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Table 1 SNPs significantly associated to early growth-related traits, from association analyses in two panels of maize

From: Association mapping for cold tolerance in two large maize inbred panels

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
  1. 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
  2. bNumber of lines with each allele
  3. cR2, proportion of total line mean variance explained by SNP as computed by Tassel software
  4. dΦPSII: Quantum efficiency of PSII
  5. eEarly vigor: subjective score from 1 = weak plants to 9 = vigorous plants