Genomic Prediction for Rust Resistance in Diverse Wheat Landraces
Hans D. Daetwyler*, Urmil K. Bansal, Harbans S. Bariana, Matthew J. Hayden and Ben J. Hayes
Theoretical and Applied Genetics, 2014
*Corresponding author:
Supplementary Information
Table S1. List of Watkins genotypes (Triticum aestivum) used in study along with their country of origin
Aus No. / Country / Aus No. / CountryAus26410 / Greece / Aus27983 / Soviet union republic
Aus26414 / Greece / Aus27307 / Soviet union republic
Aus26429 / Greece / Aus27314 / Australia
Aus26431 / Greece / Aus27315 / Australia
Aus26438 / Cyprus / Aus27317 / Australia
Aus26491 / Greece / Aus27318 / Australia
Aus26526 / Morocco / Aus27320 / Australia
Aus26552 / Portugal / Aus27339 / Australia
Aus26558 / Iran / Aus27346 / Yugoslavia
Aus26559 / Iran / Aus27348 / Yugoslavia
Aus26580 / Portugal / Aus27354 / Myanmar
Aus26624 / Spain / Aus27355 / Myanmar
Aus26667 / Tunisia / Aus27356 / Morocco
Aus26673 / Tunisia / Aus27357 / Morocco
Aus27215 / Afghanistan / Aus27361 / Spain
Aus27225 / Yugoslavia / Aus27362 / Spain
Aus27905 / Syria / Aus27363 / Spain
Aus27229 / Spain / Aus27367 / Soviet union republic
Aus27230 / Spain / Aus27374 / India
Aus27247 / Yugoslavia / Aus27375 / China
Aus27251 / Yugoslavia / Aus27376 / China
Aus27252 / Yugoslavia / Aus27379 / China
Aus27255 / Greece / Aus27380 / China
Aus27270 / Unknown / Aus27382 / China
Aus27272 / Unknown / Aus27383 / China
Aus27279 / Afghanistan / Aus27389 / China
Aus27280 / Afghanistan / Aus27401 / China
Aus27284 / Afghanistan / Aus27402 / China
Aus27286 / Afghanistan / AUS27404 / China
Aus27294 / Algeria / Aus27405 / China
Aus27299 / Algeria / Aus27406 / China
Aus27407 / China / Aus27843 / India
Aus27408 / China / Aus27848 / India
Aus27415 / China / Aus27851 / India
Aus27419 / China / Aus27852 / India
Aus27425 / China / Aus27853 / India
Aus27429 / China / Aus27854 / India
Aus27430 / China / Aus27856 / India
Aus27431 / China / Aus27857 / India
Aus27432 / China / Aus27858 / India
Aus27441 / China / Aus27861 / India
Aus27444 / China / Aus27869 / India
Aus27447 / China / Aus27873 / Soviet union republic
Aus27448 / China / Aus27878 / Italy
Aus27450 / China / Aus27881 / Italy
Aus27451 / China / Aus27882 / Italy
AUS27455 / China / Aus27885 / Italy
Aus27471 / Yugoslavia / Aus27894 / Spain
Aus27473 / Yugoslavia / Aus27899 / Morocco
AUS27474 / Yugoslavia / Aus27900 / Morocco
Aus27476 / Yugoslavia / Aus27902 / Morocco
Aus27477 / Yugoslavia / Aus27904 / Spain
Aus27492 / France / Aus27911 / Spain
