From: Genetic architecture of grain yield in bread wheat based on genome-wide association studies
Trait | Chr | Physical position (Mb)a | SNP-GWAS | Haplotype-GWAS | QTL/marker/genee | ||||
---|---|---|---|---|---|---|---|---|---|
Markerb | Environment | R2 (%)c | Haplotyped | Environment | R2 (%)c | ||||
GY | 1A | 402.9–407.4 | AX_110387060 | E3/E4/E5/E6/B | 6.9–15.5 | H1290 | E4/E5/E6/B | 10.1–19.8 |  |
1A | 434.0–439.9 | AX_110418502 | E4/E5/E6/B | 6.9–17.7 | H1313 | E4/E5/E6/B | 9.3–19.2 | QYld.abrii-1A1.2 [23] | |
1B | 539.6–542.6 | AX_110508372 | E4/E5/E6/B | 7.1–12.8 | H3650 | E4/E5/E6/B | 9.3–21.5 |  | |
1B | 673.6–675.7 | AX_109820171 | E3/E5/E6/B | 7.6–14.3 | H4268 | E4/E5/E6/B | 10.7–22.6 |  | |
2A | 30.3–31.9 | AX_94546135 | E4/E6/B | 7.1–11.6 | H5187 | E4/E6/B | 9.3–17.6 |  | |
2B | 106.1–108.9 | AX_111210290 | E2/E4/B | 7.0–12.5 | H7877 | E1/E4/E5/E6/B | 9.1–20.8 |  | |
2D | 643.1–650.8 | AX_109941480 | E4/E5/E6/B | 7.0–12.3 | H10738 | E4/E5/E6/B | 9.3–14.6 |  | |
3A | 721.3–724.0 | AX_111492146 | E5/E6/B | 7.1–11.7 | H11976 | E3/E5/E6/B | 9.1–18.2 |  | |
3B | 20.5–22.0 | AX_109881378 | E4/E5/E6/B | 7.4–10.7 | H12363 | E4/E5/E6/B | 9.3–17.6 |  | |
3D | 570.8–572.8 | AX_95257733 | E3/E4/E6/B | 7.1–9.9 | H15950 | E1/E4/E4/E6/B | 9.2–16.6 |  | |
5A | 570.2–570.3 | AX_110523824 | E3/E4/B | 7.8–14.8 | H19931 | E1/E3/E4/E5/E6/B | 10.0–20.1 | barc151 [35] | |
5B | 587.1–588.2 | AX_110995303 | E3/E6/B | 7.1–10.2 | H22191 | E1/E2/E3/E5/E6/B | 9.4–15.7 |  | |
SN | 5B | 530.8–534.0 | IWB56499 | E1/E3/E4/B | 7.1–11.9 | H21909 | E2/E3/E4/B | 9.1–12.2 |  |
5B | 696.3–700.9 | AX_109936345 | E2/E4/B | 7.1–12.1 | H22717 | E1/E2/E3/E4/B | 9.1–15.3 |  | |
6B | 605.8–607.1 | IWB51629 | E1/E3/B | 7.5–8.1 | H26344 | E1/E2/E3/E4/B | 9.5–16.6 |  | |
6B | 696.6–697.6 | AX_95260682 | E1/E3/B | 7.4–9.3 | H26799 | E1/E2/E3/B | 10.5–13.6 |  | |
6D | 468.8–471.0 | AX_110652999 | E2/E3/B | 7.2–17.1 | H27181 | E1/E2/E3/E4/B | 9.5–18.8 |  | |
7D | 75.9–76.9 | AX_111490489 | E2/E3/B | 7.7–9.0 | H31325 | E1/E2/E3/E4/B | 9.8–23.3 |  | |
KNS | 1A | 36.8–42.5 | AX_111579941 | E1/E2/E3/E5/E6/B | 7.1–11.9 | H322 | E1/E2/E3/E4/E5/E6/B | 9.2–15.8 | QGns.wa -1AS.e1 [43] |
