Table 4.
Haplotype analysis of the important loci
| Locus | Traits | No. of SNPs | No. of haplotypes | Sequence of alleles | Frequency (%) | Traits | 15LS Mean ± S.D |
16LS Mean ± S.D |
17LS Mean ± S.D |
15HS Mean ± S.D |
16HS Mean ± S.D |
17HS Mean ± S.D |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| QSl-1B | SL | 11 | 2 | TCTCATCCCCT** | 33.51 | SL | 9.65 ± 0.99 | 7.77 ± 1.01 | 8.54 ± 0.85 | 8.57 ± 1.17 | 7.31 ± 1.24 | 8.89 ± 0.98 |
| CTCTGAGATTC | 52.88 | SL | 8.95 ± 1.09 | 7.05 ± 0.96 | 7.87 ± 0.67 | 7.79 ± 1.01 | 6.71 ± 1.02 | 8.20 ± 0.90 | ||||
| QYpp-3A | YPP | 6 | 3 | CCAATG** | 5.24 | YPP | 26.56 ± 4.85 | 22.57 ± 5.17 | 24.84 ± 3.63 | 14.36 ± 1.94 | 19.37 ± 3.89 | 23.21 ± 5.17 |
| ATAATG | 77.49 | YPP | 19.33 ± 6.49 | 18.74 ± 5.24 | 19.25 ± 4.20 | 10.43 ± 3.67 | 12.96 ± 5.45 | 16.61 ± 4.95 | ||||
| ATGGGA | 4.71 | YPP | 17.65 ± 7.75 | 16.13 ± 5.59 | 18.31 ± 4.84 | 9.22 ± 4.24 | 10.02 ± 5.51 | 17.60 ± 4.04 | ||||
| QSl-3B | SL | 5 | 2 | CAGTT** | 30.37 | SL | 9.38 ± 1.50 | 7.70 ± 1.02 | – | 8.36 ± 1.48 | – | – |
| TGTCA | 65.97 | SL | 8.84 ± 1.77 | 7.16 ± 0.91 | – | 7.60 ± 1.75 | – | – | ||||
| QTkw-4A | TKW | 25 | 2 | CCGCCCGGGCGTGCGCGCTGGATCC** | 8.90 | TKW | – | 52.36 ± 5.43 | 46.03 ± 4.75 | – | 49.14 ± 5.77 | 40.20 ± 4.80 |
| TTATTGATATACCTATATCCTGAGT | 83.77 | TKW | – | 47.92 ± 6.02 | 40.92 ± 4.79 | – | 43.60 ± 9.83 | 37.65 ± 4.99 | ||||
| QPh-4D | PH | 4 | 2 | GCTG** | 68.06 | PH | 78.14 ± 20.67 | 77.55 ± 13.49 | 82.70 ± 14.71 | 63.40 ± 17.55 | 58.83 ± 15.80 | 73.26 ± 12.67 |
| TTCA | 28.27 | PH | 67.92 ± 6.00 | 65.98 ± 5.81 | 69.37 ± 6.02 | 57.58 ± 4.86 | 53.96 ± 6.53 | 60.63 ± 6.47 | ||||
| Q-5A2 | BM YPP | 4 | 2 | GACC** | 58.64 | BM | – | – | – | 22.84 ± 6.53 | – | – |
| AGAT | 37.17 | BM | – | – | – | 19.93 ± 8.86 | – | – | ||||
| GACC** | 58.64 | YPP | – | – | – | 11.35 ± 3.11 | – | – | ||||
| AGAT | 37.17 | YPP | – | – | – | 9.73 ± 4.30 | – | – | ||||
| Q-5B1 | SL BM GN YPP | 4 | 2 | AGCA** | 88.48 | BM | – | – | – | 22.46 ± 8.29 | 26.54 ± 10.51 | – |
| GTTG | 4.71 | BM | – | – | – | 15.55 ± 5.51 | 9.04 ± 6.53 | – | ||||
| AGCA** | 88.48 | SL | – | – | – | – | 6.94 ± 1.22 | – | ||||
| GTTG | 4.71 | SL | – | – | – | – | 5.45 ± 2.54 | – | ||||
| AGCA** | 88.48 | YPP | – | 19.28 ± 5.59 | – | 11.11 ± 3.93 | 13.88 ± 5.48 | – | ||||
| GTTG | 4.71 | YPP | – | 15.33 ± 4.65 | – | 7.30 ± 2.45 | 4.51 ± 3.67 | – | ||||
| QSl-5B2 | SL | 21 | 2 | CTTTTAGCGACCGGGCGGCCC** | 85.86 | SL | – | – | – | – | 6.89 ± 1.35 | – |
| TCCCCGAGAGTAAAAAATGTA | 4.71 | SL | – | – | – | – | 4.58 ± 2.88 | – | ||||
| Q-5B3 | SN BM YPP GN | 36 | 2 | GCCCCCTGGCTCCGCCACGCCGGGGGCGTCGTGGCG** | 54.45 | BM | 49.02 ± 16.02 | – | – | 23.90 ± 8.11 | – | – |
| TAAGGTCAATCATATTGTATTAATAAAACTTCCATT | 12.57 | BM | 35.86 ± 15.96 | – | – | 18.35 ± 8.87 | – | – | ||||
| GCCCCCTGGCTCCGCCACGCCGGGGGCGTCGTGGCG** | 54.45 | GN | 627.45 ± 194.97 | 415.44 ± 107.02 | – | 301.59 ± 113.55 | 310.88 ± 116.97 | – | ||||
| TAAGGTCAATCATATTGTATTAATAAAACTTCCATT | 12.57 | GN | 448.46 ± 203.83 | 361.03 ± 132.06 | – | 221.08 ± 105.19 | 255.05 ± 144.92 | – | ||||
| GCCCCCTGGCTCCGCCACGCCGGGGGCGTCGTGGCG** | 54.45 | SN | 15.43 ± 4.51 | 10.69 ± 2.34 | – | 6.75 ± 2.32 | – | – | ||||
| TAAGGTCAATCATATTGTATTAATAAAACTTCCATT | 12.57 | SN | 11.31 ± 5.38 | 9.43 ± 3.04 | – | 5.33 ± 2.46 | – | – | ||||
| GCCCCCTGGCTCCGCCACGCCGGGGGCGTCGTGGCG** | 54.45 | YPP | 21.65 ± 6.80 | – | – | 11.78 ± 3.73 | – | – | ||||
| TAAGGTCAATCATATTGTATTAATAAAACTTCCATT | 12.57 | YPP | 16.43 ± 7.39 | – | – | 9.17 ± 4.39 | – | – | ||||
| Q-7A | SL YPP | 12 | 2 | CGTTACGACCCT** | 90.58 | SL | – | 7.39 ± 1.02 | 8.18 ± 0.90 | – | – | 8.49 ± 1.12 |
| TTACGTAGATAA | 5.24 | SL | – | 6.77 ± 0.87 | 7.28 ± 1.31 | – | – | 7.76 ± 1.42 | ||||
| CGTTACGACCCT** | 90.58 | YPP | 23.71 ± 6.62 | – | – | – | – | – | ||||
| TTACGTAGATAA | 5.24 | YPP | 19.08 ± 8.93 | – | – | – | – | – |
PH plant height, SN spike number, SL spike length, GN grain number, TKW thousand kernels weight, YPP yield per plot, BM biological mass, LS low salinity treatment, HS high salinity treatment, S. D standard deviation
** represents the favorable haplotype
“--” represents no significantly difference between haplotypes