Aus27506 / France / Aus27915 / Spain
Aus27524 / Hungary / Aus27916 / Spain
Aus27525 / Hungary / Aus27919 / Spain
Aus27800 / Unknown / Aus27921 / Iran
Aus27801 / India / Aus27928 / Iran
Aus27806 / India / Aus27930 / Iran
Aus27811 / India / Aus27931 / Iran
Aus27812 / India / Aus27940 / Poland
Aus27817 / India / Aus27949 / Poland
Aus27822 / India / Aus27950 / Poland
Aus27823 / India / Aus27953 / Poland
Aus27825 / India / Aus27955 / Portugal
Aus27826 / India / Aus27959 / Portugal
Aus27830 / India / Aus27960 / Portugal
Aus27832 / India / Aus27961 / Portugal
Aus27833 / India / Aus27962 / Portugal
Aus27834 / India / Aus27969 / Portugal
Aus27835 / India / Aus27970 / Portugal
Aus27836 / India / Aus27993 / Yugoslavia
Aus27838 / India / Aus27999 / Italy
Aus27841 / India / Aus28000 / Spain
Aus27842 / India / Aus28004 / Soviet union republic
Aus28009 / Egypt / Aus28164 / Iran
Aus28011 / Tunisia / Aus28166 / Iran
Aus28012 / Soviet union republic / Aus28168 / Iran
Aus28014 / Soviet union republic / Aus28170 / Iran
Aus28015 / Soviet union republic / Aus28176 / Iran
Aus28020 / Soviet union republic / Aus28177 / Iran
Aus28022 / Soviet union republic / Aus28178 / Iran
Aus28028 / Spain / Aus28179 / Iran
Aus28042 / Spain / Aus28183 / Iran
Aus28044 / Spain / Aus28184 / Iran
Aus28050 / India / Aus28186 / Iran
Aus28052 / India / Aus28187 / Iran
Aus28055 / India / Aus28193 / Portugal
Aus28056 / India / Aus28194 / Portugal
Aus28058 / India / Aus28201 / Portugal
Aus28062 / India / Aus28202 / Portugal
Aus28066 / India / Aus28203 / Portugal
Aus28077 / India / Aus28205 / Portugal
Aus28081 / India / Aus28216 / Yugoslavia
Aus28082 / India / Aus28217 / Yugoslavia
Aus28083 / India / Aus28223 / Spain
Aus28086 / India / Aus28225 / Spain
Aus28089 / India / Aus28230 / Turkey
Aus28091 / India / Aus28232 / Turkey
Aus28095 / India / Aus28236 / Tunisia
Aus28096 / India / Aus28244 / Bulgaria
Aus28097 / India / Aus28245 / Bulgaria
Aus28099 / India / Aus28246 / Bulgaria
Aus28112 / Iraq / Aus28253 / Greece
Aus28115 / Morocco / Aus28254 / Greece
Aus28119 / Morocco / Aus28255 / Yugoslavia
Aus28124 / Morocco / Aus28261 / Greece
Aus28125 / Morocco / Aus28262 / Yugoslavia
Aus28126 / Morocco / Aus28264 / China
Aus28127 / Morocco / Aus28266 / Ethiopia
Aus28128 / Morocco / Aus28272 / Soviet union republic
Aus28138 / Spain / Aus28768 / India
Aus28139 / Spain / Aus28824 / Yugoslavia
Aus28141 / Spain / Aus29883 / United Kingdom
Aus28142 / Spain / Aus28266 / Ethiopia
Aus28146 / Spain
Aus28155 / Spain
Aus28160 / Iran
Aus28163 / Iran