1A | 497.5–498.1 | AX_108737858 | E1/E2/E3/E4/E5/E6/B | 7.1–12.7 | H1479 | E1/E5/E6/B | 9.3–12.5 | QGnu.abrii-1A1.1 [23] | |
2A | 117.2–117.3 | IWB45503 | E3/E4/E5/E6 | 7.2–8.6 | H5556 | E3/E4/E5/B | 9.5–11.5 | ||
2D | 633.2–634.5 | IWB57054 | E1/E2/E3/E4/E5/E6/B | 7.4–17.7 | H10675 | E1/E3/E6/B | 9.3–15.4 |  | |
3A | 36.8–37.2 | AX_110657474 | E1/E2/E3/E5/E6/B | 7.4–11.1 | H11017 | E1/E2/E3/E5/E6/B | 9.7–14.5 |  | |
3A | 719.3–725.8 | AX_108992368 | E2/E3/E4/E5/E6/B | 7.1–12.4 | H11953 | E3/E4/E5/E6/B | 9.1–15.1 | ||
5B | 416.4–418.0 | AX_109538915 | E1/E4/E5/E6/B | 7.1–10.5 | H21421 | E1/E4/E6/B | 9.3–14.6 | gwm213 [41] | |
5B | 489.3–492.9 | AX_109537496 | E1/E2/E3/E4/E6/B | 7.4–10.9 | H21713 | E1/E2/E3/E4/E5/E6/B | 9.5–14.8 |  | |
7A | 49.1–50.0 | AX_89571435 | E2/E3/E4/E5/E6/B | 7.2–12.6 | H27643 | E1/E3/E4/E5/E6/B | 9.3–13.9 |  | |
TKW | 1B | 658.7–662.5 | AX_111147652 | E1/E2/E4/E6/B | 7.1–10.2 | H4181 | E1/E2/E3/E4/E5/E6/B | 9.2–15.4 | QTgw.cau-1B, QGl.cau-1B.1 [51] |
2A | 760.6–760.7 | AX_111579921 | E2/E4/E5/B | 7.0–8.5 | H7248 | E1/E2/E3/E4/E5/E6/B | 9.3–18.1 |  | |
2B | 106.0–107.1 | IWB50438 | E1/E2/E4 | 6.7–9.1 | H7872 | E1/E2/E3/E4/E5/E6/B | 9.3–27.0 |  | |
4B | 40.4–44.9 | AX_110713957 | E1/E2/E3/E4/E5/E6/B | 7.1–12.7 | H17589 | E1/E2/E3/E4/E5/E6/B | 9.4–22.0 | QTgw-4B1 [48] | |
4B | 159.2–163.0 | AX_109427900 | E1/E2/E6/B | 7.1–9.2 | H17841 | E1/E2/E3/E4/E5/E6/B | 9.4–25.1 |  | |
4B | 670.4–670.5 | IWB47765 | E1/E5/E6/B | 6.9–9.2 | H18552 | E1/E2/E3/E4/E5/E6/B | 10.2–17.9 |  | |
5A | 706.2–708.0 | AX_110958315 | E1/E3/E4/E6/B | 8.2–13.0 | H20367 | E1/E2/E3/E4/E5/E6/B | 9.2–19.8 | QTKW.caas-5AL.1 [40] | |
5B | 692.7–696.4 | AX_108769612 | E3/E4/E5/E6/B | 7.2–9.9 | H22684 | E1/E2/E3/E4/E5/E6/B | 9.3–15.8 | Excalibur_c23801_115 [27]; wsnp_Ex_c16045_24471413 [45]; Ku_c7546_861 [46] | |
6B | 450.6–454.1 | AX_110368497 | E2/E3/E5/E6/B | 6.8–8.3 | H25900 | E1/E2/E3/E4/E6/B | 12.2–14.1 |  | |
6B | 675.4–677.5 | AX_109917592 | E1/E3/E6/B | 7.2–9.7 | H26662 | E1/E3/E4/E5/E6/B | 15.8–20.6 | QTKW.caas-6BL [17] | |
6D | 461.4–468.0 | AX_109481324 | E2/E3/E6 | 6.8–8.3 | H27181 | E1/E2/E3/E4/E5/E6/B | 9.3–16.5 |  | |
