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Table 1 The significant QTNs for five rice yield-related traits detected simultaneously by using two or more multi-locus GWAS methods

From: Multi-locus genome-wide association studies for five yield-related traits in rice

Trait QTN Chr Position LOD R2 (%) Method Reported genes
Grain Length qGL-1-1 1 16,255,794 3.57–6.37 0.29–1.91 1,2,3  
qGL-3-1 3 8,800,352 3.43–4.15 1.71–3.56 4,5  
qGL-3-2 3 16,182,203 3.42–5.81 1.92–2.23 1,3  
qGL-3-3 3 16,699,322 3.68–4.70 2.78–7.54 1,4 GS3
qGL-3-4 3 16,717,839 3.47–3.51 2.68–6.97 2,3 GS3
qGL-3-5 3 16,911,337 4.01–4.76 3.49–9.75 1,5 GS3
qGL-3-6 3 35,509,618 3.22–7.14 2.79–3.68 1,3 qTGW3
qGL-5-1 5 5,371,587 4.23–4.92 1.25–2.28 2,5 GSE5/GW5
qGL-5-2 5 6,215,765 3.12–5.01 3.91–5.72 1,4  
qGL-6-1 6 4,252,841 4.07–9.18 0.74–1.13 1,3  
qGL-6-2 6 22,641,242 8.54–8.57 7.17–7.35 1,3  
qGL-7-1 7 4,465,180 3.79–11.29 1.01–9.81 1,2,3  
qGL-8-1 8 1,629,499 5.01–5.78 0.67–1.33 1,3  
qGL-8-2 8 14,139,411 3.87–4.67 2.57–3.29 1,3,5  
qGL-10-1 10 4,663,209 4.49–6.46 7.66–13.25 4,5  
qGL-10-2 10 5,288,007 4.05–5.38 1.93–2.63 1,2  
qGL-12–1 12 1,135,876 3.37–3.42 0.00–1.19 2,3  
qGL-12-2 12 5,542,726 4.02–8.98 0.77–1.25 2,3  
qGL-12-3 12 14,546,343 5.74–7.38 0.08–1.73 1,3  
Grain Width qGW-3-1 3 10,817,310 3.50–4.81 0.34–3.64 2,3  
qGW-3-2 3 21,604,259 3.02–3.65 1.62–5.28 1,4  
qGW-4-1 4 26,662,080 3.95–5.95 1.77–2.83 3,4 STRK1
qGW-5-1 5 5,359,498 4.12–6.93 1.68–6.34 2,4,5 GSE5/GW5
qGW-5-2 5 5,371,587 4.92–11.55 2.83–7.20 1,3,4,5 GSE5/GW5
qGW-9-1 9 191,910 3.59–5.35 2.30–2.68 3,4  
qGW-9-2 9 1,318,664 6.74–7.74 5.97–13.97 3,4 BC12
qGW-10-1 10 22,500,927 3.31–4.41 1.04–1.50 2,4 OsCAO1
qGW-12–1 12 22,677,925 3.04–12.34 0.29–1.47 2,3  
Grain Thickness qGT-5-1 5 4,830,996 12.94–13.56 4.93–7.23 1,4  
qGT-5-2 5 7,022,361 4.94–5.14 1.85–3.20 2,4  
qGT-5-3 5 7,036,290 4.34–13.62 3.32–3.38 1,5  
qGT-5-4 5 23,605,308 3.03–4.41 0.85–5.69 1,3 OsSNAT1
qGT-6-1 6 15,688,533 3.43–4.25 3.59–4.17 1,4  
qGT-6-2 6 19,652,114 3.52–10.41 2.23–11.95 1,3 OsSPDS2
qGT-12–1 12 17,685,177 3.02–5.90 2.09–3.77 1,4  
1000-Grain Weight qTGW-1-1 1 4,853,002 6.27–6.60 1.97–2.11 1,4 GW5L
