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Table 1 Genetic regions significantly associated with resistance to the Magnaporthe oryzae isolate D41-2

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 informationKnown R genes/QTLs
Marker IDAlleleMAF (%)c− Log10(P)R2d
D-01indicaLT1id1010103–id101020515,438,604–15,649,252id1010164T/C19.64.550.16AQCT001, AQEN001, AQEN011, AQEN018
D-02indicaDLA1id1011342–id101140118,821,356–18,925,916id1011349C/A9.283.960.18AQCT001, AQEN001, AQEN011, AQEN018
D-03FullDLA2id2003636–id20036537,104,193–7,129,000id2003651C/T11.594.880.07
D-04FullDLA2id2006540-id200668716,209,277–16,648,368id2006548G/T8.284.380.06
D-05FullDLA3id3010758–ud300134423,818,976–24,280,279id3010813C/T32.014.860.06AQAF029
ud3001342T/C31.910.06
D-06FullDLA3id3016979–id301713634,609,998–34,809,786id3017114G/A12.375.410.08
D-07FullDLA4id4008106–id400833524,437,545–24,950,637id4008148T/A46.85.300.07CQAC2, Pikur1
D-08FullDLA4id4008360–id400852225,043,111–25,696,775id4008464G/A7.014.870.07CQAC2, Pikur1
D-09FullDLA4id4008601–id400868126,300,907–26,575,531id4008636G/A5.924.290.06CQAC2, Pikur1
D-10FullDLA5id5009568–id500995822,335,609–22,650,069id5009818G/T5.964.130.06AQAQ024
D-11FullDLA5id5009967–id501029422,654,409–23,102,774id5010176A/T10.23.720.05
D-12FullDLA8id8005634–ud800135720,708,815–20,937,247id8005717A/G34.655.210.07Pizh
D-13eindicaLT12ud12000652–id1200410210,218,678–10,611,754wd12001025T/A38.044.770.19AQCT008, AQEN010, AQEN017, LABR_87, LABR_88, LABR_89, Pi6(t), Pi12, Pi19(t), Pi20, Pi31(t), Pi58(t), Pi62(t), Pi157, Pita2, Pita
D-14FullLT12id12004113–id1200423410,669,467–10,900,950id12004183A/G35.644.640.07AQCT008, AQEN010, AQEN017, Pi6(t), Pi12, Pi19(t), Pi31(t), Pi58(t), Pi62(t), Pi157, Pita2, Ptr
FullDLA
indicaLTid12004196G/A15.465.030.07
id12004196G/A37.55.090.12
D-15fFullDLA12id12004251–wd1200118311,060,008–11,555,556id12004303A/G15.435.310.08AQCT008, AQEN010, AQEN017, CQAC4, LABR_90, Pi6(t), Pi12, Pi19(t), Pi31(t), Pi58(t), Pi62(t), Pi157, Pita2
D-16FullDLA12id12004432–id1200454012,065,937–12,565,383id12004538G/A16.335.370.08AQCT008, 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