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. 2021 Jun 29;12:681768. doi: 10.3389/fgene.2021.681768

TABLE 7.

Summary of marker trait associations for PGAD (glume) and PLAD (foliar) scores from four Western Australian environments in 2018–2020.

Environment Trait QTL Chromosome SNP id SNP name SNPa IWGSC-bpb Consensus map position-cMc R2 MAFd Allele effect estimate %e p-value –log10(p)
Manjimup 2018 Glume QSng.MJ18.daw-2A.1 2A IWB59332 RAC875_c57998_165 [T/C] 202,872,663 341.14 0.08 0.42 20.25 3.56E-05 4.45
QSng.MJ18.daw-2A.2 2A IWB35263 IAAV6884 [T/C] 423,204,105 341.14 0.10 0.45 −20.93 2.18E-06 5.66
QSng.MJ18.daw-2A.3 2A IWB908 BobWhite_c1634_563 [A/G] 453,520,296 341.14 0.07 0.46 16.77 7.61E-05 4.12
2A IWB51426 Ra_c21219_505 [A/G] 461,417,569 348.36 0.08 0.45 −18.86 3.85E-05 4.41
Manjimup 2019 Glume QSng.MJ19.daw-2A 2A IWB35263 IAAV6884 [T/C] 423,204,105 341.14 0.09 0.45 −20.93 1.49E-05 4.83
Manjimup 2020 Glume QSng.MJ20.daw-1D 1D IWB35174 IAAV6247 [A/G] 10,661,637 53.03 0.08 0.41 −7.72 7.20E-05 4.14
1D IWB26984 Excalibur_c4876_832 [A/G] 10,662,717 53.03 0.10 0.43 8.31 4.50E-06 5.35
1D IWB18376 D_GBF1XID01C7T2Q_63 [T/C] 10,668,578 53.03 0.09 0.40 7.92 3.90E-05 4.41
1D IWA7533 wsnp_Ra_c1020_2062200 [A/G] 10,719,634 53.03 0.09 0.45 −7.75 2.62E-05 4.58
South Perth 2020 Glume QSng.SP20.daw-1D 1D IWB8605 BS00051826_51 [A/G] 56,751,122 108.87 0.08 0.12 −13.79 7.03E-05 4.15
QSng.SP20.daw-3A 3A IWB14389 CAP7_rep_c12940_130 [T/C] 646,272,690 346.53 0.07 0.07 −15.26 4.74E-05 4.32
QSng.SP20.daw-7B 7B IWB30294 Excalibur_rep_c107796_229 [T/C] 105,559,208 229.43 0.09 0.15 −12.80 1.94E-05 4.71
Manjimup 2018 † Foliar QSnl.MJ18.daw-1B 1B IWB49491 Kukri_rep_c111213_148 [A/G] 300,949,280 206.69 0.08 0.13 −18.24 5.44E-05 4.26
1B IWB72968 Tdurum_contig63991_404 [T/C] 301,257,710 206.01 0.10 0.14 −19.32 5.17E-06 5.29
1B IWB40986 Kukri_c13156_129 [T/C] 301,257,922 206.01 0.08 0.14 17.51 4.57E-05 4.34
1B IWB55131 RAC875_c21131_3615 [T/C] 302,206,634 206.01 0.08 0.15 17.80 2.72E-05 4.56
1B IWB23446 Excalibur_c20228_135 [T/C] 305,270,049 206.01 0.09 0.14 −19.09 1.43E-05 4.84
1B IWB71062 Tdurum_contig42289_1857 [A/C] 306,072,514 206.69 0.08 0.14 −18.34 2.32E-05 4.63
1B IWB74187 tplb0024i16_800 [A/G] 307,427,828 206.69 0.08 0.14 −17.51 2.92E-05 4.53
1B IWB72756 Tdurum_contig60809_268 [T/G] 308,587,768 206.01 0.08 0.14 17.08 4.61E-05 4.34
1B IWB72755 Tdurum_contig60809_255 [T/C] 308,587,781 206.01 0.08 0.14 −17.95 2.97E-05 4.53
1B IWB37294 JD_c2834_381 [T/C] 309,387,695 206.69 0.09 0.13 −18.57 1.38E-05 4.86
1B IWB71413 Tdurum_contig43346_108 [T/C] 309,491,071 209.95 0.08 0.13 17.33 5.91E-05 4.23
1B IWB63613 RFL_Contig1354_484 [A/G] 315,383,705 208.49 0.08 0.17 −15.85 4.37E-05 4.36
1B IWB64056 RFL_Contig2784_641 [A/G] 317,320,498 206.69 0.08 0.18 −15.57 7.32E-05 4.14
