Abstract
In epigenetics, non-coding sequences are the primary matter. Transponible elements (TEs) are epigenetically marked in order to determine subsequent expression or inhibition, a process that occasionally generates the overexpression of major transcription factors (MTFs). Take this into consideration is fundamental to understanding those underlying epigenetic mechanisms and biological processes involved in the manifestation of variability (so far considered genetic variability), since this process might lead to conspicuous phenotype transformations in only one generation, which is still more noticeable in species subject to continuous selection procedures. This article reviews recent discoveries related to the genetics and epigenetics nature of tb1 and Rht loci, which are essentials in the development of maize (Zea mays) and wheat bread (Triticum aestivum) crops, respectively. In addition, an attempt is made to understand the epigenetic (paramutation, genomic imprinting) as well as environmental (hormonal) processes whose function might be related to these loci.
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References
Abe H, Urao T, Ito T, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling. Plant Cell 15(Suppl 1):63–78
Achard P, Herr A, Baulcombe D, Harberd N (2004) Modulation of floral development by a gibberellin-regulated microRNA. Development 131:3357–3365
Alvarez-Buylla E et al (2000) An ancestral MADS-box gene duplication occurred before the divergence of plants and animals. Proc Natl Acad Sci USA 97:5328–5233
Bastow R et al (2004) Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 427:164–167
Belle CR et al (2009) Control of PHERES1 Imprinting in Arabidopsis by Direct Tandem Repeats. Mol Plant 2(Suppl 4):654–660
Bolle C (2004) The role of GRAS proteins in plant signal transduction and development. Planta 218:683–692
Cao D, Hussain A, Cheng H, Peng J (2005) Loss of function of four DELLA genes leads to light- and gibberellin-independent seed germination in Arabidopsis. Planta 223:105–113
Chandler VL, Stam M (2004) Chromatin conversations: Mechanisms and implications of paramutation. Natl Rev Genet 5:532–544
Clark R, Linton E, Messing J, Doebley J (2004) Pattern of diversity in the genomic region near the maize domestication gene tb1. Proc Natl Acad Sci USA 101:700–707
Clark R, Wagler T, Quijada P, Doebley J (2006) A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nat Gen 38:594–597
Coe EH (1966) The properties, origin, and mechanism of conversion-type inheritance at the B locus in maize. Genetics 53(Suppl 6):1035–1063
Cubas P, Lauter N, Doebley J, Coen E (1999) The TCP domain: a motif found in proteins regulating plant growth and development. Plant J 2 (Suppl 18):215–222
Doebley J et al (1997) The evolution of apical dominance in maize. Nature 386:485–488
Dussert Y et al (2013) Polymorphism pattern at a miniature inverted-repeat transposable element locus downstream of the domestication gene Teosinte-branched1 in wild and domesticated pearl millet. Mol Ecol 22(Suppl 2):327–340
Floyd S, Bowman J (2005) MicroRNAs: micro-managing the plant genome. In: Meyer P (ed) Plant epigenetics. Blackwell, Oxford, pp 244–279
Gehring M, Bubb KL, Henikoff S (2009) Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324:1447–1451
Gentil MV, Maury S (2007) Characterization of Epigenetic Biomarkers Using New Molecular Approaches. In: Varshney RK (ed) Genomics-Assisted Crop Improvement, vol 1. Springer, Dordrecht, pp 351–370
Haseneyer G et al (2008) High level of conservation between genes coding for the GAMYB transcription factor in barley (Hordeum vulgare L.) and bread wheat (Triticum aestivum L.) collections. Theor Appl Genet 117:321–331
Hedden P (2003) The genes of the Green Revolution. Trends Genet 19:5–9
Hirsch S, Oldroyd GED (2009) GRAS-domain transcription factors that regulate plant development. Plant Signal Behav 4(Suppl 8):698–700
Hsieh TF et al (2011) Regulation of imprinted gene expression in Arabidopsis endosperm. Proc Natl Acad Sci USA 108:1755–1762
Iltis HH (1983) From teosinte to maize: the catastrophic sexual transmutation. Science 222:886–894
Kinoshita Y et al (2007) Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats. Plant J 49:38–45
Köhler C, Grossniklaus U (2005) Seed development and genomic imprinting in plants. Prog Mol Sub Biol 38:237–262