7D | 63.0–69.7 | AX_109927697 | E2/E3/E4/E5/E6/B | 7.1–12.3 | H31315 | E1/E2/E3/E4/E5/E6/B | 10.4–17.8 | QKL.caas-7DS [17] QGw.ccsu-7D.1 [44] | |
KL | 1B | 26.9–30.8 | AX_110032293 | E3/E4/E5/E6/B | 7.1–12.7 | H2345 | E2/E3/E4/E5/E6/B | 9.2–13.5 |  |
1B | 642.6–642.7 | AX_108849700 | E1/E2/E3/E5/E6/B | 7.0–9.6 | H4081 | E2/E5/E6/B | 9.2–12.0 | ||
2A | 740.4–745.0 | IWB32119 | E1/E2/E3/E4/E5/E6/B | 7.2–14.2 | H7042 | E1/E2/E3/E4/E5/E6/B | 9.2–13.8 | TaFlo2-A1 [49] | |
3B | 782.9–783.0 | AX_111116403 | E1/E2/E5/E6/B | 7.2–9.9 | H15574 | E2/E5/E6/B | 9.3–11.9 |  | |
5B | 52.9–55.2 | IWB50649 | E1/E2/E3/E4/E5/E6/B | 7.2–11.7 | H20632 | E3/E5/E6/B | 10.5–12.6 | ||
5D | 475.8–476.3 | AX_111122970 | E1/E2/E3/E4/E6/B | 7.2–12.4 | H22993 | E1/E2/E3/E4/E5/E6/B | 9.4–15.4 |  | |
KW | 1A | 9.6–12.0 | IWB6999 | E2/E3/E4/B | 7.1–9.3 | H46 | E1/E2/E3/E4/E5/E6/B | 9.1–17.5 | QGw.ccsu-1A.1 [44] |
1A | 532.6–533.4 | IWB7676 | E2/E3/E4/E6/B | 7.0–10.4 | H1679 | E1/E2/E3/E4/E5/E6/B | 9.2–16.3 | QTgw.cau-1A [47] | |
2A | 27.3–29.9 | AX_111037158 | E1/E3/E4/E5/E6 | 7.2–9.6 | H5176 | E1/E2/E3/E4/E5/E6/B | 9.4–20.2 | wmc177 [42] | |
2A | 758.6–760.7 | AX_111579921 | E2/E4/E5/E6 | 7.1–10.9 | H7248 | E2/E3/E4/E5/E6/B | 9.2–22.4 |  | |
2B | 105.8–108.7 | AX_111634754 | E1/E2/E3/E4/E5/E6/B | 7.0–15.0 | H7877 | E1/E2/E3/E4/E5/E6/B | 9.1–36.7 |  | |
2B | 415.0–418.9 | AX_111819405 | E2/E3/E4/E5/E6/B | 7.0–10.6 | H8418 | E1/E2/E3/E4/E5/E6/B | 9.4–16.3 |  | |
3A | 714.4–716.3 | AX_111047166 | E2/E3/E4/E5/B | 7.0–10.9 | H11918 | E1/E2/E3/E4/E5/E6/B | 9.1–27.2 | QTgw-3A1 [48] | |
3D | 570.2–575.5 | IWB17930 | E2/E3/E4/E5/E6/B | 6.8–10.3 | H15950 | E1/E2/E3/E4/E5/E6/B | 9.2–21.4 |  | |
4A | 670.0–676.0 | AX_110046841 | E2/E3/E4/E6/B | 7.0–10.3 | H17106 | E1/E2/E3/E4/E6/B | 12.1–19.1 | ||
4B | 670.4–672.9 | IWB47765 | E1/E3/E6/B | 7.0–12.4 | H18552 | E2/E3/E4/E5/E6/B | 11.5–18.8 |  | |
5A | 569.2–573.0 | AX_110523824 | E3/E4/E6/B | 7.0–11.7 | H19921 | E2/E3/E4/E6/B | 9.2–20.9 | QGl.cau-5A.1 [47] | |
5A | 702.1–708.1 | AX_110958315 | E3/E4/E5/E6/B | 7.4–13.3 | H20333 | E2/E3/E4/E5/E6/B | 9.4–22.2 | QTKW.caas-5AL.1 [40] | |
5B | 520.8–520.9 | IWB20926 | E1/E2/E3/E6/B | 7.2–10.1 | H21840 | E1/E2/E3/E4/E5/E6/B | 9.2–19.4 | QTgw.abrii-5B1.2 [23] | |