Table S2. The 40 SNPs with the largest absolute allele substitution effects for the second allele for leaf, stem and stripe rust ordered by genomic region. SNP effects presented as absolute values*
SNP name/rust / SNPEffect / Chromosome / Map order / Gene / QTLStripe rust
wsnp_Ex_c7252_12452995 / 0.00281 / 1A / 21.0 / Uncharacterized
wsnp_Ex_c42282_48901252 / 0.00259 / 1A / 87.2 / Unpublished / QTL1
wsnp_Ex_c12336_19687074 / 0.00244 / 1A / 87.2
wsnp_Ku_c21364_31103315 / 0.00227 / 1A / 102.3
wsnp_JD_c13384_13393159 / 0.00233 / 1A / 113.8
wsnp_RFL_Contig3542_3718200 / 0.00293 / 1A / 117.5
wsnp_BE444305A_Td_2_1 / 0.00290 / 1A / 117.5
wsnp_Ex_c10631_17340809 / 0.00254 / 1A / 155.3 / Uncharacterized
wsnp_BE637971B_Ta_1_20 / 0.00260 / 1B / 9.6 / Uncharacterized
wsnp_Ex_rep_c102909_87976721 / 0.00269 / 1B / 64.1 / Uncharacterized
wsnp_BF485168B_Ta_2_1 / 0.00230 / 1B / 66.5
wsnp_Ex_c27176_36393952 / 0.00245 / 1B / 101.9 / Uncharacterized
wsnp_CAP12_c1337_682282 / 0.00249 / 1B / 121.9
wsnp_Ra_c21104_30458226 / 0.00239 / 2A / 4.1 / Uncharacterized / QTL2,3
wsnp_Ex_rep_c102538_87682273 / 0.00278 / 2A / 134.6 / Yr41 / QTL2,3,4
wsnp_Ra_c8430_14289874 / 0.00257 / 2A / 150.5
wsnp_Ex_c4272_7708423 / 0.00229 / 2B / 44.0 / Uncharacterized
wsnp_Ra_c31353_40494768 / 0.00228 / 2B / 188.8 / Yr43, Yr44, Yr53 / QTL56
wsnp_Ku_c15498_24122936 / 0.00288 / 2B / 208.5 / Uncharacterized / QTL7
wsnp_Ex_c24135_33382700 / 0.00295 / 2B / 208.7
wsnp_BE488779D_Ta_1_2 / 0.00248 / 2D / 81.6 / Uncharacterized
wsnp_Ra_c16278_24893033 / 0.00236 / 3A / 42.8 / Uncharacterized
wsnp_Ku_c40218_48484410 / 0.00258 / 3A / 43.3
wsnp_Ex_c16615_25147492 / 0.00254 / 3A / 69.2 / Uncharacterized
wsnp_Ex_c15269_23492289 / 0.00238 / 3A / 83.2 / Uncharacterized
wsnp_BE446462D_Ta_2_1 / 0.00321 / 3B / 0.7 / Unpublished
wsnp_CAP11_c1214_700133 / 0.00263 / 3B / 52.8 / Yr30 / QTL8
wsnp_JD_c9805_10591233 / 0.00268 / 3B / 62.4
wsnp_Ex_c5074_9009245 / 0.00234 / 3B / 88.1 / Uncharacterized
wsnp_JD_rep_c49010_33257826 / 0.00259 / 3B / 96.2
wsnp_BE490599A_Ta_2_1 / 0.00241 / 4A / 67.0 / Uncharacterized
wsnp_RFL_Contig3024_2910610 / 0.00243 / 4A / 67.0
wsnp_BE443291A_Ta_2_1 / 0.00244 / 4A / 67.0
wsnp_Ex_c4331_7808746 / 0.00237 / 4A / 165.4 / Yr51 / QTL9
wsnp_RFL_Contig4475_5295587 / 0.00278 / 4A / 178.6
wsnp_BE442666B_Ta_2_2 / 0.00291 / 4B / 36.5 / Uncharacterized
wsnp_Ex_c14812_22928900 / 0.00240 / 5A / 45.0 / Uncharacterized
wsnp_Ex_c12678_20148981 / 0.00251 / 5A / 91.6 / Uncharacterized / QTL2
wsnp_Ku_c12211_19780409 / 0.00242 / 5A / 95.6