qTGW-1-2 1 33,427,348 3.19–4.48 0.60–1.57 3,4  
qTGW-2-1 2 2,529,182 4.94–10.21 0.56–5.62 2,3  
qTGW-3-1 3 16,776,481 6.15–7.49 0.89–2.76 1,3,4 GS3
qTGW-4-1 4 31,950,052 3.14–4.28 0.42–1.42 3,4  
qTGW-4-2 4 32,409,784 4.54–5.22 1.47–2.41 2,4 FLO2
qTGW-5-1 5 4,859,527 7.33–8.91 0.86–3.90 1,3,4,5  
qTGW-5-2 5 7,115,594 4.35–12.71 0.34–4.51 1,3,4,5  
qTGW-7-1 7 18,639,992 3.57–11.64 1.39–6.37 3,4,5  
qTGW-7-2 7 18,895,502 4.22–7.48 1.70–4.99 3,5 OsSPL13
qTGW-7-3 7 19,391,625 4.26–11.43 0.44–4.99 1,3,5 OsSPL13
qTGW-7-4 7 23,476,357 3.77–5.02 0.48–3.88 1,3  
qTGW-7-5 7 26,928,988 3.89–7.12 0.60–1.40 3,4  
qTGW-8-1 8 25,590,176 3.10–4.53 0.34–1.35 3,4,5  
qTGW-8-2 8 26,309,952 5.51–6.94 1.06–1.95 1,3 GW8/OsSPL16/qGW8
qTGW-9-1 9 2,009,389 3.01–3.70 0.45–2.50 3,4  
qTGW-10-1 10 2,107,100 5.81–11.33 1.29–5.77 3,4,5  
qTGW-11–1 11 18,100,034 4.54–9.46 0.35–2.83 1,3,4 OsBDG1
qTGW-11–2 11 20,067,792 3.52–6.31 0.87–2.95 1,2,4  
qTGW-11-3 11 25,914,037 3.04–7.25 0.88–1.53 3,5  
qTGW-12–1 12 9,394,697 8.15–10.58 1.72–4.77 1,3  
qTGW-12-2 12 16,332,104 3.01–4.30 0.13–0.89 3,4  
Yield Per Plant qYPP-2-1 2 26,731,138 3.01–3.80 1.13–3.13 4,5  
qYPP-3-1 3 7,685,085 4.19–11.64 3.11–5.26 1,4,5  
qYPP-4-1 4 513,812 4.81–5.88 2.67–3.98 1,5  
qYPP-4-2 4 25,868,074 4.96–6.52 2.15–3.25 1,4,5 LABA1
qYPP-5-1 5 28,202 3.72–6.29 3.59–4.01 1,5  
qYPP-5-2 5 25,806,082 4.43–8.85 1.17–6.77 3,4,5 OsRab7
qYPP-5-3 5 29,791,637 3.71–5.36 2.38–3.89 1,5  
qYPP-6-1 6 15,037,982 5.50–6.92 3.75–3.87 4,5  
qYPP-6-2 6 30,797,769 3.42–4.60 0.65–1.80 2,5  
qYPP-7-1 7 337,826 8.93–9.51 1.86–5.81 1,3  
qYPP-7-2 7 20,669,197 3.08–6.62 0.28–1.79 1,2,3,4,5  
qYPP-8-1 8 79,975 4.58–5.62 1.65–1.86 2,5  
qYPP-8-2 8 19,396,188 3.12–5.64 0.27–3.08 1,3 PAY1
qYPP-10-1 10 5,854,315 3.21–4.64 0.33–2.03 2,3,5  
qYPP-10-2 10 20,388,038 3.81–12.61 0.57–6.99 2,3,4,5  
qYPP-11–1 11 994,705 3.40–3.62 0.59–2.97 3,4 ONAC122
qYPP-12–1 12 10,578,786 3.15–4.20 1.65–3.60 4,5  
  1. Methods 1–5 represnet mrMLM, FASTmrEMMA, pLARmEB, pKWmEB, and ISIS EM-BLASSO, respectively
  2. R2 (%): the proportion of total phenotypic variance explained by each QTN