Table 4.
DNA polymorphisms responsible for flowering time variation in the mini-core collection as revealed by multiple regression analysis
| Data set | SNP No. | SNP name | Physical positiona |
Glyma ID | Descriptionb | Alleles | Effectc | MAF | Parameters estimated by linear regression |
Contribution rate (%) | |||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chromosome | bp | βd | s.e. | P-valuee | |||||||||
| 2011 | |||||||||||||
| E2 | rs124971350 (e2) | Chr10 | 45310798 | Glyma.10G221500 | GIGANTEA (E2) | A/T | Stop_gained | 0.42 | −5.21 | 1.51 | 2.5E-03** | 21 | |
| SNP379 | e3tr f | Chr19 | 47641562 | Glyma.19G224200 | Phytochrome A (E3) | Large deletion | Loss of exon 4 | 0.17 | −9.88 | 3.05 | 3.9E-03** | 19 | |
| SNP156 | rs125308117 | Chr12 | 5520945 | Glyma.12G073900 | Two-component response regulator-like | T/C | Stop_lost | 0.31 | 11.24 | 3.53 | 4.5E-03** | 12 | |
| 2012 | |||||||||||||
| E2 | rs124971350 (e2) | Chr10 | 45310798 | Glyma.10G221500 | GIGANTEA (E2) | A/T | Stop_gained | 0.42 | −5.44 | 1.47 | 1.3E-03** | 22 | |
| SNP379 | e3tr f | Chr19 | 47641562 | Glyma.19G224200 | Phytochrome A (E3) | Large deletion | Loss of exon 4 | 0.17 | −8.50 | 2.95 | 9.0E-03** | 19 | |
| SNP156 | rs125308117 | Chr12 | 5520945 | Glyma.12G073900 | Two-component response regulator-like | T/C | Stop_lost | 0.31 | 9.65 | 3.42 | 1.0E-02* | 10 | |
| 2013 | |||||||||||||
| E2 | rs124971350 (e2) | Chr10 | 45310798 | Glyma.10G221500 | GIGANTEA (E2) | A/T | Stop_gained | 0.42 | −5.36 | 1.66 | 4.0E-03** | 20 | |
| SNP379 | e3tr f | Chr19 | 47641562 | Glyma.19G224200 | Phytochrome A (E3) | Large deletion | Loss of exon 4 | 0.17 | −12.18 | 3.34 | 1.5E-03** | 13 | |
| SNP156 | rs125308117 | Chr12 | 5520945 | Glyma.12G073900 | Two-component response regulator-like | T/C | Stop_lost | 0.31 | 12.69 | 3.86 | 3.5E-03** | 19 | |
| SNP349 | rs127928573 | Chr19 | 45183701 | Glyma.19G194300 | TERMINAL FLOWER 1 | T/A | Missense_variant | 0.09 | 11.23 | 5.11 | 3.9E-02* | 0.5 | |
MAF: minor allele frequency; s.e.: standard error.
a
Physical position on Gmax275.
b
Gene description was obtained from Phytozome 12.
c
Effect to gene function annotated by snpEff. Effect of AMPL1040314 was defined by manually.
d
Standardized regression coefficients.
e
Adjusted P-value was obtained from multivariate models days to flowering and genotype as covariates. Signification codes: ‘**’ 0.01 ‘*’ 0.05.
f
Large deletion on E3 estimated by coverage of four amplicon on 4th exon.