QSnl.MJ18.daw-5A 5A IWB35961 IACX448 [T/C] 588,377,301 453.34 0.08 0.39 −12.57 6.90E-05 4.16
QSnl.MJ18.daw-5B 5B IWB43679 Kukri_c29267_215 [T/C] 539,460,125 252.96 0.09 0.07 18.24 1.52E-05 4.82
Manjimup 2019 Foliar QSnl.MJ19.daw-1A 1A IWB6426 BS00011521_51 [T/C] 579,830,542 431.50 0.07 0.49 9.83 7.65E-05 4.12
QSnl.MJ19.daw-2B 2B IWB9450 BS00065105_51 [T/C] 69,648,943 262.16 0.07 0.08 −19.36 6.06E-05 4.22
QSnl.MJ19.daw-4B.1 4B IWB57527 RAC875_c39524_181 [A/G] 126,323,033 182.55 0.10 0.06 −21.86 8.18E-06 5.09
QSnl.MJ19.daw-4B.2 4B IWB41569 Kukri_c16392_1468 [T/C] 558,051,887 209.83 0.08 0.12 −20.16 5.66E-05 4.25
4B IWB38540 Ku_c16392_2687 [A/C] 558,053,253 209.83 0.08 0.11 19.30 6.33E-05 4.20
4B IWB52053 Ra_c41921_1056 [T/G] 558,053,925 209.83 0.09 0.11 −20.63 2.40E-05 4.62
4B IWB35570 IAAV8975 [T/C] 558,057,833 209.83 0.09 0.12 −22.16 7.61E-06 5.12
4B IWB63337 RAC875_rep_c95493_490 [T/C] 558,059,510 209.83 0.08 0.10 −20.31 2.58E-05 4.59
4B IWB53588 RAC875_c12762_791 [T/C] 558,580,422 209.83 0.08 0.07 20.59 4.46E-05 4.35
QSnl.MJ19.daw-5A 5A IWB7820 BS00031117_51 [T/C] 588,375,856 453.34 0.07 0.42 −13.46 7.21E-05 4.14
Manjimup 2020 Foliar QSnl.MJ20.daw-1A.1 1A IWB45604 Kukri_c46010_872 [T/G] 32,894,182 ND 0.08 0.12 11.12 1.30E-05 4.89
1A IWB26996 Excalibur_c4887_1814 [T/C] 35,533,570 184.34 0.07 0.16 9.45 5.64E-05 4.25
QSnl.MJ20.daw-1A.2 1A IWB10491 BS00070695_51 [T/C] 586,914,453 462.61 0.11 0.45 8.95 7.30E-07 6.14
QSnl.MJ20.daw-5B 5B IWA7227 wsnp_Ku_c6464_11320381 [T/C] 402,843,711 152.47 0.09 0.34 8.53 1.58E-05 4.80
5B IWB8558 BS00049793_51 [T/G] 402,843,834 152.47 0.08 0.37 8.39 5.01E-05 4.30
South Perth 2020 Foliar QSnl.SP20.daw-3D 3D IWB17658 D_F5XZDLF02HWOJZ_227 [A/G] 31,764,661 284.57 0.07 0.05 −24.50 6.69E-05 4.17
QSnl.SP20.daw-6D 6D IWB70297 Tdurum_contig31718_229 [T/C] 307,881,449 183.08 0.08 0.36 12.53 2.35E-05 4.63
6D IWB36455 Jagger_c1746_113 [T/C] 307,882,817 183.08 0.08 0.36 −12.00 5.53E-05 4.26
QSnl.SP20.daw-7A 7A IWB52779 Ra_c8937_191 [A/G] 81,498,302 332.69 0.08 0.27 13.66 5.47E-05 4.26
7A IWB64358 RFL_Contig3447_1177 [A/G] 81,498,578 332.69 0.07 0.27 13.46 6.22E-05 4.21

All SNP markers within QTL have moderate to high level of significance based on threshold values of P<7.65 × 10–5 (−log10(p) > 4.12). aDesirable SNP for reduced disease, based on the allele effect estimate, is in bold and underlined. bBase pair (bp) location of the single base change in the IWGSC RefSeq v1.0. cConsensus map position as reported in Wang et al. (2014), cM: centimorgans. dMAF: minor allele frequency. eThe effect estimates the difference between the average phenotypic values of the homozygous A genotype relative to the homozygous B genotype. †Data previously reported in Francki et al. (2020). ND, Not determined.