6B | 706.9–709.2 | AX_109820966 | E3/E4/E5/E6/B | 6.9–10.3 | H26817 | E1/E2/E3/E4/E5/E6/B | 9.4–17.9 |  | |
7D | 58.5–66.5 | AX_109396082 | E1/E2/E3/E4/E5/E6/B | 7.0–12.5 | H31312 | E3/E4/E6/B | 9.5–20.0 | QKL.caas-7DS [17] QGw.ccsu-7D.1 [44] | |
SL | 2B | 44.6–47.3 | AX_109985540 | E1/E2/E3/E4/E5/B | 7.0–14.3 | H7643 | E1/E3/E4/E5/B | 9.2–14.0 | BS00022060_51 [27] |
5A | 510.1–510.3 | AX_109367907 | E1/E3/E4/E5/E6/B | 7.4–12.8 | H19589 | E4/E5/B | 9.0–11.8 | QSL.caas-5AL.2 [17] | |
5A | 534.9–540.1 | AX_110919697 | E1/E2/E3/E4/E5/E6/B | 6.7–11.8 | H19737 | E1/E2/E3/E4/B | 9.3–14.9 |  | |
5A | 568.3–574.3 | AX_110523824 | E1/E2/E3/E4/E5/E6/B | 7.3–13.0 | H19954 | E2/E5/E6/B | 9.8–10.3 | QSl-5A1 [48] | |
5B | 398.2–398.3 | AX_94562344 | E3/E4/E5/E6/B | 8.0–11.0 | H21291 | E2/E3/E5/E6/B | 9.2–15.1 |  | |
5B | 590.5–591.1 | AX_110971192 | E1/E3/E4/E6/B | 7.4–10.3 | H22208 | E1/E3/E4/E6/B | 9.1–12.6 |  | |
7B | 723.9–727.6 | IWB71567 | E1/E2/E3/E4/E5/E6/B | 7.1–13.8 | H30972 | E1/E2/E3/E4/E6/B | 9.1–19.3 |  | |
7D | 621.9–630.4 | AX_110645784 | E1/E2/E3/E4/E5/E6/B | 7.6–15.0 | H31712 | E1/E2/B | 10.7–20.0 |  | |
SDW | 1A | 568.5–573.5 | AX_95255804 | E3/E4/E5/E6/B | 7.2–9.7 | H2018 | E3/E4/E6/B | 9.1–12.6 |  |
3A | 721.3–725.8 | IWA94 | E3/E4/E5/E6/B | 7.1–19.0 | H11992 | E3/E4/E5/E6/B | 9.5–15.2 |  | |
4B | 89.5–95.1 | IWB35533 | E3/E4/E6/B | 7.1–10.7 | H17675 | E4/E5/B | 9.3–11.4 |  | |
5B | 473.9–477.8 | AX_111183518 | E3/E5/E6/B | 7.0–16.3 | H21628 | E3/E4/E5/E6/B | 9.7–18.5 |  | |
5B | 698.0–698.5 | AX_111051286 | E3/E4/E6/B | 7.1–10.6 | H22718 | E3/E4/B | 9.9–11.2 |  | |
HD | 2A | 27.3–27.4 | AX_111037158 | E1/E2/E3/E4/E5/B | 7.5–12.2 | H5170 | E1/E2/E3/E4/E5/E6/B | 11.3–15.7 |  |
2A | 704.8–710.1 | AX_89674107 | E1/E2/E3/E4/E6/B | 6.8–8.6 | H6769 | E1/E2/E6 | 9.3–13.9 |  | |
2A | 755.8–757.0 | AX_109964711 | E1/E2/E3/E4/E6/B | 6.8–9.4 | H7248 | E1/E2/E4/E6 | 9.2–13.8 | wPt-1499 [51] | |
2B | 106.0–108.7 | AX_110624209 | E1/E2/E3/E4/E5/E6/B | 6.6–10.7 | H7877 | E1/E2/E4/E6/B | 9.4–22.0 |  | |
5B | 520.1–524.4 | IWB20926 | E1/E2/E4/E6/B | 6.6–10.7 | H21844 | E1/E2/E4/E6 | 9.1–15.9 | wPt-1409 [51] | |
7A | 511.5–517.4 | AX_109921812 | E1/E2/E3/E4/E5/B | 6.9–9.4 | H28667 | E1/E3/E5/B | 9.2–14.2 |  | |