wsnp_Ex_c898_1739090 / 0.00238 / 5A / 118.2
wsnp_Ex_c898_1738424 / 0.00237 / 5A / 118.2
wsnp_BE499835B_Ta_2_5 / 0.00211 / 5B / 23.3 / Yr47
wsnp_Ku_c21465_31217980 / 0.00246 / 5B / 201.8 / Uncharacterized / QTL3,5,7,10,11
wsnp_Ku_c3151_5892200 / 0.00246 / 5B / 205.0
wsnp_Ex_c1857_3498746 / 0.00230 / 5B / 214.2
wsnp_Ex_rep_c68491_67318138 / 0.00236 / 5D1 / 6.0 / Uncharacterized
wsnp_Ex_c3422_6283568 / 0.00234 / 5D2 / 34.6
wsnp_RFL_Contig2424_1966870 / 0.00236 / 6A / 0.9 / Uncharacterized
wsnp_JD_c3441_4455541 / 0.00266 / 6A / 45.3 / Uncharacterized / QTL12,13
wsnp_CAP11_c1114_653767 / 0.00325 / 6A / 45.7
wsnp_Ex_c2236_4189774 / 0.00290 / 6A / 180.2 / Uncharacterized
wsnp_Ex_c34597_42879693 / 0.00282 / 6A / 180.2
wsnp_Ex_c7191_12352173 / 0.00255 / 6B / 7.1
wsnp_Ex_c45081_50974769 / 0.00250 / 6B / 48.8 / Uncharacterized / QTL1,7,14,15
wsnp_Ex_c25505_34771897 / 0.00289 / 6B / 52.9
wsnp_Ex_c38198_45786860 / 0.00230 / 6B / 59.5
wsnp_Ex_c2849_5262624 / 0.00228 / 6B / 60.1
wsnp_Ku_c5623_9966516 / 0.00234 / 6B / 95.0 / Uncharacterized
wsnp_Ra_c35443_43984445 / 0.00231 / 6B / 95.0
wsnp_CAP11_c1432_806102 / 0.00283 / 6B / 105.2
wsnp_RFL_Contig308_2996797 / 0.00254 / 7A / 5.6 / Uncharacterized
wsnp_Ku_c139_279238 / 0.00245 / 7A / 40.6 / Uncharacterized / QTL14
wsnp_Ex_c25644_34905425 / 0.00255 / 7A / 51.2
wsnp_Ex_c11636_18742884 / 0.00243 / 7A / 82.3 / Uncharacterized
wsnp_Ex_c18352_27178687 / 0.00234 / 7A / 82.3
wsnp_Ex_c15988_24402251 / 0.00235 / 7A / 82.3
wsnp_Ex_c42836_49314564 / 0.00239 / 7A / 82.3
wsnp_Ra_rep_c104968_88985755 / 0.00238 / 7A / 87.2
wsnp_JD_c15333_14824351 / 0.00236 / 7A / 92.8
wsnp_BQ160404A_Ta_1_1 / 0.00251 / 7A / 116.5 / Uncharacterized
wsnp_Ku_c8497_14429303 / 0.00280 / 7B / 31.6 / Uncharacterized / QTL7
wsnp_CAP8_c3593_1773371 / 0.00236 / 7B / 45.3
wsnp_Ku_c19037_28455905 / 0.00261 / 7B / 57.4
wsnp_RFL_Contig1205_284961 / 0.00239 / 7B / 57.4
wsnp_BG262287B_Td_2_5 / 0.00247 / 7B / 108.7 / Yr39, Yr52
Leaf rust
wsnp_Ex_c38203_45790396 / 0.00175 / 1A / 22.5 / Uncharacterized
wsnp_Ex_c6452_11213329 / 0.00150 / 1A / 97.5 / Uncharacterized
wsnp_Ex_c20489_29564938 / 0.00143 / 1A / 97.5
wsnp_BG606986A_Ta_2_1 / 0.00148 / 1A / 114.3
wsnp_BG606986A_Ta_2_4 / 0.00140 / 1A / 114.6
wsnp_JD_c20553_18260731 / 0.00133 / 1A / 128.9
wsnp_Ku_c13768_21859275 / 0.00164 / 1A / 153.5 / Uncharacterized
wsnp_Ex_c9600_15889471 / 0.00163 / 1A / 179.2
wsnp_Ex_c33654_42106735 / 0.00130 / 1B / 22.9 / Lr44, Lr71
wsnp_Ex_c14832_22953906 / 0.00130 / 1B / 22.9
