Table 2.
List of SNPs related to senescence traits in comparison with biomass traits.
| S. No | Marker 1 | Chr 2 | Site 3 | Allele | Sen | BIOMASS | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GM | RM | GDW | RDW | |||||||||||||
| Trait 4 | Sig 5 | Eff 6 | R2 (%) 7 | Sig 5 | Eff 6 | Sig 5 | Eff 6 | Sig 5 | Eff 6 | Sig 5 | Eff 6 | |||||
| 1 | S1_100824497 | 1 | 103,203,345 | C/T | VSH | 3.32 × 10−5 | −0.54 | 5.11 | 1.71 × 10−3 | −18.80 | 3.35 × 10−3 | −42.18 | 1.16 × 10−2 | −7.69 | 8.18 × 10−3 | −9.24 |
| 2 | S1_100903343 | 1 | 103,279,958 | C/T | VSH | 1.63 × 10−6 | −0.67 | 7.50 | 1.89 × 10−3 | −19.79 | 1.54 × 10−3 | −48.29 | 2.37 × 10−2 | −7.29 | 2.49 × 10−3 | −11.21 |
| 3 | S1_141282152 | 1 | 143,508,124 | C/T | VSH | 8.79 × 10−5 | −0.53 | 4.32 | 7.16 × 10−3 | −16.73 | 3.62 × 10−2 | −31.01 | 1.17 × 10−1 | −4.84 | 1.14 × 10−2 | −8.94 |
| 4 | S1_209120152 | 1 | 212,105,133 | C/G | VSH | 5.80 × 10−6 | 0.79 | 5.84 | 3.86 × 10−3 | 22.88 | 5.49 × 10−2 | 36.59 | 1.04 × 10−1 | 6.59 | 4.80 × 10−4 | 16.33 |
| PA | 7.15 × 10−6 | 5.41 | 5.75 | |||||||||||||
| 5 | S1_22259426 | 1 | 22,612,531 | C/G | VSH | 7.98 × 10−5 | −0.61 | 4.66 | 1.50 × 10−1 | −10.05 | 7.76 × 10−1 | −4.81 | 1.27 × 10−1 | −5.48 | 1.78 × 10−1 | −5.52 |
| 6 | S1_296203927 | 1 | 301,677,536 | C/T | VSH | 8.21 × 10−6 | 0.73 | 6.18 | 1.71 × 10−3 | 23.14 | 2.61 × 10−1 | 20.24 | 6.11 × 10−2 | 7.05 | 4.37 × 10−3 | 12.28 |
| 7 | S1_63150814 | 1 | 63,980,587 | C/G | VSH | 1.45 × 10−6 | −1.16 | 6.87 | 8.87 × 10−4 | −36.13 | 3.99 × 10−2 | −53.77 | 1.23 × 10−1 | −8.75 | 4.71 × 10−3 | −18.45 |
| 8 | S1_6423401 | 1 | 6,420,128 | A/C | VSH | 5.05 × 10−5 | 0.91 | 5.03 | 9.46 × 10−2 | 16.81 | 7.62 × 10−1 | −7.42 | 2.76 × 10−1 | 5.68 | 2.30 × 10−1 | 7.14 |
| 9 | S2_13299973 | 2 | 13,592,073 | A/C | SC | 5.56 × 10−5 | 0.03 | 4.85 | 1.17 × 10−1 | 16.33 | 3.27 × 10−2 | 53.83 | 1.07 × 10−1 | 8.85 | 4.11 × 10−3 | 18.20 |
| 10 | S2_152505815 | 2 | 157,225,727 | A/G | VSP | 8.92 × 10−5 | 0.61 | 4.34 | 5.51 × 10−3 | 15.09 | 6.05 × 10−4 | 46.11 | 4.30 × 10−2 | 5.71 | 2.75 × 10−3 | 9.69 |
| 11 | S2_184012260 | 2 | 189,518,660 | C/G | PHVDIF | 6.45 × 10−5 | −0.46 | 5.29 | 2.03 × 10−1 | −7.86 | 2.05 × 10−2 | −34.66 | 6.02 × 10−1 | 1.61 | 1.04 × 10−1 | −5.74 |
