1466 −12.5548
SUN_36153637 UN 36153637 4.92E-06 0.4923 0.0399 0.1511 12.9378
MVC18 S3B_5601689 3B 5601689 4.87E-09 0.4897 0.1426 0.3115 −22.4636
S3B_6309966 3B 6309966 5.65E-10 0.4948 0.1426 0.3344 −24.5208
S3B_6309968 3B 6309968 7.64E-10 0.4948 0.1426 0.3312 24.2253
S3B_6309973 3B 6309973 3.51E-09 0.4923 0.1426 0.3150 −23.3131
S3D_4068757 3D 4068757 1.14E-09 0.4923 0.1426 0.3269 −23.7960
S3D_4068759 3D 4068759 1.17E-09 0.4948 0.1426 0.3266 23.7896
S3D_4068764 3D 4068764 9.19E-10 0.5000 0.1426 0.3292 −23.8661
S3D_909572 3D 909572 3.61E-08 0.4871 0.1426 0.2908 20.9861
SUN_234960006 UN 234960006 1.57E-08 0.4871 0.1426 0.2993 21.2737
SUN_242439365 UN 242439365 9.10E-10 0.4974 0.1426 0.3293 24.0836
SUN_242439370 UN 242439370 1.14E-09 0.4923 0.1426 0.3269 −24.0405
SUN_242439372 UN 242439372 7.64E-10 0.4948 0.1426 0.3312 24.2253
SUN_242452400 UN 242452400 7.64E-10 0.4948 0.1426 0.3312 24.2253
SUN_242452405 UN 242452405 1.35E-09 0.4923 0.1426 0.3251 −23.7279
SUN_242452407 UN 242452407 7.64E-10 0.4948 0.1426 0.3312 24.2253
SUN_34103779 UN 34103779 2.13E-08 0.4871 0.1426 0.2962 −20.8097
SUN_36153637 UN 36153637 3.62E-09 0.4923 0.1426 0.3146 22.5449