Article Figures & Data
Figures
- Figure 1.
Gene Networks Involved in Natural Variation for Flowering Responses to Vernalization and Photoperiod signals in A. thaliana, Wheat, and Rice.
Diagrams do not represent full molecular models of flowering regulation, but they show gene network components and branches known to contribute to the natural intraspecific variation existing in these species. Yellow color represents genes that contribute to the variation in a single species, which do not present known homologous genes contributing to natural variation in other species. Green color depicts homologous genes that contribute to the variation in several species. Blue and purple indicate genes accounting for the variation in one species, which show homologous protein domains with genes contributing to the variation in another species. Given their large functional homology, CO, FT, and AP1 homologs of the three species are included in the three diagrams, with small circles depicting genes that do not contribute to natural variation. See text for further details.
Tables
- Table 1.
Genes and Funtional Polymorphisms Involved in Natural Variation for Different Traits and Species
Functional Nucleotide Polymorphism Allelic Dysfunction Plant Species Locus/Gene Phenotypic Effects Molecular Function Gene Position Mutation References A. thaliana DOG1 Seed dormancy, sugar sensing Unknown Promoter Unknown ME Bentsink et al. (2006) Thale cress FRI Flowering Unknown Promoter, coding Ins, Del, nonsense Subs TP, ME Johanson et al. (2000); Shindo et al. (2005) FRL1 Flowering FRI-like Coding Nonsense Subs TP Schläppi (2006) FRL2 Flowering FRI-like Coding Missense Subs AP Schläppi (2006) FLC Flowering MADS TF Intron, coding TE insertion, nonsense Subs ME, TP Michaels et al. (2003); Werner et al. (2005a) FLW1/FLM Flowering MADS TF Promoter + coding Gene Del Null expression Werner et al. (2005b) ART1/HUA2 Flowering, shoot morphology RNA processing factor Coding Nonsense and missense Subs TP, AP Doyle et al. (2005); Wang et al. (2007) EDI/CRY2 Flowering, seedling growth, fruit size Photoreceptor Coding Missense Subs AP El-Assal et al. (2001, 2004) PHYD Flowering, seedling growth Photoreceptor Coding Del TP Aukerman et al. (1997) PHYC Flowering, seedling growth Photoreceptor Coding Nonsense Subs TP Balasubramanian et al. (2006) PHYA Seedling growth Photoreceptor Coding Missense Subs AP Maloof et al. (2001) PHYB Seedling growth Photoreceptor Coding Missense Subs AP Filiault et al. (2008) TZP/Light5 Seedling growth Zn knuckle protein Coding Ins TP Loudet et al. (2008) CAL Flower morphology MADS TF Coding Missense Subs AP Kempin et al. (1995) IIL1 Leaf morphology Leu biosynthesis enzyme Intron Ins, Del ME Sureshkumar et al. (2009) GL1 Trichome formation Myb TF Coding Del ME Hauser et al. (2001) PUB8 Self-incompatibility U box protein Promoter Unknown ME Liu et al. (2007) MUM2 Seed mucilage Galactosidase Coding Del ME Macquet et al. (2007) BRX Root growth Novel TF Coding Nonsense Subs TP Mouchel et al. (2004) LPR1 Root growth response to P Multicopper oxidase Promoter Del ME Svistoonoff et al. (2007) INV Sugar composition, root growth Invertase Unknown Unknown Unknown Sergeeva et al. (2006) Small effect QTL Biomass accumulation Protein kinase Unknown Unknown Unknown Kroyman and Mitchell-Olds (2005) DM1 Hybrid incompatibility, disease resistance NB-LRR proteins Promoter + coding Nonsense Subs, Del AP Bomblies et al. (2007) QTL3 Hybrid incompatibility, disease resistance NB-LRR proteins Unknown Unknown Unknown Alcázar et al. (2009) LD1. 1 Genetic incompatiblity, embryogenesis His biosynthesis enzyme Promoter, coding Nonsense Subs ME, TP Bikard et al. (2009) LD1.5 Genetic incompatiblity, embryogenesis His biosynthesis enzyme Promoter + coding Gene Del Null expression Bikard et al. (2009) APR2 Sulfate accumulation Sulfate reductase Coding Nonsense Subs AP Loudet et al. (2007) MOT1 Mo accumulation Sulfate transporter Promoter Del ME Baxter et al. (2008) HMA5 Cu toxicity Cu ATPase transporter Coding Missense Subs AP Kobayashi et al. (2008) HKT1 Na accumulation Na+ transporter Promoter Del ME Rus et al. (2006) A. lyrata FRI Flowering FRI-like Coding Indel AP Kuittinen et al. (2008) B. rapa BrFLC1 Flowering MADS TF Unknown Unknown Unknown Kole et al. (2001) Turnip BrFLC2 Flowering MADS TF Unknown Unknown Unknown Schranz et al. (2002) S. lycopersicum SUN Fruit shape IQ67 domain protein Coding + promotor Gene duplication ME Xiao et al. (2008) Tomato OVATE Fruit shape Nuclear protein Coding Nonsense Subs TP Cong et al. (2002) FAS Fruit shape Yabby TF Intron Ins ME Cong et al. (2008) Fw2.2 Fruit size Cell cycle control Promoter Subs, indel ME Frary et al. (2000) Sw4. 