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Table 3 MTAs identified through GWAS for seven productivity related traits in AM panel of 346 O. rufipogon accessions

From: Genotyping-by-Sequencing Based Investigation of Population Structure and Genome Wide Association Studies for Seven Agronomically Important Traits in a Set of 346 Oryza rufipogon Accessions

SNP

Primary trait (p-value, effect)

Secondary trait (p-value, effect)

Previously reported QTLs/genes

S1_1931325

CT(9.20E−05, 3.5%), HGW (2.24E−05, 3.42%)

 

gw1 (Yu et al. 1997)

S1_35199996

CT (4.86E−05, 6.17%)

PH (0.011, 6.80%)

 

S2_21858276

CT (5.95E−06, 4.12%)

PB ( 4.98E−02, 3.19%)

AQFP026/bct2b (Mu et al. 2004)

S3_15,462,193

CT (1.70E−06, 6.75%)

PH (0.026303753, 5.56%), PB (0.021535861, 6.26%)

 

S6_16,241,331

CT (7.80E−05, 6.44%)

 

AQDZ008 (Kashiwagi and Ishimaru 2004)

S7_1,592,572

CT (8.89 E−05, 3.73%)

PB ( 2.20792E−4, 5.48%)

 

S7_18,874,511

CT (2.79E−05, 7.83%)

 

AQDZ009 (Kashiwagi and Ishimaru 2004)

S7_24,536,919

CT (2.99E−05, 7.27%)

PH (8.47 E−03, 13.23%)

 

S9_21,545,679

CT (8.02E−06, 3.98%)

  

S11_21,499,010

CT (9.40E−05, 3.56%)

PB (1.58 E−04, 5.46%), PH (1.88E−02, 3.18%)

bct11c (Mu et al. 2004)

S2_30,762,305

PL (5.91E−05, 2.13%)

PH (0.021162648, 3.20%)

pl2a/AQDQ013 (Zhuang et al. 1997)

S3_32,359,666

PL (1.17E−05, 4.39%)

 

qPL-3–2/CQX12 (Yamamoto et al. 2016)

S4_34,899,389

PL (5.89E−05, 4.06)

  

S6_6,597,022

PL (1.37E−07, 4.70%)

PH(4.67879E−04, 7.92%), PB(0.005270489, 7%)

qPL-6/AQGM011, AQDY083, AQDY082, AQCU085 (Suh et al. 2005; Kobayashi et al. 2003; Mei et al. 2003)

S6_11,174,827

PL(3.76E−06, 3.4%)

CT( 0.020179035, 3.17%), GW(0.026049429, 1.61%)

AQCU085 (Mei et al. 2003)

S8_11,774,122

PL(4.83E−07, 8.34%)

PB(0.035139693, 10.31%)

AQCU085 (Mei et al. 2003)

S9_4,933,781

PL(4.62E−05, 2.08%)

 

AQCU149 (Mei et al. 2003)

S10_14,320,467

PL(3.59E−07, 3.1%)

PH(0.002110037, 4.37%)

 

S10_16,385,834

PL(2.00E−06, 5.40%)

PH(0.030803675, 6.90%), PB(0.00164866, 10.75%)

 

S11_7,438,223

PL(3.00E−05, 2.08%)

  

S4_30,721,851

PB(7.49E−05, 5.56%)

 

qPRB-4a (Teng et al. 2002)

S7_24,282,724

PB(5.57E−05, 7.60%)

PH(0.042017316, 3.63%)

 

S6_24,807,445

GL(6.01E−05, 1.89%)

 

qGL-6 (Li et al. 2003)

S8_5,775,398

GL(9.86E−05, 1.84%)

  

S1_40,142,074

GW(7.92E−05, 2.67%)

 

qGW-1 (Wan et al. 2005)

S2_7,048,091

GW(6.96E−05, 2.25%)

  

S2_22,216,515

GW(1.62E−05, 2.75%)

  

S3_7,917,671

GW(5.35E−05, 4.64%)

  

S4_12,374,542

GW(3.99E−06, 4.88%)

  

S4_34,598,600

GW(8.93E−05, 3.35%)

  

S5_19,130,617

GW(7.87E−06, 3.87%)

  

S5_23,720,696

GW(4.31E−05, 2.90%)

  

S5_28,157,471

GW(5.68E−06, 2.44%)

PH(0.002417007, 3.94%), HGW(0.002092217, 2.68%)

 

S8_20,423,775

GW(9.81E−06, 3.00%)

  

S8_24,621,885

GW(3.61E−06, 3.92%)

PB(0.022511555, 5.8%), PH(0.020274467, 5.36%)

 

S10_111,061

GW(5.03E−06, 4.29%)

  

S10_19,109,511

GW(1.47E−05, 2.4%)

  

S10_19,238,621

GW(2.16E−05, 3.91%)

  

S1_38,370,584

HGW(6.88E−07, 7.38%)

 

gw1.2, qTGW1-2, gw1.1 (Moncada et al. 2001; Hittalmani et al. 2002; Septiningsih et al. 2003)

S2_2,875,772

HGW(6.46E−05, 3.49%)

GL(0.035508538, 0.98%), PH(0.001764352, 3.4%)

QKw2b (Li et al. 1997)

S2_3,873,759

HGW(1.55E−05, 6.38%)

GL(0.005263071, 2.61%)

QKw2b (Li et al. 1997)

S4_4,499,266

HGW(1.34E−10, 9.46%)

  

S4_26,914,103

HGW(9.69E−07, 6.17%)

 

AQE053, gw4 (Xiao et al. 1998; Brondani et al. 2002)

S4_31,316,844

HGW(5.89E−06, 5.43%)

 

AQEO021 (Redoña and Mackill 1998)

S4_35,115,087

HGW(3.76E−05, 6.58%)

CT(0.002310095, 6.00%)

 

S5_24,316,574

HGW(7.99E−08, 8.85%)

 

gw5b, gw5(Xiao et al 1998; Hua et al. 2002)

S11_19,062,952

HGW(5.30E−07, 8.05%)

 

gw11.1 (Moncada et al. 2001)