7A | 556.2–561.0 | AX_111660137 | E1/E2/E3/E4/E5/B | 6.7–12.3 | H28779 | E1/E2/E4/E5/E6 | 9.4–12.9 | wPt-4796 [51] | |
7B | 701.0–703.7 | IWB75191 | E1/E2/E3/E4/E5/E6/B | 6.6–13.1 | H30856 | E1/E2/E3/E4/E5/E6/B | 9.3–16.3 |  | |
PH | 1A | 434.1–440.2 | AX_109449226 | E1/E2/E3/E4/E5/E6/B | 6.9–13.1 | H1306 | E1/E2/E3/E4/E5/E6/B | 9.3–16.1 |  |
1B | 539.6–542.6 | AX_94564150 | E1/E2/E4/E5/E6/B | 7.0–21.1 | H3651 | E1/E2/E3/E4/E5/E6/B | 10.4–22.8 |  | |
1B | 673.9–675.7 | AX_109820171 | E1/E2/E4/E5/E6/B | 6.8–30.8 | H4268 | E1/E2/E3/E4/E5/E6/B | 9.5–38.0 |  | |
2A | 30.9–32.0 | AX_110988136 | E1/E2/E4/E5/B | 7.0–11.3 | H5187 | E1/E2/E3/E4/E5/B | 11.4–19.8 | QUIL.caas-2AS.1 [17] | |
2A | 715.3–721.6 | AX_94494373 | E1/E2/E4/E6/B | 6.7–10.5 | H6911 | E1/E2/E3/E4/E5/E6/B | 10.9–16.5 | QPH.caas-2AL, QUIL.caas-2AL [17] | |
3A | 716.5–721.3 | AX_111577195 | E1/E2/E4/E5/E6/B | 6.9–14.8 | H11943 | E1/E2/E3/E4/E5/E6/B | 9.2–18.4 | barc1113 [19] | |
3B | 116.1–120.4 | AX_109413472 | E1/E2/E3/E4/E5/E6/B | 6.8–12.8 | H12783 | E1/E2/E3/E4/E5/E6/B | 9.0–17.4 | gwm566 [19] | |
4D | 16.6–19.7 | AX_108916749 | E1/E2/E4/E5/E6/B | 6.7–14.5 | H18598 | E1/E2/E3/E4/E5/E6/B | 10.2–16.1 | ||
5A | 669.2–671.2 | AX_110446653 | E1/E2/E3/E4/E5/E6/B | 6.9–14.7 | H20207 | E1/E2/E3/E4/E5/E6/B | 10.8–17.5 |  | |
5A | 708.4–708.8 | IWA2646 | E2/E3/E5/B | 6.7–8.0 | H20356 | E1/E2/E3/E4/E5/E6/B | 9.4–18.0 | QPh.hwwgr5AL [53] | |
5B | 576.3–580.9 | AX_108921249 | E1/E2/E4/E5/B | 7.0–13.3 | H22142 | E1/E2/E3/E4/E5/E6/B | 12.2–20.4 |  | |
6B | 1.4–4.9 | AX_110482029 | E1/E2/E4/E5/B | 7.0–18.1 | H24673 | E1/E2/E3/E4/E5/E6/B | 9.4–25.9 |  | |
6B | 42.7–42.8 | AX_110671479 | E1/E2/E4/B | 7.2–10.8 | H24862 | E1/E2/E3/E4/E5/E6/B | 9.4–19.0 |  | |
7A | 556.2–560.9 | AX_109384874 | E1/E2/E3/E5/E6/B | 6.9–15.1 | H28784 | E1/E2/E3/E4/E5/E6/B | 10.5–18.6 |  | |
UIL | 1A | 142.6–148.6 | AX_109901254 | E1/E5/E6/B | 7.5–11.1 | H608 | E1/E2/E5/E6/B | 9.2–17.4 |  |
1A | 434.4–440.2 | AX_109449226 | E1/E2/E5/E6/B | 6.9–12.9 | H1306 | E1/E2/E5/E6/B | 9.1–16.3 |  | |
1B | 539.6–542.6 | AX_94564150 | E1/E2/E5/B | 6.8–16.1 | H3650 | E1/E2/E5/B | 9.6–17.9 |  | |
1B | 674.8–675.7 | AX_109820171 | E1/E2/E5/B | 8.4–16.4 | H4239 | E1/E2/E5/E6/B | 9.2–24.0 |  | |