1 Seed size Transporter Unknown Unknown Unknown Orsi and Tanksley (2009) Brix9-2-5/LIN5 Fruit sugar content Invertase Coding Missense Subs AP Fridman et al. (2004) Cnr Fruit ripening SBP TF Promoter DNA methylation ME Manning et al. (2006) Pisum sativum LF/PsTFL1c Flowering TFL1-like protein Promoter, coding Gene Del Null expression Foucher et al. (2003) Pea R Seed composition and morphology Starch branching enzyme Coding TE insertion TP, ME Bhattacharyya et al. (1990) Lynaria vulgaris Lcyc Flower simetry TCP TF Promoter + coding DNA methylation ME Cubas et al. (1999) Toadflax T. aestivum VRN1 Flowering AP1-like MADS TF Promoter, intron Del, Ins ME Yan et al. (2003) Bread wheat VRN3 Flowering FT-like protein Promoter TE insertion ME Yan et al. (2006) Q Seed free-thressing AP2-like TF Coding Missense Subs AP Simons et al. (2006) RhtB1, RhtD1 Plant and leaf size GAI-like protein Coding Nonsense Subs TP Peng et al. (1999) Gpc-B1/NAM-B1 Senescence; Zn, Fe, and protein content NAC TF Coding Del, gen Del TP Uauy et al. (2006) Triticum monococum VRN1 Flowering AP1-like MADS TF Promoter Del ME Yan et al. (2003) Einkorn wheat VRN2 Flowering CCT domain protein Promoter, coding Missense Subs AP Yan et al. (2004a) H. vulgare VRN2 Flowering CCT domain protein Promoter + coding Gene Del Null expression Yan et al. (2004a) Barley VRN3 Flowering FT-like protein Intron Subs ME Yan et al. (2006) Ppd1 Flowering Response regulator Coding Missense Subs AP Turner et al. (2005) Nud Seed free-threshing ERF TF Promoter + coding Gene Del Null expression Taketa et al. (2008) Vrs1 Seed number, ear morphology HD TF Coding Ins TP Komatsuda et al. (2007) Bot1 Boron toxicity tolerance Boron efflux transporter Promoter + coding Gene duplication ME Sutton et al. (2007) O. sativa qLTG3 Germination Unknown Coding Del ME Fujino et al. (2008) Rice Rc Germination, seed color bHLH TF Coding Del TP Sweeney et al. (2006) Hd1 Flowering CO-like TF Coding Del, TE insertion TP, ME Yano et al. (2000); Doi et al. (2004) Hd3a Flowering FT-like protein Unknown Unknown ME Kojima et al. (2002) Hd6 Flowering Protein kinase CK2 Coding Nonsense Subs TP Takahashi et al. (2001) Ehd1 Flowering Response regulator Coding Missense Subs AP Doi et al. (2004) Ghd7 Flowering, plant height, seed yield CCT domain protein Coding Gene Del, nonsense Subs Null expression Xue et al. (2008) sh4 Shattering Myb TF Coding Missense Subs AP Li et al. (2006) qSH1 Shattering HD TF Promoter Missense Subs ME Konishi et al. (2006) qSW5 Seed size Unknown Coding, promoter Del ME Shomura et al. (2008) GW2 Seed size RING protein Coding Del TP Song et al. (2007) GS3 Seed size Unknown Coding Missense Subs TP Fan et al. (2006) Gn1a Seed number CK oxidase/dehydrogenase Promoter Del ME Ashikari et al. (2005) Wx Seed starch composition Starch biosynthesis enzyme Intron Splice site Subs TP Isshiki et al. (1998) SKC1 Salt tolerance HKT transporter Coding Missense Subs AP Ren et al. (2005) Z. mays Vgt1 Flowering AP2-like TF Promoter enhancer TE insertion, indel ME Salvi et al. (2007) Maize tb 1 Inflorescence architecture TCP TF Promoter enhancer Unknown ME Doebley et al. (1997) tga1 Seed morphology SBP TF Coding Missense Subs AP Wang et al. (2005) Wx Starch composition Starch biosynthesis enzyme Promoter, intron, coding TE insertion ME Varagona et al. (1992) TF: Transcription factor; TE: Transposable element; Subs: substitution; Ins: insertion; Del: deletion; TP: truncated protein; AP: altered protein; ME: Misexpression
What Has Natural Variation Taught Us about Plant Development, Physiology, and Adaptation?
