Table 4 Chromosomal regions with most significant SNPs (Bonferroni and holm P value < 0.01) traits associated with cold tolerance.
From: Genomic-regions associated with cold stress tolerance in Asia-adapted tropical maize germplasm
Trait | Stage of cold stress | SNP | Chr | Bin | Gene model | Pos. (Mb) | P value | maf | effect | Phenotypic variance (%) | Associated protein/enzymes |
|---|---|---|---|---|---|---|---|---|---|---|---|
Grain Yield | Vegetative | S2_14539348 | 2 | 2.02 | GRMZM2G314396 | 15 | 3.7E−08 | 0.09 | 0.27 | 37.02 | Calcium dependent protein Kinase5 |
S2_45988012 | 2 | 2.04 | GRMZM2G028258 | 46 | 1.5 E−08 | 0.21 | − 0.22 | 38.13 | Potassium channel SKOR | ||
S3_169264156 | 3 | 3.06 | 169 | 1.8 E−07 | 0.12 | − 0.24 | 6.21 | ||||
Flowering | S1_286656232 | 1 | 1.11 | 287 | 1.1 E−09 | 0.20 | 0.19 | 8.39 | |||
S2_213163019 | 2 | 2.08 | GRMZM2G703373, GRMZM5G895355 | 213 | 7.0 E−10 | 0.06 | 0.37 | 24.74 | Pentatricopeptide repeat-containing protein | ||
S3_143356181 | 3 | 3.05 | GRMZM2G053343 | 143 | 9.3 E−11 | 0.19 | 0.24 | 11.10 | Elongation factor G | ||
S7_162341622 | 7 | 7.04 | 162 | 5.7 E−09 | 0.11 | 0.23 | 11.15 | ||||
Days to 50% anthesis | Vegetative | S2_196110540 | 2 | 2.07 | 196 | 1.7 E−09 | 0.49 | − 0.88 | 7.88 | ||
S3_185976288 | 3 | 3.06 | GRMZM2G021881 | 186 | 1.2 E−07 | 0.10 | 1.29 | 10.56 | Calcium uniporter protein | ||
S4_158607550 | 4 | 4.06 | GRMZM2G106795 | 159 | 6.9 E−08 | 0.19 | 0.87 | 5.77 | ADP-ribosylation factor B1B | ||
S7_104175420 | 7 | 7.02 | GRMZM2G032160 | 104 | 1.8 E−07 | 0.07 | − 1.32 | 21.56 | endo-1,3(4)-beta-glucanase | ||
S8_149609962 | 8 | 8.06 | 150 | 3.4 E−08 | 0.09 | 1.25 | 8.62 | ||||
S9_90843159 | 9 | 9.03 | GRMZM2G056093 | 91 | 3.0 E−08 | 0.44 | 0.78 | 6.52 | Tetratricopeptide repeat (TPR)-like superfamily protein | ||
Flowering | S1_21543873 | 1 | 1.02 | 22 | 2.1 E−07 | 0.35 | 0.48 | 12.52 | |||
S1_250912433 | 1 | 1.09 | 251 | 4.0 E−11 | 0.13 | − 1.07 | 28.18 | ||||
S5_196412134 | 5 | 5.06 | 196 | 2.4 E−09 | 0.25 | 0.68 | 14.82 | ||||
Across | S3_186214261 | 3 | 3.06 | 186 | 3.6 E−09 | 0.10 | 1.06 | 48.04 | |||
S9_90843159 | 9 | 9.03 | GRMZM2G056093 | 91 | 1.6 E−09 | 0.45 | 0.57 | 17.32 | Tetratricopeptide repeat (TPR)-like superfamily protein | ||
Days to 50% Silking | Vegetative | S1_53467993 | 1 | 1.04 | 53 | 1.6 E−07 | 0.34 | 0.87 | 15.19 | ||
S8_149609962 | 8 | 8.06 | 150 | 1.0 E−09 | 0.09 | 1.63 | 28.27 | ||||
Flowering | S5_196412120 | 5 | 5.06 | 196 | 3.2 E−11 | 0.33 | 0.81 | 33.65 | |||
S9_147965995 | 9 | 9.07 | 148 | 9.1 E−08 | 0.35 | − 0.64 | 22.12 | ||||
Plant height (cm) | Flowering | S3_153769448 | 3 | 3.05 | 154 | 5.3 E−08 | 0.09 | − 3.62 | 64.05 | ||
S6_93497825 | 6 | 6.02 | GRMZM2G161680 | 93 | 7.0 E−08 | 0.50 | 1.91 | 11.98 | CCAAT-HAP5 transcription factor | ||
Across | S3_152451938 | 3 | 3.05 | GRMZM2G170689 | 152 | 6.3 E−08 | 0.07 | 3.06 | 17.34 | S-formylglutathione hydrolase | |
S3_153769448 | 3 | 3.05 | 154 | 1.1 E−09 | 0.09 | − 2.93 | 17.78 | ||||
S5_206305411 | 5 | 5.07 | GRMZM2G039855 | 206 | 4.3 E−10 | 0.06 | − 3.46 | 31.46 | |||
S8_72384070 | 8 | 8.03 | GRMZM2G063880 | 72 | 5.9 E−08 | 0.35 | 1.56 | 6.69 | WRKY-transcription factor 106 |
