Table 3 Summary of significant SNPs associated with yield component traits identified in GWAS
From: Genome-wide association studies for yield component traits in a macadamia breeding population
Trait | SNP | Scaffolda | Position (bp) | Alleles | MAF | p | pMR | BLUE |
|---|---|---|---|---|---|---|---|---|
NWc | s2204 | scaffold926|size239084 | 212,122 | A/G | 0.027 | 3.68E-06 | 4.46e-06 | 0.084 |
s4163 | scaffold285|size451335 | 314,657 | C/T | 0.027 | 8.03E-06 | NS | ||
s1434 | scaffold_177|size983250 | 804,678 | T/C | 0.019 | 2.65E-05 | NS | ||
s1643 | scaffold44|size832018 | 129,241 | A/C | 0.021 | 3.46E-05 | NS | ||
s1121 | scaffold653|size305054 | 6573 | A/G | 0.021 | 3.82E-05 | NS | ||
s5182 | – | – | A/T | 0.035 | 6.29E-05 | NS | ||
s2256 | scaffold710|size289053 | 142,496 | G/T | 0.026 | 6.45E-05 | NS | ||
KWc | s3540b | ∫ | ∫ | G/A | 0.482 | 1.34E-05 | ||
KR | s1707b | scaffold_72|size1196525 | 587,142 | C/T | 0.061 | 2.37E-05 | ||
WK | s0201 | scaffold213|size509421 | 186,179 | G/A | 0.093 | 8.81E-06 | 1.11E-06 | 4.608 |
s3239 | scaffold361|size1112638 | 1,087,419 | G/C | 0.037 | 3.39E-05 | 2.45E-04 | −10.359 | |
s1917 | – | – | A/G | 0.163 | 1.23E-05 | NS | ||
s2607 | – | – | T/C | 0.177 | 2.91E-05 | NS | ||
TC | s3169 | scaffold146|size572432 | 176,797 | T/C | 0.230 | 1.29E-07 | 1.13E-07 | −1.343 |
s1885 | ∫ | ∫ | C/T | 0.319 | 8.57E-05 | 4.85E-05 | −1.706 | |
s2320 | scaffold81|size707423 | 173,614 | C/A | 0.083 | 1.02E-04 | 3.90E-05 | 4.088 | |
s3332 | scaffold1221|size537814 | 497,497 | T/C | 0.285 | 1.97E-06 | 3.98E-04 | 2.167 | |
s1208 | ∫ | ∫ | C/T | 0.179 | 3.14E-04 | 6.96E-04 | −2.383 | |
s3291 | ∫ | ∫ | G/T | 0.267 | 4.09E-05 | 7.52E-04 | 0.540 | |
s4709 | ∫ | ∫ | G/A | 0.106 | 4.74E-04 | 2.62E-03 | −11.946 | |
s3311 | – | – | A/C | 0.043 | 3.90E-04 | 3.81E-03 | −4.442 | |
s3828 | ∫ | ∫ | G/A | 0.093 | 4.03E-04 | 4.47E-03 | −2.009 | |
s2230 | scaffold_88 | 424,720 | G/T | 0.884 | 2.03E-04 | 6.15E-03 | −2.360 |