Skip to main content

Table 2 Genetic regions significantly associated with resistance to the Magnaporthe oryzae isolate 12YL-DL3-2

From: Genome-wide association study of rice genes and loci conferring resistance to Magnaporthe oryzae isolates from Taiwan

No.PopulationPhenotypeChr.RangeaPhysical position (bp)bHighest marker informationbKnown R genes/QTLs
Marker IDAlleleMAF (%)c− Log10(P)R2d
Y-01indicaDLA1id1013754–id101403423,732,729–23,934,283id1013942T/G364.470.21AQCT001, AQEN001, LABR_10
Y-02indicaDLA1id1015101–id101528225,284,622–25,681,092id1015101A/G35.066.830.31AQAH002, AQCT001, AQEN001, Pitp(t)
LT35.064.850.28
Y-03indicaDLA2id2007485–id200751618,977,320–19,192,422id2007494G/T41.095.370.26
Y-04indicaDLA2id2008594–id200864421,493,161–21,607,823id2008601A/G39.244.880.22Pid(t)1
Y-05indicaDLA2id2009379–id200940323,397,267–23,466,199id2009379T/C34.214.420.21
Y-06indicaDLA3id3017643–id301772535,480,048–35,558,427id3017643C/G33.334.190.19
Y-07indicaDLA5id5002016-id50020753,483,482-3,586,560id5002075C/T304.060.18
Y-08indicaDLA5wd5001198–wd500134410,351,569–10,848,969id5004839, id5004859C/T22.794.150.19AQEN004, Pi23
A/G23.750.18
Y-09indicaDLA6id6004112–id60042356,458,990–6,636,955id6004212C/T46.154.370.20AQCT004, AQEN005, Pii1, Pi8, Pi59(t), Pi27(t)
Y-10indicaDLA8id8000511–id80005441,744,391–1,839,119id8000544A/G32.884.660.23
Y-11indicaDLA8id8000658–id80006952,130,616–2,184,609id8000663C/T26.674.470.21
Y-12indicaDLA12id12002136–id120022194,731,647–4,872,049id12002210A/G11.544.520.21Pi6(t), Pi62(t)
Y-13japonicaDLA12id12003134–id120034327,827,050–8,296,350id12003144T/C7.644.090.10AQCT008, AQEN010, AQEN017, Pi6(t), Pi12, Pi20, Pi31(t), Pi58(t), Pi62(t)
Y-14japonicaDLA12ud12000485–id120036088,383,596–8,874,826id12003547C/T7.94.040.10AQCT008, AQEN010, AQEN017, Pi6(t), Pi12, Pi19(t), Pi20, Pi31(t), Pi58(t), Pi62(t), Pi157
id12003562A/T7.94.040.10
Y-15japonicaDLA12id12003642–ud120005668,914,661–9,231,272id12003728T/A8.13.930.10AQCT008, AQEN010, AQEN017, Pi6(t), Pi12, Pi19(t), Pi20, Pi31(t), Pi58(t),, Pi62(t), Pi157
Y-16eFullLT12id12003919–id1200411310,058,758–10,669,467id12004093G/A105.670.11AQCT008, AQEN010, AQEN017, LABR_87, LABR_88, LABR_89, Pi6(t), Pi12, Pi19(t), Pi20, Pi31(t), Pi58(t), Pi62(t), Pi157, Pita2, Pita
japonicaLTid12004007A/T74.820.02
japonicaDLAwd12001025T/A8.24.620.13
Y-17fFullLT12id12004251–wd1200118311,060,008–11,555,556id12004284C/G8.525.870.11AQCT008, AQEN010, AQEN017, CQAC4, LABR_90, Pi6(t), Pi12, Pi19(t), Pi31(t), Pi58(t), Pi62(t), Pi157, Pita2
Y-18FullLT12id12004546–id1200468512,567,686–13,060,942id12004554C/A42.115.40.10AQCT008, AQCT009, AQEN010, AQEN017, CQAC4, Pi6(t), Pi12, Pi19(t), Pi51(t), Pi62(t), Pi157, Pita2
  1. aThe left-border marker and right-border marker of the QTL
  2. bThe physical map position is based on MSU version 7.0 Nipponbare rice reference genome
  3. cMAF: minor allele frequency
  4. dR2 represents the proportion of the phenotypic variation explained by the single nucleotide polymorphism
  5. e, fSame or largely overlapped genetic region identified by using D41-2 and 12YL-DL3-2