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Table 1 Significant associations between SNP genotypes and blast resistance in the analyzed rice accessions

From: Genome wide association studies for japonica rice resistance to blast in field and controlled conditions

Category MTA
ID
Peak Marker/Region (bp) Chr. -log10(p) #SNP Associated region (bp) Peak marker R2 a LD block (bp) SNP alleles at peak markerb Average blast score Allelic frequence (%)
       Start End Size   Start-End    Total K1 K2 Adm.
Field BRF01 S1_32855693 1 4.369 1 6.23% 32,855,693-33,101,889 A 7.39 93.5 92.0 100.0 90.9
G 5.26 6.5 8.0 0.0 9.1
Field BRF04 S4_31566281 4 14.594 31 31,257,415 32,476,401 1,218,986 19.54% T 7.59 91.4 96.4 75.9 91.7
G 3.23 8.6 3.6 24.1 8.3
Field BRF06–1 S6_10184497 6 5.889 17 10,108,408 11,927,672 1,819,264 7.77% C 7.60 92.4 94.4 92.2 74.2
A 4.52 7.6 5.6 7.8 25.8
Field BRF06–2 S6_29136506 6 3.963 1 5.08% A 7.06 58.8 57.4 59.6 64.9
G 7.44 41.2 42.6 40.4 35.1
Field BRF07 S7_23126442 7 4.723 1 6.18% A 7.35 94.5 92.3 100.0 100.0
G 4.95 5.5 7.7 0.0 0.0
Field BRF10 S10_14442878 10 4.450 2 14,421,776 14,442,878 21,102 5.79% G 6.75 58.6 47.9 79.3 83.8
A 7.86 41.4 52.1 20.7 16.2
Field BRF11–1 S11_27464620 11 5.476 28 26,482,681 27,672,972 1,190,291 7.26% 26,090,712-28,791,205 C 7.57 91.7 99.5 72.4 83.8
T 4.12 8.3 0.5 27.6 16.2
Field BRF11–2 S11_28957771 11 6.304 2 28,900,124 28,957,771 57,647 8.43% 28,807,359-29,018,344 T 7.64 83.8 91.3 56.9 86.5
G 5.05 16.2 8.7 43.1 13.5
Growth chamber BRGC01 S1_1719121 1 3.872 1 5.65%   A 3.48 80.4 97.9 26.4 68.6
G 2.71 19.6 2.1 73.6 31.4
Growth chamber BRGC06 S6_10390066 6 6.068 20 9,906,359 10,685,711 779,352 9.55%   C 3.51 89.1 94.7 86.5 63.9
T 2.00 10.9 5.3 13.5 36.1
Growth chamber BRGC07 S7_22505151 7 4.167 1 6.14%   G 3.41 92 90.4 92.5 100.0
A 2.47 8 9.6 7.5 0.0
Growth chamber BRGC11–1 S11_25555354 11 4.413 5 24,811,878 25,555,354 743,476 6.03% 24,068,338-26,090,282 T 3.54 87 97.3 67.3 61.1
G 1.95 13 2.7 32.7 38.9
Growth chamber BRGC11–2 S11_27672972 11 5.975 25 26,482,681 28,167,315 1,684,634 8.34% 26,090,712-28,791,205 C 3.47 92.4 97.9 75.5 88.9
T 1.65 7.58 2.1 24.5 11.1
Growth chamber BRGC11–3 S11_28957771 11 7.143 34 28,809,430 29,007,377 197,947 11.54% 28,807,359-29,018,344 T 3.54 84.1 91.0 58.5 86.1
G 2.25 15.9 9.0 41.5 13.9
  1. For each trait, the peak marker (SNP with the highest p-value) is reported. avariance explained by the marker/region; bMajor allele is written in bold letters