Table 1.
SNPs significantly associated to early growth-related traits, from association analyses in two panels of maize
| Inbred panel | Chromosome | Position | SNP | P-value | SNP alleles | Additivea effect | Nb | R 2c |
|---|---|---|---|---|---|---|---|---|
| Days to emergence | ||||||||
| Flint | 3 | 145737736 | PUT-163a-78121249-4393 | 3.3 × 10−6 | T/C | 0.67 | 201/40 | 0.11 |
| Chlorophyll content (SPAD) | ||||||||
| Dent | 1 | 201477347 | PZE-101159230 | 1.4 × 10−5 | C/T | 0.34 | 234/57 | 0.08 |
| Dent | 4 | 172689894 | SYN2344 | 1.5 × 10−5 | A/G | 0.18 | 157/131 | 0.08 |
| ΦPSIId | ||||||||
| Flint | 1 | 73380804 | PZE-101084685 | 8.1 × 10−6 | A/C | 59.5 | 27/213 | 0.10 |
| Flint | 4 | 20738948 | SYN24026 | 8.0 × 10−6 | T/G | 56.6 | 38/203 | 0.09 |
| Early vigore | ||||||||
| Dent | 1 | 110914351 | PZE-101106625 | 1.2 × 10−5 | C/T | 0.05 | 231/62 | 0.08 |
| Flint | 5 | 27247368 | PZE-105041198 | 8.3 × 10−6 | C/T | 0.21 | 62/179 | 0.11 |
| Flint | 5 | 27857856 | PZE-105041551 | 3.4 × 10−6 | C/T | 0.21 | 123/97 | 0.14 |
| Flint | 7 | 153421340 | PZE-107098206 | 2.4 × 10−6 | C/T | 0.21 | 121/118 | 0.10 |
aThe additive effect was calculated as half the difference between the mean of the homozygotes for the minor and the mean of the homozygotes for the major allele
bNumber of lines with each allele
cR2, proportion of total line mean variance explained by SNP as computed by Tassel software
dΦPSII: Quantum efficiency of PSII
eEarly vigor: subjective score from 1 = weak plants to 9 = vigorous plants