wsnp_Ex_c6022_10553838 / 0.00143 / 1B / 38.2
wsnp_Ex_c4436_7981188 / 0.00143 / 1B / 123.4 / Lr46
wsnp_Ex_c866_1684236 / 0.00167 / 2A / 63.7 / Lr17a, Lr17b
wsnp_Ra_c4503_8155485 / 0.00131 / 2A / 150.5 / Uncharacterized
wsnp_Ku_c4042_7375053 / 0.00129 / 2B / 80.8 / Lr13, Lr23, Lr48
wsnp_RFL_Contig2666_2354537 / 0.00127 / 2B / 110.8
wsnp_CAP8_c7453_3441062 / 0.00139 / 2B / 149.4 / Uncharacterized
wsnp_BF291674B_Ta_2_1 / 0.00140 / 2B / 149.4
wsnp_Ku_c12037_19549078 / 0.00143 / 2B / 165.9
wsnp_Ex_c16425_24923685 / 0.00131 / 2B / 185.7
wsnp_JD_c4343_5462565 / 0.00133 / 2B / 191.0 / Lr16
wsnp_Ex_rep_c103064_88104690 / 0.00140 / 2B / 230.1
wsnp_Ex_c25311_34578436 / 0.00146 / 2D / 113.1 / Uncharacterized
wsnp_Ra_c16278_24893033 / 0.00175 / 3A / 42.8 / Uncharacterized / QTL16,17
wsnp_Ex_c24432_33676448 / 0.00158 / 3A / 42.8
wsnp_Ku_c40218_48484410 / 0.00170 / 3A / 43.3
wsnp_Ku_c3286_6111264 / 0.00151 / 3A / 102.9 / Uncharacterized
wsnp_Ex_c15100_23284292 / 0.00153 / 3A / 102.9
wsnp_Ex_c9510_15761235 / 0.00153 / 3A / 102.9
wsnp_Ex_rep_c104125_88923836 / 0.00169 / 3A / 162.4
wsnp_Ex_c6223_10857649 / 0.00133 / 3B / 80.9 / Uncharacterized
wsnp_Ex_c18624_27492167 / 0.00139 / 3B / 80.9
wsnp_Ex_c2352_4405961 / 0.00167 / 4A / 136.3 / Uncharacterized
wsnp_JD_c17976_16616890 / 0.00158 / 4B / 123.4 / Uncharacterized
wsnp_JD_rep_c51623_35119179 / 0.00153 / 4D / 20.6 / Uncharacterized
wsnp_Ex_rep_c67296_65839761 / 0.00165 / 4D / 22.4
wsnp_Ex_c34252_42593715 / 0.00142 / 4D / 69.9 / Lr67 / QTL16,17
wsnp_Ku_c9559_16000086 / 0.00133 / 5A / 17.4 / Uncharacterized
wsnp_Ex_c49211_53875600 / 0.00132 / 5A / 83.0
wsnp_Ex_c49211_53875575 / 0.00132 / 5A / 83.0
wsnp_Ex_rep_c101994_87256479 / 0.00149 / 5A / 136.7 / Uncharacterized
wsnp_Ex_c23787_33024604 / 0.00146 / 5A / 140.6
wsnp_BF201102B_Ta_2_5 / 0.00131 / 5B / 23.6 / Lr52
wsnp_Ex_c214_422365 / 0.00142 / 5B / 39.4 / Uncharacterized
wsnp_Ex_c24577_33826666 / 0.00147 / 5B / 57.1
wsnp_BE497820B_Ta_2_3 / 0.00135 / 5B / 79.1
wsnp_BE495277B_Ta_2_5 / 0.00142 / 5B / 101.6
wsnp_JD_rep_c63083_40243538 / 0.00137 / 5B / 127.0 / Uncharacterized / QTL17
wsnp_Ex_c8659_14515623 / 0.00209 / 5B / 130.4
wsnp_Ra_c9155_15344108 / 0.00188 / 5B / 142.5
wsnp_Ra_c20970_30293078 / 0.00137 / 5B / 155.8
wsnp_Ex_c3422_6283568 / 0.00132 / 5D2 / 34.6 / Uncharacterized
wsnp_JD_c34368_25929293 / 0.00136 / 6A / 103.9 / uncharacterized
wsnp_JD_rep_c48797_33040150 / 0.00139 / 6A / 103.9
wsnp_JD_c3839_4902725 / 0.00131 / 6A / 111.9
wsnp_BQ167224B_Ta_2_1 / 0.00148 / 6B / 32.3 / Uncharacterized / QTL14
