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Table 2 ‘Hub’ genes of interest. Turquoise module ‘hub’ genes upregulated in the highland (A) and lowland (B) landraces; yellow module ‘hub’ genes upregulated in the highland (C) and lowland (D) landraces organized by functional categories

From: Differentiated transcriptional signatures in the maize landraces of Chiapas, Mexico

Functional category Maize gene ID MaizeTF TAIR symbol Arabidopsis TAIR10 definition
A. Turquoise module – Highland landraces
 Transcription GRMZM2G010920 ZmGLK18 - myb-like HTH transcr. Regulator family
GRMZM2G097275 ZmSBP27 SPL2 squamosa promoter binding protein-like 2
GRMZM2G154169 - GIF3 GRF1-interacting factor 3
GRMZM2G398124 - TAF9 TATA binding protein associated factor 21 kDa subunit
GRMZM2G414141 - - transcription coactivators
GRMZM5G828396 ZmbHLH81 CIB2 basic helix-loop-helix (bHLH) DNA-binding superfamily protein
 Kinases GRMZM2G053117 - MPK20 MAP kinase 20
GRMZM2G079303 - RLP48 receptor like protein 48
GRMZM2G144028 - LRK10L1.2 Protein kinase superfamily protein
GRMZM2G144245 - NARA5 pfkB-like carbohydrate kinase family protein
GRMZM2G160853 - - S-locus lectin protein kinase family protein
GRMZM2G473104 - NARA5 pfkB-like carbohydrate kinase family protein
GRMZM2G049510 - KIP1 Kinase interacting (KIP1-like) family protein
B. Turquoise module – Lowland landraces
 Transcription GRMZM2G033413 ZmbZIP100 ABF4 ABRE binding factor 4
GRMZM2G035103 - ZAT10 salt tolerance zinc finger
GRMZM2G067624 ZmSBP29 SPL4 squamosa promoter binding protein-like 4
GRMZM2G113078 ZmEREB117 WRI1 Integrase-type DNA-binding superfamily protein
GRMZM2G138976 ZmARID4 - ARID/BRIGHT DNA-binding domain
GRMZM5G842484 ZmHMG12 SSRP1 high mobility group
GRMZM5G873335 - - ARID/BRIGHT DNA-binding domain
 Kinases GRMZM2G159678 - - Domain of unknown function (DUF303)
GRMZM2G172900 - NEK5 NIMA-related kinase 5
GRMZM2G474546 - - Protein kinase superfamily protein
C. Yellow module – Highland landraces
 Transcription AC186524.3_FG005 - HMGB4 high mobility group B4
GRMZM2G052667 ZmEREB102 HRE1 Integrase-type DNA-binding superfamily
GRMZM2G098227 - ARIA ARM repeat protein interacting with ABF2
GRMZM2G308034 ZmMYB46 MYB103 myb domain protein 103
 Kinases GRMZM2G126858 - - Leucine-rich repeat transmembrane protein kinase
GRMZM2G139157 - - protein kinase superfamily protein
  GRMZM2G316907 - - Leucine-rich repeat protein kinase family
  GRMZM2G403719 - CRK23 cysteine-rich RLK (RECEPTOR-like protein kinase) 23
D. Yellow module – Lowland landraces
 Transcription GRMZM2G077197 - NPR1 regulatory protein (NPR1)
GRMZM2G327349 ZmWRKY99 WRKY42 WRKY family transcription factor
 Kinases GRMZM2G002542 - - kinase family protein w/leucine-rich repeat
GRMZM2G119714 - - protein kinase superfamily protein
GRMZM2G316474 - - Leucine-rich repeat protein kinase family
  1. Functional category, broad categories defining function; Maize gene IDs, gene IDs from MaizeGDB; Maize TF; TF IDs from the Grassius GrassTFDB; TAIR symbol, gene symbol from The Arabidopsis Information Resource (TAIR); Arabidopsis TAIR10 definition, functional annotation from Phytozome; Hyphens, nonexistent data