Table 6.
Summary of significant (−log10(PVal) ≥ 3) marker-trait associations identified by GWA based on the FV/FM trait and the corresponding candidate genes from the Blast results
| Environment | Marker name | Position | GWA statistics | BLAST results | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Chr | cM | -log10(P) | MAFa | Effect | SEb | Gene | cM | Description | ||
| GH13A | 12_30482 | 3H | 128.6 | 4.2 | 0.26 | 0.014 | 0.003 | - | - | - |
| SCRI_RS_98443 | 4H | 22.2 | 3.5 | 0.17 | 0.016 | 0.004 | MLOC_75098.2 | 18.5 | Cupin 1; Germin, Mn binding site | |
| 12_30239 | 51.0 | 3.4 | 0.14 | -0.015 | 0.004 | MLOC_82113.1 | 49.7 | PSII PsbN | ||
| AK357955 | 54.3 | Protein phosphatase 2C (PP2C) Mn/Mg aspartate binding site | ||||||||
| SCRI_RS_142924 | 51.0 | 3.4 | 0.14 | -0.015 | 0.004 | AK249774.1 | 54.3 | PSII PsbP, oxygen evolving complex | ||
| 12_30987 | 100.6 | 3.7 | 0.43 | 0.012 | 0.003 | MLOC_40094.1 | 99.1 | PSI PsaA/PsaB | ||
| SCRI_RS_131671 | 101.6 | 3.2 | 0.43 | 0.011 | 0.003 | |||||
| SCRI_RS_157125 | 111.3 | 3.1 | 0.13 | -0.015 | 0.004 | AK367749 | 111.3 | Cupin 1; Germin, Mn binding site | ||
| SCRI_RS_235762 | 111.3 | 3.1 | 0.13 | -0.015 | 0.004 | |||||
| SCRI_RS_56 | 6H | 4.9 | 3.4 | 0.30 | 0.011 | 0.003 | - | - | - | |
| 12_30149 | 7H | 62.4 | 3.1 | 0.36 | 0.011 | 0.003 | - | - | - | |
| SCRI_RS_184488 | 120.8 | 3.1 | 0.01 | 0.039 | 0.011 | MLOC_3173.4 | 124.6 | PP2C Mn/Mg aspartate binding site | ||
| MLOC_77860.1 | 124.6 | PSII PsbP, oxygen evolving complex | ||||||||
| GH13B | SCRI_RS_144892 | 6H | 72.2 | 3.1 | 0.30 | -0.013 | 0.004 | - | - | - |
| KS11 | SCRI_RS_137249 | 5H | 50.0 | 3.1 | 0.13 | -0.019 | 0.005 | AK368229 | 47.9 | Chlorophyll a/b binding protein |
| MLOC_18354.1 | 51.3 | Chlorophyll a/b binding protein | ||||||||
| 11_10254 | 159.5 | 3.7 | 0.13 | -0.021 | 0.006 | AK251925.1 | 159.5 | PSII Psb28, class 1 | ||
| SCRI_RS_199298 | 159.5 | 3.1 | 0.13 | 0.019 | 0.006 | |||||
| SCRI_RS_235652 | 159.5 | 3.6 | 0.13 | 0.020 | 0.005 | |||||
| 11_10870 | 159.5 | 3.6 | 0.12 | 0.022 | 0.006 | |||||
| SCRI_RS_237948 | 167.6 | 3.7 | 0.36 | -0.015 | 0.004 | - | - | - | ||
| SCRI_RS_174123 | 167.7 | 3.6 | 0.31 | -0.015 | 0.004 | |||||
| SCRI_RS_239569 | 169.4 | 3.0 | 0.50 | -0.012 | 0.004 | |||||
| LJ13 | 12_30823 | 2H | 140.8 | 3.4 | 0.11 | 0.019 | 0.005 | - | - | - |
| SCRI_RS_73620 | 142.3 | 3.3 | 0.40 | -0.015 | 0.004 | |||||
| SCRI_RS_231015 | 147.3 | 7.4 | 0.18 | -0.027 | 0.005 | |||||
| 12_30002 | 3H | 51.4 | 3.5 | 0.33 | -0.025 | 0.007 | MLOC_38362.2 | 51.6 | Chlorophyll a/b binding protein | |
| 12_31372 | 51.4 | 3.5 | 0.32 | -0.025 | 0.007 | |||||
| 11_10365 | 51.6 | 4.5 | 0.32 | 0.029 | 0.007 | |||||
| SCRI_RS_173348 | 51.6 | 3.1 | 0.32 | -0.023 | 0.007 | |||||
| 11_20890 | 51.6 | 3.3 | 0.32 | 0.024 | 0.007 | |||||
| 11_20102 | 51.6 | 3.5 | 0.32 | 0.025 | 0.007 | |||||
| SCRI_RS_137552 | 51.6 | 3.5 | 0.32 | 0.025 | 0.007 | |||||
| SCRI_RS_186504 | 51.6 | 3.5 | 0.32 | 0.025 | 0.007 | |||||
| 11_10224 | 51.7 | 3.5 | 0.33 | 0.025 | 0.007 | |||||
| SCRI_RS_238114 | 51.8 | 3.4 | 0.33 | -0.024 | 0.007 | AK374059 | 52.6 | PP2C Mn/Mg aspartate binding site | ||
| 11_10349 | 51.8 | 3.1 | 0.33 | 0.023 | 0.007 | |||||
| 12_31011 | 52.1 | 3.1 | 0.35 | 0.019 | 0.006 | |||||
| 12_31393 | 52.6 | 3.4 | 0.33 | 0.021 | 0.006 | |||||
| 11_21511 | 52.6 | 4.3 | 0.35 | 0.025 | 0.006 | |||||
| 11_20276 | 52.9 | 3.4 | 0.33 | 0.021 | 0.006 | |||||
| 11_20325 | 53.1 | 3.1 | 0.32 | -0.020 | 0.006 | |||||
| 11_10225 | 53.3 | 3.8 | 0.33 | -0.022 | 0.006 | |||||
| SCRI_RS_201987 | 59.6 | 3.6 | 0.28 | 0.016 | 0.004 | - | - | - | ||
| SCRI_RS_76971 | 61.7 | 3.6 | 0.28 | 0.016 | 0.004 | AK369292 | 68.2 | PSII PsbW, class 2 | ||
| 11_21414 | 5H | 49.9 | 6.5 | 0.21 | 0.023 | 0.004 | AK368229 | 47.9 | Chlorophyll a/b binding protein | |
| MLOC_18354.1 | 51.3 | Chlorophyll a/b binding protein | ||||||||
aMinor Allele Frequency
bStandard error
Allelic effect sign is estimated with respect to the minor allele. SNPs are ordered by environment and genome position