wsnp_Ku_c4910_8793327 / 0.00144 / 6B / 139.8 / Uncharacterized / QTL17
wsnp_Ex_c5341_9443380 / 0.00129 / 7A / 53.6 / Uncharacterized
wsnp_Ex_c5341_9442913 / 0.00129 / 7A / 53.6
wsnp_Ku_rep_c105954_91953127 / 0.00141 / 7A / 56.8
wsnp_bq170165A_Ta_1_1 / 0.00153 / 7A / 97.6
wsnp_Ex_c14248_22204549 / 0.00131 / 7B / 51.3 / Uncharacterized
wsnp_BE605194B_Ta_2_7 / 0.00138 / 7B / 105.5 / Lr68 / QTL16,18,19
wsnp_BE605194B_Ta_2_1 / 0.00142 / 7B / 105.7
wsnp_BE498985A_Ta_2_1 / 0.00156 / 7B / 106.1
wsnp_JD_c13673_13606066 / 0.00163 / 7B / 132.8
Stem rust
wsnp_Ex_c48087_53105842 / 0.00077 / 1A / 33.1 / Uncharacterized
wsnp_Ex_c4092_7395646 / 0.00094 / 1B / 28.2 / Uncharacterized
wsnp_Ex_c16581_25100502 / 0.00096 / 1B / 28.2
wsnp_RFL_Contig1952_1128597 / 0.00097 / 1B / 28.2
wsnp_Ex_c26860_36084209 / 0.00153 / 1B / 80.2 / Uncharacterized / QTL20
wsnp_Ku_c41261_49287074 / 0.00089 / 1B / 90.7
wsnp_Ex_c2569_4780450 / 0.00113 / 1B / 91.4
wsnp_Ex_c3147_5817088 / 0.00105 / 1B / 91.4
wsnp_CAP11_c1043_618449 / 0.00096 / 1D / 50.8 / Uncharacterized / QTL21
wsnp_Ku_c53270_57959459 / 0.00087 / 1D / 67.3
wsnp_CAP11_c1556_864919 / 0.00098 / 2A / 114.7 / Uncharacterized
wsnp_Ex_c12219_19526749 / 0.00102 / 2A / 141.0
wsnp_CAP11_c3271_1608092 / 0.00104 / 2B / 20.5 / Uncharacterized / QTL21,22,23
wsnp_Ku_c2486_4751761 / 0.00090 / 2B / 23.2
wsnp_Ku_c2486_4751695 / 0.00093 / 2B / 23.2
wsnp_RFL_Contig3118_3061389 / 0.00094 / 2B / 23.2
wsnp_BE497494B_Ta_2_1 / 0.00139 / 2B / 76.0 / Uncharacterized
wsnp_CAP11_c3947_1866837 / 0.00128 / 2B / 76.0
wsnp_CAP11_c3947_1867089 / 0.00115 / 2B / 76.0
wsnp_Ex_c62404_62055681 / 0.00114 / 2B / 76.0
wsnp_Ex_c2430_4546479 / 0.00115 / 2B / 76.0
wsnp_Ex_c20786_29874875 / 0.00115 / 2B / 76.4
wsnp_Ex_c20786_29875033 / 0.00128 / 2B / 76.4
wsnp_Ex_rep_c68704_67559626 / 0.00129 / 2B / 76.4
wsnp_Ex_c42316_48926687 / 0.00108 / 2B / 77.5
wsnp_Ex_c12671_20140014 / 0.00107 / 2B / 77.5
wsnp_Ex_c6537_11338763 / 0.00095 / 2B / 80.4
wsnp_CAP7_rep_c12606_5316797 / 0.00094 / 2B / 94.0 / Uncharacterized
wsnp_Ex_c6537_11339130 / 0.00094 / 2B / 94.0
wsnp_Ex_c41558_48356814 / 0.00085 / 2B / 158.1 / Unpublished
wsnp_Ex_c17700_26446810 / 0.00089 / 2B / 160.4
wsnp_Ku_c48694_54811376 / 0.00096 / 2B / 219.9 / Sr9b, Sr23 / QTL22
wsnp_Ex_c34303_42642389 / 0.00101 / 2B / 254.7 / Uncharacterized
wsnp_Ex_rep_c102478_87635370 / 0.00106 / 3A / 41.7 / Uncharacterized
wsnp_Ex_rep_c106152_90334299 / 0.00090 / 3A / 46.2
wsnp_BF292295A_Ta_2_1 / 0.00105 / 3A / 46.8
wsnp_Ex_c15036_23203474 / 0.00107 / 3A / 47.1