| 12 | S2_2088378 | 2 | 2,085,417 | C/G | PA | 3.43 × 10−5 | −3.33 | 5.59 | 8.89 × 10−2 | −9.28 | 2.79 × 10−3 | −39.55 | 1.34 × 10−2 | −6.94 | 2.19 × 10−3 | −9.87 |
| 13 | S2_42234632 | 2 | 44,077,439 | A/G | PHVDIF | 3.21 × 10−5 | −0.65 | 5.22 | 1.54 × 10−2 | −19.51 | 1.89 × 10−2 | −46.97 | 2.25 × 10−2 | −9.50 | 4.14 × 10−4 | −16.88 |
| 14 | S3_148031626 | 3 | 149,339,963 | C/T | PHVDIF | 5.25 × 10−6 | 0.68 | 6.70 | 2.53 × 10−2 | 17.76 | 2.56 × 10−1 | 21.75 | 5.01 × 10−2 | 7.96 | 1.16 × 10−1 | 7.33 |
| 15 | S3_151970626 | 3 | 153,385,457 | A/G | PHVDIF | 6.27 × 10−6 | 0.44 | 6.19 | 1.02 × 10−2 | 13.24 | 1.39 × 10−1 | 18.53 | 8.31 × 10−2 | 4.56 | 3.27 × 10−1 | 2.94 |
| 16 | S3_217840430 | 3 | 221,449,552 | G/T | VSH | 3.73 × 10−6 | −1.04 | 7.38 | 5.42 × 10−3 | −27.78 | 4.54 × 10−4 | −87.79 | 5.13 × 10−1 | −3.44 | 8.70 × 10−1 | 0.98 |
| 17 | S3_223310403 | 3 | 227,056,710 | A/C | VSH | 8.54 × 10−5 | −0.54 | 5.54 | 5.63 × 10−2 | −11.91 | 4.63 × 10−1 | −11.17 | 2.64 × 10−1 | −3.58 | 3.66 × 10−1 | −3.29 |
| 18 | S3_5884845 | 3 | 5,057,742 | C/T | PA | 3.45 × 10−5 | −3.42 | 5.39 | 1.32 × 10−4 | −21.65 | 3.25 × 10−3 | −40.11 | 5.01 × 10−2 | −5.52 | 5.46 × 10−3 | −8.99 |
| SC | 1.07 × 10−5 | −0.02 | 6.01 | |||||||||||||
| 19 | S4_181727580 | 4 | 184,669,210 | A/C | VSH | 6.93 × 10−5 | −0.48 | 4.91 | 2.36 × 10−2 | −12.46 | 3.65 × 10−3 | −38.16 | 3.38 × 10−2 | −5.87 | 4.60 × 10−2 | −6.34 |
| 20 | S4_202887002 | 4 | 207,316,178 | A/T | VSP | 5.65 × 10−5 | 1.20 | 4.86 | 7.34 × 10−3 | 27.74 | 4.95 × 10−3 | 72.45 | 1.29 × 10−2 | 13.28 | 2.09 × 10−3 | 18.73 |
| 21 | S5_154600488 | 5 | 158,376,423 | A/G | PA | 3.36 × 10−5 | −4.15 | 5.45 | 3.84 × 10−2 | −15.06 | 1.31 × 10−2 | −42.16 | 3.28 × 10−3 | −10.55 | 2.39 × 10−2 | −9.32 |
| 22 | S5_147166110 | 5 | 150,672,499 | C/T | VSP | 1.69 × 10−5 | −0.85 | 5.97 | 1.12 × 10−3 | −22.69 | 3.55 × 10−3 | −47.37 | 5.24 × 10−2 | −6.61 | 2.48 × 10−2 | −8.81 |
| VSH | 4.83 × 10−6 | −0.69 | 6.76 | |||||||||||||
| 23 | S5_167009258 | 5 | 170,916,787 | C/T | PA | 9.04 × 10−5 | −6.48 | 4.78 | 3.87 × 10−2 | −22.47 | 4.76 × 10−2 | −53.38 | 9.19 × 10−2 | −9.48 | 3.86 × 10−2 | −13.27 |
| SC | 9.83 × 10−5 | −0.04 | 4.67 | |||||||||||||
| 24 | S5_172396840 | 5 | 176,501,182 | C/G | VSH | 4.28 × 10−5 | 0.61 | 4.86 | 2.19 × 10−1 | 8.42 | 3.28 × 10−2 | 35.03 | 8.99 × 10−1 | 0.43 | 1.22 × 10−1 | 6.04 |
