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Table 3 Identified QTLs for the assessed salinity responsive traits

From: Genome-wide association study of seedling stage salinity tolerance in temperate japonica rice germplasm

Trait QTL Chr QTL interval (Mb) Peak position (bp) SNP Marker F value p value Marker R2
PD18 qPD18_2.1 2 24.38–24.51 24,382,186 10,224,382,186 18.11 3.53E-05 0.1119
PD18 qPD18_4.1 4 17.08–17.09 17,083,910 10,417,083,910 19.43 1.87E-05 0.1134
PD18 qPD18_11.1 11 24.64–24.65 24,645,753 11,124,645,753 19.92 1.50E-05 0.1174
SES18 qSES18_2.1 2 24.38–24.51 24,382,186 10,224,382,186 20.23 1.31E-05 0.1255
SES18 qSES18_4.1 4 17.06–17.09 17,083,910 10,417,083,910 19.28 2.01E-05 0.1127
SES18 qSES18_11.1 11 24.64–24.65 24,645,753 11,124,645,753 20.89 9.55E-06 0.1234
SDW0 qSDW0_2.1 2 6.98–7.12 6,992,556 10,206,992,556 16.02 9.29E-05 0.092
SDW0 qSDW0_9.1 9 7.77–7.78 7,779,630 10,907,779,630 8.57 2.95E-04 0.1111
SNa+0 qSNa0_2.1 2 4.79–6.56 5,610,544 10,205,610,544 22.43 4.54E-06 0.1283
SNa+0 qSNa0_6.1 6 27.17–29.49 27,397,942 10,627,397,942 19.86 1.52E-05 0.12
SNa+0 qSNa0_8.1 8 21.49–21.51 21,498,898 10,821,498,898 16.21 8.59E-05 0.0997
SNa+0 qSNa0_8.2 8 26.56–26.57 26,568,663 10,826,568,663 10.12 7.13E-05 0.1225
SNa+0 qSNa0_9.1 9 6.77–7.42 7,411,725 10,907,411,725 16.83 6.47E-05 0.1043
SNa+12 qSNa12_4.1 4 20.33–20.57 20,374,274 10,420,374,274 11.62 1.91E-05 0.1427
SNa+12 qSNa12_10.1 10 14.91–16.19 15,893,435 11,015,893,435 16.29 8.30E-05 0.0988
SNa+D qSNaD_5.1 5 10.28–11.25 10,287,595 10,510,287,595 17.9 3.83E-05 0.1062
SNa+D qSNaD_6.1 6 23.74–23.85 23,820,480 10,623,820,480 16.49 7.53E-05 0.0984
SK+D qSKD_1.1 1 32.96–38.59 38,584,909 10,138,584,909 20.12 1.33E-05 0.1155
SK+D qSKD_2.1 2 24.49–25.43 24,686,915 10,224,686,915 30.49 1.23E-07 0.1754
SK+D qSKD_2.2 2 28.40–28.92 28,694,339 10,228,694,339 24.25 1.97E-06 0.1391
SK+D qSKD_3.1 3 3.69–3.81 3,805,384 10,303,805,384 28.01 3.69E-07 0.1611
SK+D qSKD_4.1 4 4.49–4.72 4,509,563 10,404,509,563 30.72 4.08E-12 0.3525
SK+D qSKD_12.1 12 16.55–17.62 16,556,527 11,216,556,527 18.41 2.95E-05 0.1056
SNa+/K+0 qSNa/K0_3.1 3 3.72–3.81 3,805,384 10,303,805,384 29.01 2.37E-07 0.168
SNa+/K+0 qSNa/K0_11.1 11 17.62–17.63 17,624,102 11,117,624,102 8.4 3.45E-04 0.1012
SNa+/K+D qSNa/KD_3.1 3 23.88–24.08 24,079,731 10,324,079,731 15.67 1.10E-04 0.1019