wsnp_Ex_c1660_3158776 / 0.00084 / 3A / 76.0 / Uncharacterized
wsnp_Ra_c7280_12576178 / 0.00090 / 3A / 81.4
wsnp_Ku_rep_c68861_68030775 / 0.00086 / 4A / 73.4 / Uncharacterized
wsnp_BG313770B_Ta_1_1 / 0.00089 / 4A / 154.3 / Uncharacterized
wsnp_Ra_c22775_32274079 / 0.00121 / 4A / 164.3
wsnp_Ex_c49319_53953814 / 0.00078 / 4B / 61.0 / Uncharacterized / QTL21,24
wsnp_BE497368A_Ta_2_1 / 0.00109 / 5A / 46.0 / Uncharacterized
wsnp_BE442892A_Ta_2_2 / 0.00096 / 5A / 46.0
wsnp_CD453438A_Ta_2_1 / 0.00090 / 5A / 46.0
wsnp_Ex_c15163_23357477 / 0.00093 / 5A / 46.0
wsnp_Ku_c39334_47795461 / 0.00084 / 6A / 10.0 / Uncharacterized
wsnp_Ex_c14975_23127669 / 0.00099 / 6A / 78.7 / Uncharacterized
wsnp_Ex_c99215_85409445 / 0.00098 / 6A / 78.7
wsnp_CAP11_c3219_1585635 / 0.00090 / 6B / 0.6 / Sr54
wsnp_Ex_c1988_3742022 / 0.00109 / 6D / 0.7 / Uncharacterized
wsnp_RFL_Contig2789_2553657 / 0.00089 / 7A / 41.0 / Uncharacterized
wsnp_Ra_c31751_40835513 / 0.00087 / 7A / 74.2 / Uncharacterized
wsnp_Ku_c4591_8286024 / 0.00088 / 7A / 98.4
wsnp_CAP11_c827_513472 / 0.00095 / 7A / 104.9
wsnp_CAP7_c949_486485 / 0.00089 / 7A / 104.9
wsnp_Ex_c5177_9174930 / 0.00093 / 7A / 105.5
wsnp_Ex_rep_c68047_66792559 / 0.00099 / 7A / 118.2
wsnp_CAP8_c334_304253 / 0.00103 / 7B / 0.0 / Uncharacterized
wsnp_CAP11_c589_398835 / 0.00100 / 7B / 0.0
wsnp_BM137749D_Ta_2_1 / 0.00106 / 7B / 133.4 / Unpublished
wsnp_Ex_c65899_64135487 / 0.00091 / 7D / 2.6 / Uncharacterized
The locations of Yr, Lr and Sr genes as per the USDA–ARS Cereal Disease Lab (
*Unpublished genes were identified through BSA using 9K SNP chip in mapping populations developed from Watkins genotypes and are yet to be named (Bansal and Bariana unpublished results). QTL if reported in the same region are mentioned as well. It may or may not be the same locus.
1Bariana et al. (2010); 2Lowe et al. (2011); 3Boukaten et al. (2002); 4Carter et al. (2009); 5Mallard et al. (2005); 6Powell et al. (2013); 7Suenaga et al. (2003); 8Singh et al. (2000); 9Prins et al. (2011); 10Lu et al. (2009); 11Yang et al. (2013); 12Hao et al. 2011(2011); 13Lin and Chen (2009); 14Ren et al. 2012(2012); 15Santra et al. (2008); 16 Messmer et al (2000); 17Chu et al. (2009); 18William et al. (1997); 19Xu et al. (2005); 20Haile et al. (2012); 21Kaur et al. (2009); 22Bhavani et al. (2011); 23Singh et al. (2013), 24Njau et al. (2013)
Table S3. P-values and goodness of fit (R2) when regressing genomic prediction accuracy on releationship measures (mean relationship, Gmean; Mean of top X, GtopX).
