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Table 3 Candidate genes from the association analyses for cold tolerance traits in two association panels of maize

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

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
  1. 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
  2. bEarly vigor: subjective score from 1 = weak plants to 9 = vigorous plants