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Table 1 The list of selected genes involved in grain yield.

From: Dissecting grain yield pathways and their interactions with grain dry matter content by a two-step correlation approach with maize seedling transcriptome

Probe ID Annotation Mean FD Association Step Ref§ Figure
     grain yield GDMC    
MZ00013618 CIPK9-like protein 9.0 1.7 P - F [3]  
MZ00014057 Dynamin-related protein 1A, putative 9.8 2.0 P N F   Fig. 3
MZ00014612 ARID/BRIGHT DNA-binding domain-containing protein, putative 7.8 1.6 N P F   
MZ00014822 Ribulosebisphosphate carboxylase. {Zea mays;} 9.7 3.7 N - F   
MZ00015132 O-methyltransferase ZRP4 (EC 2.1.1.-) (OMT) {Zea mays} 8.9 2.1 P - F [1]  
MZ00016342 SEUSS transcriptional co-regulator, homologue 9.3 1.4 N P F   
MZ00017365 Serine/threonine-protein kinase SAPK3, putative 10.3 1.5 P - F   
MZ00018334 High light protein {Hordeum vulgare} 8.8 1.5 P - F   
MZ00018444 2-Hydroxyisoflavanone dehydratase, putative 8.4 1.6 P N F   
MZ00018517 2-Hydroxyisoflavanone dehydratase, putative 10.7 2.8 P N F   
MZ00020198 Thioredoxin M-type, chloroplast precursor (TRX-M) {Zea mays} 13.3 2.1 N - S   
MZ00021090 DNA-3-methyladenine glycosylase (MAG), homologue 8.4 1.4 P - F   
MZ00022903 Leucine-rich repeat transmembrane protein kinase, putative 8.6 2.7 N - F   
MZ00023941 Histone deacetylase 2c (Zm-HD2c) {Zea mays} 8.2 3.4 P - S   
MZ00024407 Agamous-like MADS box protein AGL9 homolog, putative 7.5 1.4 P N F   
MZ00026127 Development regulation gene OsNAC4, homologue 9.2 1.8 P - F   
MZ00026879 Putative receptor-mediated endocytosis 1 isoform I/calcium-binding EF hand family protein 10.5 1.3 N - F   
MZ00029320 Isoflavone reductase homolog, putative 9.5 6.2 P N S   
MZ00033058 Plasma membrane ATPase 1, putative 8.2 1.7 N - F   
MZ00044236 Putative calcium-dependent protein kinase 8.9 1.5 P - F   
MZ00046983 Glycosyl transferase family 17 protein, putative 8.3 1.3 N - F   
MZ00056596 24-methylenesterol C-methyltransferase 2(SMT2), homologue 8.8 2.1 N - F   Fig. 3
MZ00057130 Dof-type zinc finger domain-containing/OBP1-like protein, orthologue 8.0 1.9 P - F   
MZ00057320 Putative ribulose-5-phosphate-3-epimerase 9.0 1.6 P - F [3]  
Carbohydrates and energy        
MZ00005490 Beta-fructofuranosidase/vacuolar invertase {Zea mays} 8.2 1.9 P - F [1] Fig. 2
MZ00013514 UDP-glucose pyrophosphorylase, homolgue 8.2 1.5 P - F   Fig. 2
MZ00013816 Adenosine kinase/phosphofructokinase (PFK) {Zea mays} 9.9 3.3 P - F   Fig. 2
MZ00014260 Glucose-6-phosphate isomerase, cytosolic {Zea mays} 11.2 1.6 N - F   Fig. 2
MZ00015645 Pyrophosphate-fructose 6-phosphate 1-phosphotransferase (PFP) alpha subunit, putative 8.7 1.6 N - F [1] Fig. 2
MZ00017454 Putative GDP-mannose pyrophosphorylase 10.1 1.5 N - F   Fig. 2
MZ00024012 Pyrophosphate-fructose 6-phosphate 1-phosphotransferase (PFP) beta subunit, putative 10.7 2.7 P - F [3] Fig. 2
MZ00024213 Pyrophosphate-fructose 6-phosphate 1-phosphotransferase (PFP) alpha subunit, putative 12.0 1.6 P - F   Fig. 2
MZ00026683 Putative beta-fructofuranosidase/cytosolic invertase 10.3 1.4 P - F   Fig. 2
MZ00033179 Beta-fructofuranosidase/cell wall invertase {Zea mays} 8.8 2.0 P - F [2] Fig. 2
MZ00036953 Triosephosphate isomerase, cytosolic, putative 9.7 3.1 N P S [3] Fig. 2
MZ00039244 Phosphoglycerate kinase, putative 10.4 1.7 P - F   Fig. 2
MZ00042300 Putative hexokinase (HXK) 8.9 1.4 P N F   Fig. 2
Cell cycle, DNA processing, and cell fate        
MZ00004156 Endo-1,3-beta-D-glucosidase, putative 9.0 1.9 P - F   Fig. 3
MZ00013343 Histone H4, similarity 12.3 1.8 P - F [2, 3] Fig. 3
MZ00013961 V-type H+ATPase, putative 7.7 1.4 P - F   Fig. 3
MZ00017273 CDK regulatory subunit 9.2 2.1 P - S   
MZ00017440 CDC2/B-type CDK, homologue 8.5 2.9 N - S   Fig. 3
MZ00017840 DNA ligase, putative 9.0 1.6 P - F   Fig. 3
MZ00017975 CDK-activating kinase assembly factor-related 9.2 1.3 P N F   
MZ00021340 Putative beta-expansin 8.1 1.4 P - F [2] Fig. 3
