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Table 4 Examples of genes for which expression levels are (anti-)correlated with leaf size-related traits

From: Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population

MapMan Gene Maize description Arabidopsis orthologs Arabidopsis symbol Arabidopsis description LL Lwe LA Lwi Arabidopsis orthologs with phenotype Phenotype Reference
Regulation of transcription GRMZM2G361659   AT3G48160a DEL1, E2FE, E2L3 DP-E2F-like 1 −−   AT3G48160a Overexpression results in smaller leaves due to repression of cell proliferation [76]
AT3G01330c
AT5G14960c
GRMZM2G462623   AT5G02470b AT5G03415a DPA, DPB Transcription factor DP ++ ++ ++   AT5G02470b DPa acts together with E2F as stimulator of cell proliferation [75]
GRMZM2G099862 Putative growth-regulating factor AT2G22840b ATGRF1, ATGRF2 Growth-regulating factor 1, growth-regulating factor 2 ++ + +   AT2G22840b Overexpression results in larger cotyledons and leaves due to increase in cell number [74]
AT4G37740a,b AT4G37740a,b
GRMZM2G470307   AT4G32730b ATMYB3R-1, ATMYB3R1, MYB3R-1, MYB3R1, PC-MYB1, AtMYB3R4, MYB3R-4 Homeodomain-like protein, myb domain protein 3r-4   + + ++ AT5G11510a,b Loss of function mutants are more compact [77]
AT5G11510a,b
GRMZM2G053298   AT1G20640b   Plant regulator RWP-RK family protein + ++ ++ + AT1G20640b Loss of function mutants have smaller rosettes [77]
AT1G76350a,b,c
AT2G17150b,c
AT4G35270b
AT4G38340b
GRMZM2G067624   AT1G53160a,b SPL4, FTM6, SPL3, SPL5 Squamosa promoter binding protein-like, FLORAL TRANSITION AT THE MERISTEM6 + ++ ++ + AT1G53160a,b Promotor of vegetative phase change; influencing the duration of the vegetative phase can affect number and size of leaves [78, 149]
AT2G33810b
AT3G15270b
Hormone metabolism GRMZM2G144701   AT2G42820c HVA22F HVA22-like protein F + ++ +   AT2G42820c Downregulation of HVA22-like genes results in plants with dwarf and bushy stature with a reduced seed set [80]
GRMZM2G130548 HVA22-like protein a AT1G74520a HVA22A HVA22 homologue A   ++ ++ ++ AT1G74520a Downregulation of HVA22-like genes results in plants with dwarf and bushy stature with a reduced seed set [80]
GRMZM2G102347   AT1G75700a,b HVA22G HVA22-like protein G ++     AT1G75700a,b Downregulation of HVA22-like genes results in plants with dwarf and bushy stature with a reduced seed set [80]
AT5G42560b
AT1G19950b
GRMZM2G135978   AT1G12820c AFB3, AFB2, TIR1, AFB1, GRH1 Auxin signaling F-box 3, auxin signaling F-box 2, F-box/RNI-like superfamily protein, GRR1-like protein 1 ++ + +   AT3G62980a,b,c Mutations in TIR1 that enhance the degradation of auxin/IAA display more lateral roots, smaller rosettes and reduced number of axillary branches [59, 77]
AT3G26810c
AT3G62980a,b,c
AT4G03190b,c
GRMZM2G057000 Brassinosteroid biosynthesis-like protein AT3G19820a,b,c CBB1, DIM, DIM1, DWF1, EVE1 Cell elongation protein/DWARF1/DIMINUTO (DIM) −−   AT3G19820a,b,c Brassinosteroid dwarfs have more roundish, dark green leaves next to short, robust inflorescence and reduced fertility [81]
GRMZM2G125943 Histidine kinase AT1G27320c AHK3, HK3, AHK4, ATCRE1, CRE1, WOL, WOL1, AHK2, HK2 Histidine kinase 3, CHASE domain containing histidine kinase protein, histidine kinase 2 + ++ ++ + AT1G27320c Ectopic expression of ZmHK6 in Arabidopsis results in strongly enhanced shoot development, next to smaller seeds and a smaller root system; loss of function mutants in Arabidopsis orthologs have severe phenotypes, including smaller leaves due to a strong reduction in the number of cells [150, 151]
