Table 2 GWAS results: significant SNPs for association mapping using the carioca diversity panel (CDP) genotyped by 1,516 SNPs, evaluating seed coat lightness at harvest (HL) and seed coat post-harvest darkening (L30 and ΔL*)
Trait | SNP | Chr | Position | p value | REF.a | ALT.a | MAF | Effect | nG |
|---|---|---|---|---|---|---|---|---|---|
HL | ss715650237 | Pv04 | 8,305,412 | 2.2E-05 | C | A | 0.09 | -1.14 | 65 |
ss715650318 | Pv04 | 38,357,623 | 2.7E-06 | T | C | 0.12 | -1.05 | 38 | |
ss715640503 | Pv10 | 2,562,874 | 4.4E-06 | T | C | 0.27 | 0.66 | 88 | |
L30 | ss715646867 | Pv01 | 42,399,057 | 5.3E-07 | C | T | 0.12 | -1.02 | 100 |
ss715648328 | Pv04 | 5,499,065 | 5.1E-07 | C | T | 0.13 | -1.11 | 83 | |
ss715650318 | Pv04 | 38,357,623 | 1.6E-06 | T | C | 0.12 | -0.94 | 38 | |
ss715647732 | Pv07 | 32,272,598 | 1.8E-06 | G | A | 0.14 | 1.41 | 110 | |
ss715645851 | Pv07 | 35,650,852 | 2.2E-05 | A | G | 0.08 | -1.19 | 113 | |
ΔL | ss715645575 | Pv03 | 51,275,803 | 1.4E-05 | C | T | 0.21 | 0.37 | 118 |
ss715646652 | Pv08 | 58,966,240 | 7.8E-07 | G | A | 0.29 | 0.45 | 109 | |
ss715646104 | Pv08 | 61,479,072 | 1.9E-06 | A | G | 0.24 | -0.43 | 235 | |
ss715646121 | Pv08 | 61,915,670 | 1.4E-05 | C | T | 0.15 | -0.40 | 235 | |
ss715645744 | Pv09 | 7,807,479 | 2.7E-06 | C | T | 0.32 | -0.38 | 92 | |
ss715640510 | Pv10 | 2,582,807 | 2.8E-05 | C | T | 0.26 | -0.31 | 88 |