Association mapping for cold tolerance in two large maize inbred panels

BMC Plant Biology

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	Additive^a effect	N^b	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
ΦPSII^d
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 vigor^e
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

ISSN: 1471-2229