AT2G01830a,b AT2G01830a,b
AT5G35750c AT5G35750c
GRMZM2G158252 Histidine kinase 3 AT1G27320c AT5G35750a,b,c AHK3, HK3, AHK4, ATCRE1, CRE1, WOL, WOL1, AHK2, HK2 Histidine kinase 3, CHASE domain containing histidine kinase protein, histidine kinase 2 ++ ++ ++ + AT1G27320c AT5G35750a,b,c Ectopic expression of ZmHK1 in Arabidopsis results in strongly enhanced shoot development, next to smaller seeds and a smaller root system; loss of function mutants in Arabidopsis orthologs have severe phenotypes, including smaller leaves due to a strong reduction in the number of cells [150, 151]
GRMZM2G067225 Allene oxide synthase AT5G42650a,b,c DDE2, AOS, CYP74A DELAYED DEHISCENCE 2, allene oxide synthase, CYTOCHROME P450 74A −− AT5G42650a,b,c aos mutants have larger leaves and rosettes [83, 152]
Protein degradation GRMZM2G041561 BRCA1-associated protein AT2G26000a,b,c BRIZ2 Zinc finger (C3HC4-type RING finger) family protein ++ ++ ++ ++ AT2G26000a,b,c Loss of function mutants show severe phenotype; genes involved in seed germination and early seedling growth [91]
GRMZM2G120408   AT3G61590a,b HWS, HS HAWAIIAN SKIRT ++ + +   AT3G61590a,b Loss of function mutants display increased growth of leaves and roots, while overexpression reduces rosette size [92]
GRMZM2G116314   AT1G17110a,b,c UBP15 Ubiquitin-specific protease 15 + ++ +   AT1G17110a,b,c Overexpression results in plants with larger rosettes due to increase in leaf weight and number of leaves, while mutants display opposite phenotypes [90]
Posttranslational modifications GRMZM2G054634 ATP binding protein AT1G01740c BSK3, BSK1, BSK2 BR-signaling kinase ++ + ++   AT1G01740c Triple, quadruple and pentuple loss of function mutants show a reduced rosette size [153]
AT1G50990c AT1G50990c
AT1G63500c AT1G63500c
AT3G54030c AT3G54030c
AT4G00710c AT4G00710c
AT4G35230c AT4G35230c
AT5G41260c AT5G41260c
AT5G46570a,b,c AT5G46570a,b,c
AT5G59010c AT5G59010c
GRMZM2G004572   AT1G53730a SRF6, SRF7, SRF4, SRF5, SRF3 STRUBBELIG-receptor family protein + ++ ++ + AT3G13065c Loss of function mutants show smaller leaves while overexpressing plants display enlarged leaves [95]
AT3G13065c
AT1G78980c
AT4G03390c
Cell wall GRMZM2G328500   AT1G26570b,c UGD1, UGD2, UGD3 UDP-glucose dehydrogenase 1, UDP-glucose 6-dehydrogenase family protein −−   AT3G29360a,b,c Double mutants in the two isoforms of the enzyme udg2,3 are severely dwarfed due to defects in cell wall composition [101]
AT3G29360a,b,c AT5G15490b,c
AT5G15490b,c
AT5G39320b,c
  1. Arabidopsis orthologs were determined using PLAZA3.0 web resource [147]. a Best hit family ortholog. b Tree-based ortholog. c Orthologous gene family. Double plus signs ("++") indicate transcript levels positively correlated with phenotypic trait (q0.99). Single plus signs ("+") indicate transcript levels positively correlated with phenotypic trait (qrandom). Double minus signs ("−−") indicate transcript levels negatively correlated with phenotypic trait (q0.01). Single minus signs ("") indicate transcript levels negatively correlated with phenotypic trait (qrandom). IAA indole-3-acetic acid