Lr / Sr / YrP-value / R2 / P-value / R2 / P-value / R2
Gtop1 / 0.000003 / 0.942709 / 0.000228 / 0.833034 / 0.000025 / 0.903607
Gtop5 / 0.000011 / 0.920800 / 0.001653 / 0.729608 / 0.000672 / 0.782649
Gtop10 / 0.000177 / 0.843265 / 0.002690 / 0.695972 / 0.000158 / 0.847442
Gtop20 / 0.000575 / 0.790723 / 0.003495 / 0.676280 / 0.087855 / 0.320745
Gtop30 / 0.013141 / 0.557183 / 0.011569 / 0.570167 / 0.188512 / 0.205279
Gtop40 / 0.085383 / 0.324880 / 0.025807 / 0.482474 / 0.200709 / 0.195517
Gtop50 / 0.037644 / 0.436212 / 0.011596 / 0.569930 / 0.004206 / 0.661631
Gmean / 0.305028 / 0.130522 / 0.127606 / 0.265318 / 0.100559 / 0.300969
Table S4. Accuracy (Pearson correlation) and values for two relationship measures of validation accessions to the reference population: mean genomic relationship (Gmean) and highest genomic relationship (Gtop1).Each accuracy resulted from subsets of low or high relationship in leaf, stem and stripe rust in five repeated random cross-validations each with five folds (30 points per relationship measure).
Gmean / Accuracy / Gtop1 / AccuracyTrait
Cross-Validation / Low / High / Low / High / Low / High / Low / High
Lr CV1 / -0.017 / -0.004 / 0.104 / 0.362 / 0.622 / 1.378 / 0.027 / 0.463
Lr CV2 / -0.016 / -0.003 / 0.266 / 0.245 / 0.596 / 1.342 / 0.001 / 0.492
Lr CV3 / -0.015 / -0.002 / 0.302 / 0.348 / 0.622 / 1.367 / 0.108 / 0.486
Lr CV4 / -0.015 / -0.004 / 0.315 / 0.191 / 0.614 / 1.385 / -0.061 / 0.488
Lr CV5 / -0.013 / -0.002 / 0.264 / 0.299 / 0.617 / 1.395 / 0.116 / 0.412
Sr CV1 / -0.014 / -0.003 / 0.027 / 0.226 / 0.612 / 1.376 / -0.038 / 0.352
Sr CV2 / -0.020 / -0.001 / 0.132 / 0.174 / 0.629 / 1.380 / 0.046 / 0.253
Sr CV3 / -0.013 / -0.004 / 0.219 / 0.179 / 0.594 / 1.349 / 0.104 / 0.281
Sr CV4 / -0.017 / -0.002 / 0.244 / 0.261 / 0.598 / 1.381 / 0.147 / 0.367
Sr CV5 / -0.017 / -0.001 / 0.054 / 0.250 / 0.594 / 1.384 / 0.001 / 0.288
Yr CV1 / -0.022 / -0.003 / 0.468 / 0.394 / 0.604 / 1.351 / 0.263 / 0.566
Yr CV2 / -0.019 / -0.003 / 0.335 / 0.520 / 0.613 / 1.329 / 0.368 / 0.501
Yr CV3 / -0.016 / -0.002 / 0.308 / 0.493 / 0.608 / 1.365 / 0.261 / 0.507
Yr CV4 / -0.015 / -0.002 / 0.242 / 0.542 / 0.610 / 1.368 / 0.323 / 0.482
Yr CV5 / -0.018 / -0.003 / 0.422 / 0.444 / 0.597 / 1.359 / 0.295 / 0.549
Table S5. LogLikelihood and variance components from BLUE models including various random terms, including GxE interactions, where Var(e) is the error variance, Var(ID) is the variance due to accessions, Var(IDxSite) is the variance of accession-by-site interactions, and Var(IDxYear) is the variance of accession-by-year interactions. Models with * are significantly different from the base model that just fitted ID.
Random Model Terms / LogLikelihood / Var(e) / Var(ID) / Var(IDxSite) / Var(IDxYear)ID / -1409.5 / 1.26081 / 2.10941 / - / -
ID IDxSite* / -1354.51 / 1.07312 / 1.53346 / 0.66856 / -
ID IDxYear* / -1380.14 / 1.00154 / 2.0863 / - / 0.335315
ID IDxSite IDxYear* / -1313.34 / 0.78553 / 1.45246 / 0.72856 / 0.377454
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