Table 4.
Quantitative trait loci (QTL) detected for 11 agronomic traits studied in CK60/San Chi San RIL population
| Trait | QTL name | Environment | Chr | Position (cM) | Flanking markers | Interval (cM)a | LOD score | Additiveb | R2 (%)c |
|---|---|---|---|---|---|---|---|---|---|
| Chl-1 | qChl1-2 | 12NN | 2 | 141.3 | S2_64212168 - S2_66500907 | 136.5-147.4 | 3.5 | −0.83 | 6.06 |
| qChl1-3 | 12NN | 3 | 159.4 | S3_68886972 - S3_71854294 | 154-163.1 | 3.6 | 0.95 | 8.07 | |
| qChl1-10a | Comb-LN | 10 | 62.8 | S10_6734893 - S10_11357374 | 56.5-73.4 | 3.8 | −1.14 | 10.7 | |
| qChl1-10b | Comb-LN | 10 | 78.4 | S10_13327624 - S10_15068324 | 77.2-79.3 | 3.1 | 0.84 | 7.46 | |
| Chl-3 | qChl3-10a | 12NN | 10 | 48.2 | S10_5936786 - S10_6734839 | 44.1-52.3 | 4 | −2.9 | 13.9 |
| qChl3-10b | 12NN | 10 | 91 | S10_50340995 - S10_52987481 | 88.3-98.8 | 4.9 | 2.4 | 11.8 | |
| PH | qPH-2a | 11NN | 2 | 2.5 | S2_1477485 - S2_2197887 | 0-3.2 | 3 | 8.7 | 7.55 |
| qPH-2b | 11LN | 2 | 10.5 | S2_2459689 - S2_3418722 | 5.4-14 | 3.2 | 7 | 8.04 | |
| qPH-3a | 11, 12, Comb- LN | 3 | 21.4 | S3_2945750 - S3_4802301 | 17.4-28.4 | 3.3 | 7.9 | 9.51 | |
| qPH-6 | Comb-NN | 6 | 47.2 | S6_40065492 - S6_45811964 | 44-54 | 3.8 | −6.98 | 16.9 | |
| qPH-9 | 11NN | 9 | 85.1 | S9_50511351 - S9_50956545 | 82.6-87 | 3.3 | 8.9 | 18.0 | |
| AD | qAD-1a | 11NN | 1 | 81.2 | S1_21655969 - S1_24935643 | 77.6-91.4 | 3.4 | −1.06 | 7.06 |
| qAD-1b | 11LN | 1 | 174 | S1_58103916 - S1_62800271 | 169-178 | 3.1 | 3.73 | 10.8 | |
| qAD-2 | 12NN | 2 | 30.4 | S2_4979265 - S2_7797336 | 25.4-41.1 | 4.2 | −1.45 | 10.5 | |
| qAD-3 | 11NN | 3 | 3.1 | S3_518323 - S3_2452009 | 1.4-11.4 | 5 | −1.48 | 12.8 | |
| qAD-9 | 11NN, Comb- LN | 9 | 78.9 | S9_49568498 - S9_50744450 | 75.9-85 | 5.7 | 1.61 | 14.7 | |
| MC1 | qMC1-1 | 12LN | 1 | 169.8 | S1_57571254 - S1_59648859 | 163.9-171.3 | 3 | 0.88 | 10.67 |
| qMC1-8 | 11NN | 8 | 103.3 | S8_48291652 - S8_53690396 | 88.6-115.4 | 3.3 | −0.87 | 7.48 | |
| MC2 | qMC2-1 | 11LN | 1 | 107.7 | S1_44806835 - S1_49470786 | 101.2-111.3 | 3 | −1.82 | 7.65 |
| qMC2-9 | 12LN | 9 | 78.9 | S9_49568498 - S9_50744450 | 75.9-85 | 3.1 | 2.92 | 6.76 | |
| BY | qBY-3 | 12LN | 3 | 151.8 | S3_66370259 - S3_70192466 | 143-158.3 | 3 | 0.42 | 6.81 |
| qBY-7 | 11LN, Comb-LN | 7 | 98.7 | S7_57890877 - S7_58551650 | 97.1-100.8 | 4.1 | −1.22 | 11 | |
| qBY-8 | Comb-LN | 8 | 33.3 | S8_2528799 - S8_4381062 | 23.9-34.1 | 3.9 | −0.75 | 10.0 | |
| GY | qGY-2 | 12NN, Comb-NN | 2 | 65.9 | S2_13864242 - S2_19506339 | 65.6-71.9 | 3.1 | −0.4 | 7.48 |
| qGY-8 | 11LN | 8 | 102.3 | S8_48291652 - S8_53253482 | 85.4-111.6 | 3.6 | 0.37 | 6.63 | |
| qGY-9 | Comb-NN | 9 | 90.6 | S9_50744450 - S9_51382632 | 86.5-95.6 | 3.1 | 0.27 | 16.8 | |
| qGY-10a | 12LN | 10 | 61.8 | S10_6734839 - S10_8210492 | 50.8-63.1 | 3.1 | −0.21 | 7.09 | |
| qGY-10b | 12NN, Comb-NN | 10 | 121.3 | S10_54423190 - S10_55477998 | 117.2-125.5 | 4.6 | −0.54 | 12.9 | |
| TGW | qTGW-1 | 11LN | 1 | 2.8 | S1_1573765 - S1_5966723 | 0-12.3 | 3.3 | 1.19 | 17.6 |
| qTGW-3 | 11NN, Comb-LN | 3 | 95.1 | S3_54561579 - S3_56298715 | 92.4-98.8 | 3.7 | −1.22 | 9.19 | |
| qTGW-4 | 12NN | 4 | 11.7 | S4_4317922 - S4_5726443 | 10.6-16.4 | 3.1 | −0.78 | 7.3 | |
| GS | qGS-1 | 11LN | 1 | 36 | S1_10813941 - S1_14302572 | 25.7-36.8 | 3.2 | −0.08 | 8.11 |
Traits indicate Chl1, Chl2, Chl3 chlorophyll contents at (vegetative, anthesis, and maturity) stages, PH plant height (cm), AD days to anthesis, MC1% stover moisture content, MC2% head moisture content, BY biomass yield (t. ha−1), GY grain yield (t. ha−1), TGW thousand grain weight (g), GS grain/stover ratio (%). QTL name indicates q for QTL followed by trait name to which the QTL was detected and by the chromosome number on which it was detected. Environments: 11NN, 12NN indicate that QTLs detected in normal N treatments in 2011 and 2012 years respectively; 11LN, 12LN indicate QTLs detected in low N treatments in 2011 and 2012 years respectively; Comb-NN, Comb-LN indicates QTLs detected on trait values averaged over two years (2011 and 2012) in normal N and low N treatments respectively. Chr, chromosome on which QTL was detected. a2.0-LOD drop support interval of the QTL; bAdditive effect: positive values of the additive effect indicate that alleles from CK60 were in the direction of increasing the trait score and vice versa; cPercentage of phenotypic variation explained by the QTL. If more than one QTL were detected on the same chromosome for a trait, QTLs identified were serially numbered. QTLs highlighted in bold are the validated QTLs, which were also detected in earlier study reported by Gelli et al. [46]