| 25 | S5_184169070 | 5 | 188,797,787 | A/C | PHVDIF | 6.45 × 10−5 | −0.43 | 5.03 | 1.31 × 10−1 | −8.44 | 8.09 × 10−3 | −36.42 | 3.63 × 10−1 | −2.61 | 1.19 × 10−1 | −5.10 |
| 26 | S5_184171751 | 5 | 188,800,468 | A/T | PHVDIF | 4.64 × 10−5 | 0.47 | 5.20 | 2.64 × 10−1 | 6.79 | 1.35 × 10−1 | 21.94 | 1.91 × 10−1 | 4.03 | 1.26 × 10−1 | 5.40 |
| 27 | S5_185866560 | 5 | 190,535,974 | A/G | SC | 4.12 × 10−5 | 0.03 | 4.94 | 1.51 × 10−2 | 20.31 | 5.01 × 10−2 | 40.18 | 1.71 × 10−1 | 5.96 | 2.50 × 10−1 | 5.73 |
| 28 | S5_19709941 | 5 | 20,195,993 | C/T | SC | 1.06 × 10−5 | −0.02 | 5.81 | 1.40 × 10−1 | −7.65 | 1.47 × 10−1 | −18.29 | 7.24 × 10−2 | −4.79 | 3.67 × 10−2 | −6.38 |
| 29 | S5_214537055 | 5 | 220,409,338 | A/G | PA | 6.97 × 10−6 | −3.80 | 6.49 | 1.74 × 10−2 | −13.74 | 1.40 × 10−1 | −20.39 | 5.35 × 10−3 | −8.06 | 1.31 × 10−3 | −10.66 |
| SC | 4.56 × 10−5 | −0.02 | 5.22 | |||||||||||||
| 30 | S5_54415632 | 5 | 56,109,705 | G/T | VSP | 6.22 × 10−5 | 0.89 | 4.74 | 7.52 × 10−4 | 26.26 | 1.64 × 10−4 | 71.22 | 7.50 × 10−2 | 7.09 | 1.02 × 10−3 | 15.10 |
| 31 | S5_55394662 | 5 | 57,153,911 | A/C | PHVDIF | 5.08 × 10−5 | 0.60 | 4.84 | 4.90 × 10−2 | 15.55 | 7.30 × 10−3 | 51.32 | 5.80 × 10−1 | 2.21 | 2.18 × 10−1 | 5.63 |
| 32 | S5_61802239 | 5 | 63,587,555 | C/T | VSH | 2.68 × 10−5 | 0.74 | 5.37 | 3.81 × 10−3 | 23.31 | 1.15 × 10−2 | 48.79 | 1.15 × 10−2 | 10.03 | 4.89 × 10−2 | 8.96 |
| VSP | 3.78 × 10−6 | 1.06 | 6.66 | |||||||||||||
| 33 | S5_80969487 | 5 | 83,171,395 | C/G | VSH | 2.27 × 10−5 | 0.53 | 5.83 | 1.64 × 10−2 | 13.55 | 1.77 × 10−2 | 32.46 | 9.38 × 10−3 | 7.48 | 2.05 × 10−3 | 10.17 |
| 34 | S5_84063981 | 5 | 86,287,916 | C/T | VSP | 9.09 × 10−5 | 0.70 | 4.38 | 4.35 × 10−3 | 18.00 | 1.86 × 10−3 | 46.90 | 4.09 × 10−3 | 9.05 | 4.77 × 10−4 | 12.69 |
| 35 | S6_132457507 | 6 | 136,597,839 | G/T | PHVDIF | 5.17 × 10−5 | −0.47 | 5.24 | 2.47 × 10−3 | −18.90 | 2.91 × 10−3 | −44.78 | 3.32 × 10−2 | −6.73 | 2.10 × 10−3 | −11.14 |
| 36 | S6_141797374 | 6 | 145,913,312 | C/T | VSH | 3.08 × 10−5 | 0.98 | 5.35 | 7.53 × 10−3 | 28.34 | 2.91 × 10−3 | 77.85 | 2.77 × 10−1 | 5.93 | 8.92 × 10−3 | 16.30 |
| 37 | S6_152309276 | 6 | 156,446,826 | A/G | VSH | 7.63 × 10−5 | 0.57 | 5.25 | 1.24 × 10−1 | 10.01 | 2.55 × 10−1 | 18.05 | 2.21 × 10−2 | 7.74 | 1.18 × 10−2 | 9.68 |
