Table 1 Descriptive statistics for germination traits under low temperature and normal conditions
Trait
|
n
|
Mean
|
Median
|
Range
|
SD
|
RGR
|
222
|
0.737
|
0.787
|
0.027-0.999
|
0.220
|
RGL
|
222
|
0.486
|
0.434
|
0.087-1.229
|
0.220
|
RRL
|
222
|
0.704
|
0.718
|
0.100-1.838
|
0.285
|
RRSA
|
222
|
0.722
|
0.769
|
0.133-2.352
|
0.282
|
RRV
|
222
|
0.739
|
0.737
|
0.173-2.650
|
0.325
|
RGI
|
222
|
0.270
|
0.263
|
0.009-0.977
|
0.124
|
RVI
|
222
|
0.162
|
0.141
|
0.001-0.812
|
0.111
|
RSVI
|
222
|
0.360
|
0.340
|
0.002-0.917
|
0.186
|
XYRGR
|
222
|
0.403
|
0.420
|
0.014-0.753
|
0.172
|
XYRGL
|
222
|
0.542
|
0.538
|
0.001-0.897
|
0.869
|
XYRSVI
|
222
|
0.222
|
0.225
|
0.001-0.557
|
0.105
|
KSRGR
|
222
|
0.510
|
0.537
|
0.084-0.857
|
0.175
|
KSRGL
|
222
|
0.500
|
0.496
|
0.212-0.857
|
0.111
|
KSRSVI
|
222
|
0.261
|
0.266
|
0.018-0.535
|
0.115
|
The traits were evaluated for 222 inbred lines during germination tests under normal (25℃), and low temperature conditions (10℃). Statistics include means, median, standard deviation (SD), and range. 14 relative (R) traits were derived by dividing the directly measured trait values (GR, GL, RL, RSA, RV, GI, VI SVI, XYGR, XYGL, XYSVI, KSGR, KSGL and KSVI), under low temperature conditions by their corresponding values under normal conditions
Table 2 SNPs for low temperature germination related traits detected in 222 maize inbred lines
SNP
|
Chromosome
|
Position
|
MAF
|
P value
|
Trait
|
SYN25470
|
1
|
60897507
|
0.34
|
5.87E-05
|
RVI
|
PZE-101120376
|
1
|
148125053
|
0.138
|
1.85E-06
|
RGI
|
PZE-101192647
|
1
|
238680213
|
0.111
|
3.53E-07
|
RRV
|
PUT-163a-88747038-4526
|
1
|
282891355
|
0.279
|
4.23E-05
|
KSRGR
|
PUT-163a-149007696-748
|
2
|
8500779
|
0.077
|
3.74E-05
|
RGR
|
SYN29778
|
2
|
17713628
|
0.318
|
6.89E-05
|
RRSA
|
PZE-102099570
|
2
|
114621446
|
0.361
|
1.54E-06
|
RGI
|
PZE-102100684
|
2
|
117468629
|
0.267
|
4.92E-05
|
RVI
|
SYN21841
|
2
|
219117623
|
0.253
|
3.73E-07
|
RRV
|
PZE-103072583
|
3
|
115856771
|
0.346
|
8.88E-05
|
RRSA
|
PZE-103094415
|
3
|
151499271
|
0.182
|
6.34E-05
|
RGL
|
PZE-104024779
|
4
|
28770811
|
0.095
|
8.24E-05
|
RRV
|
SYN30173
|
5
|
10372835
|
0.401
|
3.75E-05/7.8E-05
|
RGL/RSVI
|
PZE-105034900
|
5
|
19776726
|
0.089
|
2.34E-06/3.47E-05
|
RRV/RVI
|
PZE-106003222
|
6
|
4152307
|
0.141
|
2.15E-07
|
RRV
|
PZE-106097864
|
6
|
151745619
|
0.137
|
2.34E-05
|
RGI
|
PZE-106129965
|
6
|
168030463
|
0.382
|
1.96E-07
|
RRV
|
PZE-106130106
|
6
|
168266461
|
0.359
|
2.88E-07
|
RRV
|
SYN4961
|
7
|
7156626
|
0.144
|
0.000035996
|
RSVI
|
PZE-107036384
|
7
|
56177181
|
0.257
|
1.70E-07
|
RRV
|
PZE-107098845
|
7
|
148186320
|
0.161
|
7.77E-05
|
RRL
|
PUT-163a-78076151-4108
|
8
|
1508965
|
0.282
|
9.59E-05
|
KSRSVI
|
PZE-108064544
|
8
|
113952611
|
0.141
|
2.80E-07
|
RRV
|
PZE-108068725
|
8
|
119362385
|
0.286
|
9.81E-05
|
RRSA
|
SYN26538
|
8
|
169361414
|
0.224
|
2.24E-07
|
RRV
|
PZE-109053558
|
9
|
89605923
|
0.4
|
5.75E-05/5.02E-05
|
XYRGR/XYRSVI
|
SYN5516
|
10
|
8952194
|
0.301
|
6.64E-07
|
RGI
|
PZE-110029252
|
10
|
50842298
|
0.128
|
9.84E-05
|
RRSA
|
PZE-110057591
|
10
|
110369493
|
0.113
|
4.22E-05
|
RVI
|
PZE-110060997
|
10
|
115266833
|
0.122
|
4.08E-05
|
XYRGL
|
The location is indicated by chromosome and base pair position. The P values less than 10-4 corresponding to 5% type I error are displayed as scientific notations.The frequency is indicated by the Minor Allele Frequency (MAF). MAF: Minor Allele Frequency.