Köhler C, Hennig L, Spillane C (2003) The Polycomb-group protein MEDEA regulates seed development by controlling expression of the MADS-box gene PHERES1. Gen Dev 17:1540–1553
Kusano T, Berberich T, Harada M, Suzuki N, Sugawara K (1995) A maize DNA-binding protein with bZIP motif is induced by low temperature. Mol Gener Gen 248:507–517
Lu G, Paul AL, McCarty DR, Ferl RJ (1996) Transcription factor veracity: is GBF3 responsible for ABA-regulated expression of Arabidopsis Adh? Plant Cell 8(Suppl 5):847–857
Lu C, Chen J, Zhang Y, Hu Q, Su W, Kuang H (2012) Miniature Inverted–Repeat Transposable Elements (MITEs) Have Been Accumulated through Amplification Bursts and Play Important Roles in Gene Expression and Species Diversity in Oryza sativa. Mol Biol Evol 29(Suppl 3):1005–1017
Michaels SD, Amasino RM (1999) FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell 11:949–956
Nakagawa H, Ohmiya K, Hattori T (1996) A rice bZIP protein, designated OSBZ8, is rapidly induced by abscisic acid. Plant J 9(Suppl 2):217–227
Ng M, Yanofsky MF (2001) Activation of the Arabidopsis B class homeotic genes by APETALA1. Plant Cell 13(Suppl 4):739–753
Palatnik JF et al (2003) Control of leaf morphogenesis by microRNAs. Nature 425(Suppl 6955):257–263
Patterson GI, Thorpe CJ, Chandler VL (1993) Paramutation, an allelic interaction, is associated with a stable and heritable reduction of transcription of the maize b regulatory gene. Genetics 135(Suppl 3):881–894
Pysh LD, Wysocka-Diller JW, Camilleri C, Bouchez D, Benfey PN (1999) The GRAS gene family in Arabidopsis: sequence characterization and basic expression analysis of the SCARECROW-LIKE genes. Plant J 18:111–119
Riechmann JL et al (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290:2105–2110
Sarnowska EA et al (2013) DELLA-interacting SWI3C core subunit of switch/sucrose nonfermenting chromatin remodeling complex modulates gibberellin responses and hormonal cross talk in Arabidopsis. Plant Physiol 163(Suppl 1):305–317
Stam M, Belele C, Dorweiler JE, Chandler V (2002) Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation. Gen Dev 16:1906–1918
Studer A, Zhao Q, Ross-Ibarra J, Doebley J (2011) Identification of a functional transposon insertion in the maize domestication gene tb1. Nat Genet 43:1160–1163
Suzuki S et al (2007) Retrotransposon silencing by DNA methylation can drive mammalian genomic imprinting. PLoS Genet 3:e55
Tsaftaris A, Polidoros NA, Kapazoglou A, Nives ET, Kovacevic M (2008) Epigenetics and Plant Breeding. In: Janick J (ed) Plant Breeding Reviews, vol 30. Wiley, Toronto, pp 49–145
Tsiantis M (2011) A transposon in tb1 drove maize domestication. Nat Gen 11:1048–1050
Waterland RA, Jirtle RL (2003) Transposable Elements: Targets for Early Nutritional Effects on Epigenetic Gene Regulation. Mol Cel Biol 23(Suppl 15):5293–5300
Wen W et al (2013) Sequence variations of the partially dominant DELLA gene Rht-B1c in wheat and their functional impacts. J Exp Bot 64(Suppl 11):3299–3312
Wilhelm EP et al (2013) Genetic characterization and mapping of the Rht-1 homoeologs and flanking sequences in wheat. Theor Appl Genet 26(Suppl 5):1321–1336
Willige BC et al (2007) The DELLA domain of GA INSENSITIVE mediates the interaction with the GA INSENSITIVE DWARF1A gibberellin receptor of Arabidopsis. Plant Cell 19:1209–1220
Wolff P et al (2011) High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Arabidopsis Endosperm. PLoS Genet 7:e1002126
Wu J et al (2013) Dynamic Evolution of Rht-1 Homologous Regions in Grass Genomes. PLoS ONE 8(Suppl 9):e75544. doi:10.1371/journal.pone.0075544
Yoshida T, Kawabe A (2013) Importance of Gene Duplication in the Evolution of Genomic Imprinting Revealed by Molecular Evolutionary Analysis of the Type I MADS-Box Gene Family in Arabidopsis Species. PLoS ONE 8(Suppl 9):e73588
Acknowledgments
First, I thank Dr. Manu J. Dubin whose advices helped to organize the information presented in this work. Second, I also would like to thank my English teacher, Susana Cervi, who disinterestedly made the grammatical corrections in this manuscript.
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Vaschetto, L.M. Exploring an Emerging Issue: Crop Epigenetics. Plant Mol Biol Rep 33, 751–755 (2015). https://doi.org/10.1007/s11105-014-0796-z
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DOI: https://doi.org/10.1007/s11105-014-0796-z