| 38 | S6_162646831 | 6 | 166,851,405 | C/G | VSP | 3.76 × 10−5 | 0.67 | 5.37 | 4.32 × 10−4 | 20.14 | 1.29 × 10−3 | 43.93 | 1.31 × 10−2 | 7.15 | 3.40 × 10−5 | 13.83 |
| 39 | S6_163349566 | 6 | 167,553,244 | C/G | PA | 4.42 × 10−5 | −3.11 | 4.77 | 9.63 × 10−4 | −17.46 | 5.71 × 10−2 | −23.98 | 4.00 × 10−4 | −9.33 | 3.19 × 10−3 | −8.86 |
| VSP | 5.26 × 10−5 | −0.61 | 4.78 | |||||||||||||
| VSH | 4.88 × 10−5 | −0.47 | 4.73 | |||||||||||||
| 40 | S6_167031439 | 6 | 171,178,929 | C/T | VSH | 6.13 × 10−5 | 0.87 | 5.41 | 2.51 × 10−1 | 11.19 | 8.05 × 10−1 | 5.90 | 3.30 × 10−1 | 5.00 | 2.69 × 10−2 | 12.95 |
| 41 | S7_12615372 | 7 | 13,041,805 | A/G | SC | 6.97 × 10−5 | 0.03 | 4.38 | 3.54 × 10−1 | 9.72 | 3.68 × 10−1 | 22.66 | 7.07 × 10−2 | 8.67 | 4.21 × 10−1 | 4.38 |
| 42 | S7_139201593 | 7 | 143,942,346 | C/T | SC | 1.99 × 10−5 | 0.04 | 5.04 | 9.69 × 10−2 | 18.18 | 4.29 × 10−3 | 77.67 | 1.10 × 10−1 | 9.23 | 7.35 × 10−3 | 17.76 |
| PA | 8.37 × 10−5 | 6.44 | 4.26 | |||||||||||||
| 43 | S8_96765835 | 8 | 98,565,103 | A/G | SC | 2.89 × 10−5 | 0.04 | 6.11 | 4.84 × 10−1 | 8.28 | 2.21 × 10−2 | 66.36 | 1.85 × 10−2 | 13.24 | 2.43 × 10−2 | 14.42 |
| 44 | S9_8660567 | 9 | 8,358,103 | A/G | VSH | 4.06 × 10−5 | 0.59 | 5.13 | 9.42 × 10−2 | 10.87 | 4.73 × 10−2 | 31.13 | 4.30 × 10−1 | 2.59 | 4.54 × 10−1 | 2.81 |
| 45 | S10_141078749 | 10 | 141,806,270 | G/T | VSH | 8.94 × 10−5 | 0.47 | 4.60 | 7.28 × 10−2 | 9.70 | 5.21 × 10−2 | 25.80 | 3.89 × 10−1 | 2.37 | 2.31 × 10−1 | 3.77 |
| 46 | S10_146472807 | 10 | 147,246,775 | G/T | VSH | 8.56 × 10−5 | −0.53 | 4.63 | 1.68 × 10−4 | −23.51 | 5.97 × 10−3 | −40.65 | 8.11 × 10−1 | −0.70 | 1.66 × 10−3 | −10.67 |
1 Marker—significant SNPs for the desired trait; 2 Chr—physical chromosomal position of the marker; 3 Site—physical position of the SNP in bp; 4 Trait-GM—grain moisture; RM—residual moisture; GDW—grain dry weight; residual dry weight; VSP—visual scale of the plant at 45 DAA; VSH—visual scale of husk at 45 DAA; PHVDIF—the difference between the visual scale of plant and husk at 45 DAA; PA—photosynthesis activity at 45 DAA; SC—stomatal conductance at 45 DAA; 5 SIG—significance; 6 EFF—effect; 7 R2 proportion of the phenotypic variance explained by the QTL.