Table 3.
Candidate genes from the association analyses for cold tolerance traits in two association panels of maize
| Chr. | SNP ID and position of significant SNP (bp) | Gene ID | Start (bp) | Stop (bp) | Function/Subcellular localization |
|---|---|---|---|---|---|
| Days to emergence | |||||
| 3 | PUT-163a-78121249-4393 145737736 |
GRMZM2G061206 | 145636198 | 145639549 | Antiporter |
| GRMZM2G061127 | 145642310 | 145643935 | Proteolysis/Chloroplast stroma localization | ||
| GRMZM2G174274 | 145762729 | 145764119 | Signal transduction/Intracellular | ||
| GRMZM2G174249 | 145763792 | 145766257 | Carbohydrate, response to wounding/Cell wall vacuole | ||
| GRMZM2G174221 | 145771397 | 145774255 | Vacuole | ||
| GRMZM2G174196 | 145774369 | 145777597 | Protein binding | ||
| GRMZM2G174137 | 145786387 | 145795884 | Catalytic activity | ||
| GRMZM2G074241 | 145796992 | 145799980 | ATPase activity/Membrane | ||
| GRMZM2G375807 | 145817237 | 145825052 | ATPase activity/Membrane | ||
| Chlorophyll content (SPAD) | |||||
| 1 | PZE-101159230 201477347 |
GRMZM2G419024 | 201439240 | 201443106 | Triosephosphate isomerase activity |
| GRMZM5G899800 | 201502394 | 201505169 | Protein heterodimerization activity | ||
| GRMZM2G416069 | 201513870 | 201519179 | Protein heterodimerization activity/Cohesin complex | ||
| GRMZM2G115730 | 201519254 | 201520692 | Unknown | ||
| GRMZM2G115750 | 201522268 | 201525873 | Receptor/Membrane, ER, Golgi | ||
| 4 | SYN2344 172689894 |
GRMZM2G130043 | 172635729 | 172706662 | Starch synthase |
| GRMZM2G130002 | 172714527 | 172719310 | Protein binding/Plasma membrane | ||
| GRMZM2G129979 | 172721820 | 172724795 | G10 protein/Nucleous | ||
| GRMZM2G178398 | 172777639 | 172783737 | Epsin like protein | ||
| ΦPSIIa | |||||
| 1 | PZE-101084685 73380804 |
GRMZM2G172244 | 73387395 | 73390846 | Unknown |
| GRMZM2G171420 | 20758772 | 20762634 | Unknown | ||
| 4 |
SYN24026 20738948 |
GRMZM2G171394 | 20762995 | 20764457 | Rapid alkalinization factor |
| GRMZM2G078143 | 20795669 | 20799891 | Glycine hydroxymethyltransferase/Plasma membrane | ||
| Early vigorb | |||||
| 1 | PZE-101106625 110914351 |
GRMZM2G084825 | 110955450 | 110958921 | Protein serine threonine kinase activity |
| GRMZM2G154216 | 110981685 | 110983586 | Transferase activity of acyl groups (no amino-acyl) | ||
| GRMZM2G341036 | 27150769 | 27152027 | Unknown | ||
| 5 | PZE-105041198 27247368 |
GRMZM2G102862 | 27218204 | 27224147 | Protein kinase activity |
| GRMZM2G405090 | 27787706 | 27788723 | Putative uncharacterized protein | ||
| 5 | PZE-105041551 27857856 |
GRMZM2G127510 | 153320097 | 153324724 | Nucleotide binding |
| 7 | PZE-107098206 153421340 |
GRMZM2G127499 | 153326363 | 153329791 | Unknown |
| GRMZM2G429396 | 153330870 | 153331777 | Response to high light intensity/Cytoplasm | ||
| GRMZM2G124794 | 153413756 | 153414250 | Deoxyribodipyrimidine photo-lyase activity | ||
| GRMZM2G423478 | 153416453 | 143416869 | Unknown | ||
| GRMZM2G180027 | 153457846 | 153464555 | Unknown | ||
| GRMZM2G480480 | 153464547 | 153475981 | Protein binding | ||
| GRMZM2G180080 | 153485164 | 153487062 | Nucleotide binding | ||
| GRMZM2G180082 | 153490387 | 153492351 | Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen | ||
Genes in an 200 kb interval surrounding the significant SNPs are listed with their identifier. The gene closest to the significant SNP is indicated in boldaΦPSII: Quantum efficiency of PSII
bEarly vigor: subjective score from 1 = weak plants to 9 = vigorous plants