View Full Table | Close Full ViewTable 1.

Designated name, representative single-nucleotide polymorphism (SNP; TagSNP), chromosome arm, location on the Illumina SNP9K consensus map, p-value, and R2-value of each quantitative trait loci (QTL) that was significant at a false discovery rate of 0.01 when the association panel was evaluated using Pt pathotypes Pt2013, Pt52-2, and Pt54-1.

 
Pt pathotype QTL TagSNP SNP Chromosome arm† Map location p-value R2
cM %
Pt2013 QLr.stars-1BC1 IWA435 5 1BC 60.13 2.09 × 10−13 4.76
QLr.stars-1BL1 IWA8153 1 1BL 148.23 3.31 × 10−5 1.36
QLr.stars-1BS1 IWA1566 7 1BS 48.08–57.72 2.31 × 10−11 3.64
QLr.stars-1BS1 IWA6110 3 1BS 9.06 × 10−15 4.83
QLr.stars-1DC1 IWA362 1 1DC 48.81 1.73 × 10−5 1.84
QLr.stars-2DL1 IWA1083 14 2DL 176.19–177.99 1.67 × 10−6 1.82
QLr.stars-7AL1 IWA6736 3 7AL 188.95 5.71 × 10−24 8.35
Pt52-2 QLr.stars-1BC1 IWA435 1 1BC 60.13 2.25 × 10−5 1.43
QLr.stars-1BL2 IWA6758 1 1BL 81.58 5.96 × 10−6 1.60
QLr.stars-1BL3 IWA579 3 1BL 115.79 4.08 × 10−5 1.35
QLr.stars-2DS1 IWA609 6 2DS 79.50–92.80 2.19 × 10−23 7.23
QLr.stars-4AL1 IWA2460 2 4AL 73.40–83.38 2.65 × 10−5 1.40
QLr.stars-4BL1 IWA6480 2 4BL 72.30–82.13 2.11 × 10−6 1.75
QLr.stars-5BL1 IWA4571 4 5BL 106.17–106.94 1.85 × 10−6 1.75
QLr.stars-7AS1 IWA3760 1 7AS 45.42 6.38 × 10−6 1.59
Pt54-1 QLr.stars-7AL1 IWA6736 1 7AL 188.95 6.29 × 10−8 1.95
QLr.stars-1BC1 IWA435 1 1BS 42.93 3.43 × 10−7 1.97
QLr.stars-2DS1 IWA4012 3 2DS 92.80–93.40 7.87 × 10−7 2.64
QLr.stars-2BL1 IWA1488 1 2BL 193.90 1.31 × 10−5 1.48
QLr.stars-1BS2 IWA6110 3 1BS 1.87 × 10−10 1.79
L, S, and C refer to long and short chromosome arms, and centromere, respectively.



View Full Table | Close Full ViewTable 2.

Allelic effects of the tag single-nucleotide polymorphisms (SNPs) underlying quantitative trait loci (QTL) for leaf rust resistance and the distribution of favorable alleles in six subpopulations

 
QTL name TagSNP SNP allele† Allele effects
Favorable allele frequency‡
Pt2013 Pt52-2 Pt54-1 S1 S2 S3 S4 S5 S6 All
————————————————— % —————————————————
QLr.stars-1BC1 IWA435 T/C 0.72 0.80 0.37 0.9 6.4 17.6 3.4 29.3 8.2 9.8
QLr.stars-1BL1 IWA8153 T/C 0.52 2.1 30.8 29.3 66.0 15.0 11.7 29.2
QLr.stars-1BS1 IWA6110 A/G 2.27 1.70 0.0 25.6 0.5 5.5 0.0 0.0 2.8
QLr.stars-1DC1 IWA362 T/C 0.26 78.8 16.7 35.2 29.3 77.4 56.1 48.4
QLr.stars-2DL1 IWA1083 T/C 0.60 2.1 30.8 29.7 65.4 14.3 11.7 29.1
QLr.stars-7AL1 IWA6736 T/C 1.26 0.69 5.0 74.4 33.4 67.8 6.8 19.9 33.9
QLr.stars-1BL2 IWA6758 A/G 0.40 2.1 6.4 14.9 10.3 44.4 15.2 11.6
QLr.stars-1BL3 IWA579 T/C 0.31 40.6 6.4 9.8 9.2 84.2 68.4 29.3
QLr.stars-2BL1 IWA1488 A/G 1.00 3.8 0.0 1.6 4.2 14.3 7.0 4.4
QLr.stars-2DS1 IWA609 A/G 2.50 3.2 5.1 2.3 2.1 23.8 9.0 5.1
QLr.stars-2DS1 IWA4012 A/G 1.02 5.3 22.2 4.5 7.7 29.2 14.9 10.2
QLr.stars-4AL1 IWA2460 T/C 0.42 1.5 3.8 13.7 8.4 70.7 14.6 14.2
QLr.stars-4BL1 IWA6480 A/C 0.56 96.5 16.7 28.4 20.3 78.9 97.7 52.0
QLr.stars-5BL1 IWA4571 T/C 0.30 81.4 88.5 71.6 92.3 70.7 93.0 80.9
QLr.stars-7AS1 IWA3760 A/C 0.48 1.8 74.4 33.4 71.0 14.3 36.3 39.2
The favorable alleles are in bold type.
S1, Iranian landrace group 1; S2, eastern European cultivar group; S4, western European cultivar group; S5, east-Asian accession group; S6, Iranian landrace group 2.