Table 3 Functions of candidate genes directly associated with derived germination traits.
Trait
|
SNP
|
Gene ID
|
Gene function
|
RGR
|
PUT-163a-149007696-748
|
GRMZM2G012088
|
uncharacterized
|
RGL/RSVI
|
SYN30173
|
GRMZM2G158359
|
probable receptor protein kinase TMK1
|
RSVI
|
SYN4961
|
GRMZM2G107309
|
histone deacetylase
|
RRSA
|
PZE-103072583
|
GRMZM2G390374
|
protein ROOT HAIR DEFECTIVE 3 homolog 1
|
RRSA
|
SYN29778
|
GRMZM2G101383
|
Pseudouridine synthase family protein
|
RRSA
|
PZE-108068725
|
GRMZM2G173195
|
glycerol-3-phosphate dehydrogenase
|
RRV
|
PZE-104024779
|
GRMZM2G007734
|
polyadenylation and cleavage factor homolog 4
|
RRV
|
PZE-108064544
|
GRMZM2G092000
|
uncharacterized
|
RRV/RVI
|
PZE-105034900
|
GRMZM2G001772
|
NA
|
RGI
|
SYN5516
|
GRMZM2G118286
|
long chain acyl-CoA synthetase 9, chloroplastic
|
RVI
|
SYN25470
|
GRMZM2G402584
|
uncharacterized
|
XYRGL
|
PZE-110060997
|
GRMZM2G059110
|
uncharacterized
|
KSRGR
|
PUT-163a-88747038-4526
|
GRMZM2G152921
|
seed maturation protein
|
KSRSVI
|
PUT-163a-78076151-4108
|
GRMZM2G005980
|
DNA-binding protein
|
All candidate genes contain either an associated SNP.
Table 4 Candidate genes contained in DEGs inconsistent between the CT_102vsCT_55 and LT_102vsLT_55 comparison groups
Gene ID
|
CT_102vsCT_55
|
LT_102vsLT_55
|
Gene function
|
Arabidopsis best hit
|
Rice best hit
|
GRMZM2G038964
|
no
|
down
|
inositolphosphorylceramide-B C-26 hydroxylase
|
(ATFAH1, FAH1) fatty acid hydroxylase 1
|
fatty acid hydroxylase putative expressed
|
GRMZM2G059042
|
no
|
down
|
photoperiod responsive protein
|
(ATCMPG2, CMPG2) CYS MET PRO and GLY protein 2
|
U-box domain containing protein expressed
|
GRMZM2G009223
|
no
|
down
|
glucose-6-phosphate/phosphate translocator 2
|
(ATGPT2, GPT2) glucose-6-phosphate/phosphate translocator 2
|
transporter family protein putative expressed
|
GRMZM2G052129
|
no
|
down
|
uncharacterized
|
Pleckstrin homology (PH) domain-containing protein
|
pleckstrin homology domain-containing protein-related taxo putative expressed
|
GRMZM2G073861
|
no
|
down
|
uncharacterized
|
no
|
AT hook motif family protein expressed
|
GRMZM2G101408
|
no
|
down
|
uncharacterized
|
no
|
coiled-coil domain-containing protein 124 putative expressed
|
GRMZM2G101383
|
no
|
up
|
Pseudouridine synthase family protein
|
Pseudouridine synthase family protein
|
coiled-coil domain-containing protein 139 putative expressed
|
AC213621.5_FG004
|
no
|
up
|
uncharacterized
|
(SOS5) Fasciclin-like arabinogalactan family protein
|
fasciclin-like arabinogalactan protein putative expressed
|
GRMZM2G402584
|
no
|
up
|
uncharacterized
|
(sks3) SKU5 similar 3
|
monocopper oxidase putative expressed
|
The list consists of six parts: gene ID, gene function description, up or down regulation in CT_102vsCT_55 and LT_102vsLT_55 comparison groups, Arabidopsis and rice best hit.
Table 5 GO analysis of candidate genes related to RNA-Seq result
Gene ID
|
GO
|
GRMZM2G038964
|
GO:0005783; GO:0006631; GO:0080132
|
GRMZM2G059042
|
GO:0004842; GO:0005737; GO:0010200; GO:0016567
|
GRMZM2G009223
|
GO:0034219; GO:0034219
|
GRMZM2G052129
|
GO:0004550; GO:0005634; GO:0009507
|
GRMZM2G073861
|
no
|
GRMZM2G101408
|
GO:0003674; GO:0005737; GO:0008150
|
GRMZM2G101383
|
GO:0005634
|
AC213621.5_FG004
|
GO:0000139; GO:0005794; GO:0006004; GO:0006486; GO:0007155; GO:0016021; GO:0016757; GO:0071555
|
GRMZM2G402584
|
GO:0005507; GO:0009505; GO:0009506; GO:0016722; GO:0003674; GO:0005739; GO:0008150; GO:0016021
|
Table 6 Distribution of genes and pathway elated to RNA-Seq results
pathway_id
|
pathway_name
|
Gene ID
|
KO_Entry
|
EC
|
ko00230
|
Purine metabolism
|
si618049h06(54)
|
K00940
|
EC:2.7.4.6
|
ko00240
|
Pyrimidine metabolism
|
si618049h06(54)
|
K00940
|
EC:2.7.4.6
|
ko04016
|
MAPK signaling pathway - plant
|
si618049h06(54)
|
K00940
|
EC:2.7.4.6
|