Table 5.
Summary of quantitative trait loci identified for grain Cd concentrations in rice.
| Locus | Dataset | Chr.a | SSNb | Peak SNPc | Location | Alleled | MAFe | Effectf | P-value |
|---|---|---|---|---|---|---|---|---|---|
| qGCD1 | ALL | 6 | 1 | SNP-6.26611875 | 26612873 | T/C | 0.12 | -0.03 | 5.50 × 10-6 |
| qGCD2 | ALL | 8 | 1 | SNP-8.6451524 | 6452520 | A/T | 0.23 | 0.03 | 9.55 × 10-6 |
| qGCD3 | ALL | 8 | 1 | SNP-8.8506719 | 8507716 | C/T | 0.14 | 0.02 | 9.14 × 10-7 |
| qGCD4 | ALL | 10 | 1 | SNP-10.1059961 | 1060986 | G/T | 0.17 | -0.02 | 1.74 × 10-6 |
| qGCD5 | ALL | 11 | 1 | SNP-11.3083997 | 3088095 | C/A | 0.12 | -0.02 | 9.80 × 10-6 |
| qGCD6 | ALL | 12 | 1 | SNP-12.21730362 | 21763816 | A/T | 0.06 | 0.04 | 7.41 × 10-6 |
| qGCD7 | ALL | 12 | 1 | SNP-12.25531108 | 25564714 | T/C | 0.07 | -0.03 | 1.54 × 10-6 |
| qGCD8 | IND | 1 | 1 | SNP-1.42352675 | 42353720 | A/G | 0.26 | 0.05 | 4.52 × 10-6 |
| qGCD9 | IND | 2 | 1 | SNP-2.20960147 | 20966016 | A/G | 0.09 | 0.07 | 8.34 × 10-6 |
| qGCD10 | IND | 2 | 1 | SNP-2.29758238 | 29764108 | T/C | 0.11 | 0.07 | 6.27 × 10-6 |
| qGCD11 | IND | 9 | 1 | SNP-9.6772609 | 6773610 | T/C | 0.12 | 0.06 | 5.82 × 10-6 |
| qGCD12 | TEJ | 3 | 1 | SNP-3.22814291 | 22815803 | T/C | 0.32 | 0.04 | 3.96 × 10-6 |
| qGCD13 | TEJ | 4 | 1 | SNP-4.20446300 | 20618258 | T/C | 0.28 | 0.04 | 9.48 × 10-6 |
| qGCD14 | TEJ | 6 | 2 | SNP-6.24657474 | 24658472 | C/T | 0.45 | 0.04 | 5.57 × 10-6 |
| qGCD15 | TEJ | 7 | 1 | SNP-7.12536853 | 12537847 | C/A | 0.20 | 0.05 | 9.91 × 10-6 |
| qGCD16 | TRJ | 2 | 1 | SNP-2.28662504 | 28668374 | T/G | 0.09 | 0.04 | 2.37 × 10-6 |
| qGCD17 | TRJ | 3 | 1 | SNP-3.34365461 | 34372592 | G/A | 0.12 | 0.04 | 5.70 × 10-6 |
Threshold for significance, P-value < 1.00 × 10-5. aChr., chromosome. bSSN, significant SNP number. cSNP with the best P-value. dAllele, minor/major alleles. eMAF, minor allele frequency. fEffect, allele effect with respect to the minor allele.