3A | 721.3–723.7 | AX_111610555 | E1/E2/E5/B | 7.3–9.7 | H11922 | E1/E2/E5/E6/B | 9.1–17.3 | barc1113 [19] | |
5A | 665.6–671.2 | IWA5929 | E1/E2/E5/E6/B | 7.1–11.3 | H20205 | E1/E2/E5/E6/B | 9.6–18.5 |  | |
6B | 1.4–4.9 | AX_109526332 | E1/E2/E5/B | 7.0–11.4 | H24673 | E1/E2/E5/E6/B | 9.3–24.8 |  | |
6B | 42.7–46.9 | IWB12568 | E1/E2/E5/E6/B | 7.1–9.5 | H24865 | E1/E2/E5/E6/B | 9.8–20.4 |  | |
6B | 563.3–567.8 | AX_86165710 | E1/E2/E5/E6/B | 6.7–10.5 | H26273 | E1/E2/E5/E6/B | 9.3–15.6 |  | |
6D | 396.5–403.7 | AX_109331000 | E1/E2/E5/E6/B | 7.0–12.6 | H27113 | E1/E2/E5/E6/B | 15.3–19.0 | barc96 [19] | |
6D | 460.7–465.0 | IWB2743 | E1/E2/E5 | 7.2–10.5 | H27272 | E1/E2/E5/E6/B | 9.4–14.1 |  | |
7B | 630.6–632.7 | AX_109492373 | E1/E2/E5/B | 7.1–12.3 | H30631 | E1/E2/E5/E6/B | 9.9–22.1 |  | |
FLL | 1A | 8.3–11.0 | AX_109621606 | E3/E4/E5/E6/B | 7.1–16.9 | H99 | E3/E4/E5/E6/B | 9.0–20.8 |  |
2A | 2.5–7.8 | AX_109880304 | E2/E3/E5/E6/B | 7.4–19.6 | H5121 | E2/E3/E4/E5/E6/B | 10.9–29.1 |  | |
2A | 87.8–87.9 | AX_95085564 | E4/E5/E6/B | 8.6–12.7 | H5461 | E2/E3/E5/E6/B | 9.6–17.5 |  | |
2B | 46.4–50.4 | AX_111027654 | E2/E6/B | 7.0–19.6 | H7632 | E2/E3/E4/E5/E6/B | 9.4–25.5 | QFLL-2B [57] | |
3A | 716.9–722.5 | AX_108908243 | E3/E4/E6 | 7.2–9.7 | H11976 | E3/E4/E5/E6/B | 9.4–22.7 |  | |
5A | 556.6–559.7 | IWB4576 | E3/E4/E6/B | 6.9–9.6 | H19845 | E2/E3/E4/E5/E6/B | 9.6–16.2 | QFlw.cau-5A.2, QFlan.cau-5A.3 [56] | |
6B | 704.9–708.7 | AX_109459603 | E5/E6/B | 8.8–9.6 | H26801 | E2/E3/E4/E5/E6/B | 9.5–22.0 |  | |
6D | 455.5–462.2 | AX_110876641 | E3/E6/B | 7.6–8.8 | H27138 | E2/E3/E4/E5/E6/B | 9.8–18.0 | QFll.cau-6D [56] | |
FLW | 1A | 440.4–445.5 | AX_111540798 | E2/E3/E4/E6/B | 7.0–11.4 | H1318 | E2/E3/E4/B | 9.1–17.3 |  |
3B | 23.9–24.4 | AX_111655083 | E4/E6/B | 7.3–9.7 | H12389 | E2/E3/E4/E5/E6/B | 9.2–19.7 |  | |
5B | 531.5–533.5 | IWB41225 | E2/E6/B | 6.9–7.9 | H21876 | E2/E3/E4/E5/E6/B | 9.1–14.7 |  | |
5B | 557.1–559.4 | AX_109519234 | E2/E3/E4/E5/B | 7.0–9.0 | H22030 | E2/E3/E4/E5/E6/B | 9.3–16.7 |  | |
6B | 461.4–465.5 | AX_108771909 | E2/E3/E5/B | 7.0–9.9 | H25955 | E2/E3/E4/E5/E6/B | 9.6–12.2 | QFlw.cau-6B [56] |