MZ00021442 Cyclin-dependent kinase inhibitor 7 (ICK7), homologue 8.9 1.5 P - F   Fig. 3
MZ00022872 Putative beta-expansin 8.3 1.7 P - F [3] Fig. 3
MZ00026530 Enhancer of rudimentary, putative 9.7 3.0 P - F   Fig. 3
MZ00027266 Putative cell division protein FtsZ (CH) 10.1 1.5 P - S   Fig. 3
MZ00027598 Putative replication factor subunit 9.5 1.8 P - F   Fig. 3
MZ00030457 Putative alpha-expansin 8.3 1.3 P - F   Fig. 3
MZ00030567 Putative alpha-expansin 1 precursor 8.5 2.1 N - F [1, 3] Fig. 3
MZ00041750 Prolifera protein (PRL)/DNA replication licensing factor Mcm7 (MCM7) 8.7 2.4 P - F [3] Fig. 3
MZ00043527 Aquaporins/tonoplast membrane integral protein ZmTIP3-1 {Zea mays} 8.2 2.8 P - F [3] Fig. 3
MZ00044246 Putative CDC48-like protein 8.6 1.5 P - F   
Ubiquitin pathway        
MZ00000787 F-box/tubby family protein, putative 8.7 2.0 P - F [1] Fig. 3
MZ00012603 RWD domain containing 1-like protein, putative 8.9 1.8 P N F   
MZ00012765 RING finger subunit, putative 7.6 1.9 P N F   Fig. 3
MZ00020431 E3 ubiquitin ligase APC1, putative 8.1 1.5 P - F   Fig. 3
MZ00026276 Ubiquitin-conjugating enzyme E2-17 kDa, putative 9.2 2.4 P N S [3]  
MZ00030283* CCS52A class, homologue 8.5 1.2 P -    Fig. 3
MZ00036978 SKP1 family, putative 11.0 1.9 N - F   
MZ00039271 F-box/LRR protein, putative 8.9 1.6 P - F   Fig. 3
MZ00056403 Ubiquitin-conjugating enzyme E2-17 kDa, putative 9.7 2.0 P - S [3]  
Phytohormone pathway        
MZ00003819 Putative ethylene-responsive transcriptional coactivator (MBF1) 8.7 2.7 P - F [1] Fig. 3
MZ00012636 Glutathione S-transferase GST 29 (auxin-induced) {Zea mays} 8.4 2.0 N - F   
MZ00013540 14-3-3-like protein, putative 10.5 3.1 P - F   
MZ00013608 Beta-glucosidase aggregating factor {Zea mays} 12.1 2.8 P - F [2, 3]  
MZ00014891 Contains similarity to gibberellin-stimulated transcript 1 like protein, putative 8.7 1.5 P - F [3]  
MZ00018299 Ethylene-responsive protein, putative 8.7 1.5 P - F   
MZ00021497 Auxin-responsive family protein, putative 8.7 1.3 P - F   
MZ00024781 Putative auxin-responsive factor (ARF1) 8.5 1.4 P - S [2]  
MZ00025819 BRI1-associated receptor, homologue 10.0 1.8 P - F   
MZ00026772 bHLH/IAA-LEUCINE RESISTANT3, homologue 10.4 1.5 N P S   
MZ00028517 Abscisic acid-insensitive 4 (ABI4)-like protein, putative 7.6 1.3 P - F   
MZ00030444 Glutathione S-transferase, putative 9.1 1.3 P N F   
MZ00031351 Two-component responsive regulator 2/response regulator 4 (ARR4)-like protein {Zea mays} 9.4 1.7 P - F   
MZ00034947 Glycosyl hydrolase family 1/Beta-glucosidase-like protein, putative 8.6 1.2 N P F   
MZ00035426 Beta-glucosidase {Zea mays} 8.0 2.6 P N F [2]  
MZ00038300 Auxin response factor 2, putative 7.9 3.2 P - S   
MZ00040986 IAA-alanine resistance protein, putative 8.1 1.2 N - F   
MZ00044325 Auxin-responsive protein -related, similarity 10.4 2.2 P N S   
Stress         
MZ00001535 Heat shock protein, putative 8.0 1.6 N P F   
MZ00004615 Pathogenesis-related protein, putative 10.1 3.3 P - F   
MZ00013860 DNAJ heat shock protein, putative 10.5 2.3 P - F   
MZ00017699 Putative drought-induced protein, related 10.5 2.0 P - F   
MZ00022225 AN1-like protein/ZmAN18 {Zea mays} 9.9 3.1 P - F   
MZ00036400 LEA3 family protein, putative 10.6 2.2 P N F   
MZ00056817 Cold-shock DNA-binding family protein, homologue 8.2 1.6 P - F   
Transporter         
MZ00017748 Putative peptide transporter 12.2 1.7 P - F   
MZ00018481 Putative Potassium channel protein 9.3 1.7 P - F [1]  
MZ00026499 Glucose-6-phosphate/phosphate-translocator precursor, homolog 10.0 1.6 P - F   
MZ00043904 ABC transporter family protein 9.0 1.8 P - F   
  1. The grain yield-involved genes are collected in Step 1 (F) and Step 2 (S). For each gene, mean and fold-change (FD) of mid-parent expression are calculated; the positive (P) and negative (N) association to grain yield and grain dry matter content (GDMC) are also provided.
  2. §1, Fernandes et al., 2008 [10]; 2, Zhu et al., 2009 [6]; 3, Liu et al., 2008 [5].
  3. * Probes (genes) with marginal significance included for discussion.