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Ivaničová Z, Valárik M, Pánková K, Trávníčková M, Doležel J, Šafář J, Milec Z. Heritable heading time variation in wheat lines with the same number of Ppd-B1 gene copies. PLoS One 2017; 12:e0183745. [PMID: 28846721 PMCID: PMC5573275 DOI: 10.1371/journal.pone.0183745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 08/10/2017] [Indexed: 11/18/2022] Open
Abstract
The ability of plants to identify an optimal flowering time is critical for ensuring the production of viable seeds. The main environmental factors that influence the flowering time include the ambient temperature and day length. In wheat, the ability to assess the day length is controlled by photoperiod (Ppd) genes. Due to its allohexaploid nature, bread wheat carries the following three Ppd-1 genes: Ppd-A1, Ppd-B1 and Ppd-D1. While photoperiod (in)sensitivity controlled by Ppd-A1 and Ppd-D1 is mainly determined by sequence changes in the promoter region, the impact of the Ppd-B1 alleles on the heading time has been linked to changes in the copy numbers (and possibly their methylation status) and sequence changes in the promoter region. Here, we report that plants with the same number of Ppd-B1 copies may have different heading times. Differences were observed among F7 lines derived from crossing two spring hexaploid wheat varieties. Several lines carrying three copies of Ppd-B1 headed 16 days later than other plants in the population with the same number of gene copies. This effect was associated with changes in the gene expression level and methylation of the Ppd-B1 gene.
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Affiliation(s)
- Zuzana Ivaničová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ Olomouc, Czech Republic
| | - Miroslav Valárik
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ Olomouc, Czech Republic
| | | | - Martina Trávníčková
- Crop Research Institute, Drnovská 507, Prague, Czech Republic
- Czech University of Life Sciences Prague, Kamýcká 129, Prague 6, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ Olomouc, Czech Republic
| | - Zbyněk Milec
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ Olomouc, Czech Republic
- * E-mail:
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Kumar R, Bohra A, Pandey AK, Pandey MK, Kumar A. Metabolomics for Plant Improvement: Status and Prospects. FRONTIERS IN PLANT SCIENCE 2017; 8:1302. [PMID: 28824660 PMCID: PMC5545584 DOI: 10.3389/fpls.2017.01302] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/11/2017] [Indexed: 05/12/2023]
Abstract
Post-genomics era has witnessed the development of cutting-edge technologies that have offered cost-efficient and high-throughput ways for molecular characterization of the function of a cell or organism. Large-scale metabolite profiling assays have allowed researchers to access the global data sets of metabolites and the corresponding metabolic pathways in an unprecedented way. Recent efforts in metabolomics have been directed to improve the quality along with a major focus on yield related traits. Importantly, an integration of metabolomics with other approaches such as quantitative genetics, transcriptomics and genetic modification has established its immense relevance to plant improvement. An effective combination of these modern approaches guides researchers to pinpoint the functional gene(s) and the characterization of massive metabolites, in order to prioritize the candidate genes for downstream analyses and ultimately, offering trait specific markers to improve commercially important traits. This in turn will improve the ability of a plant breeder by allowing him to make more informed decisions. Given this, the present review captures the significant leads gained in the past decade in the field of plant metabolomics accompanied by a brief discussion on the current contribution and the future scope of metabolomics to accelerate plant improvement.
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Affiliation(s)
- Rakesh Kumar
- Department of Plant Sciences, University of Hyderabad (UoH)Hyderabad, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Abhishek Bohra
- Crop Improvement Division, Indian Institute of Pulses Research (IIPR)Kanpur, India
| | - Arun K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University (IGNTU)Amarkantak, India
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Pilu R. Paramutation phenomena in plants. Semin Cell Dev Biol 2015; 44:2-10. [DOI: 10.1016/j.semcdb.2015.08.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 08/26/2015] [Indexed: 02/05/2023]
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Brzeski J, Brzeska K. The maze of paramutation: a rough guide to the puzzling epigenetics of paramutation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:863-74. [PMID: 21976288 DOI: 10.1002/wrna.97] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Epigenetic mechanisms maintain gene expression states through mitotic and sometimes meiotic cell divisions. Paramutation is an extreme example of epigenetic processes. Not only an established expression state is transmitted through meiosis to the following generations but also an information transfer occurs between alleles and leads to heritable changes in expression state. As a consequence the expression states can rapidly propagate in population, violating Mendelian genetics. Recent findings unraveled an essential role for siRNA-dependent processes in paramutation. Despite significant progress, the overall picture is still puzzling and many important questions remain to be answered.
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Affiliation(s)
- Jan Brzeski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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Pilu R. Paramutation: just a curiosity or fine tuning of gene expression in the next generation? Curr Genomics 2011; 12:298-306. [PMID: 22131875 PMCID: PMC3131737 DOI: 10.2174/138920211795860099] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 04/12/2011] [Accepted: 04/12/2011] [Indexed: 12/31/2022] Open
Abstract
Gene silencing is associated with heritable changes in gene expression which occur without changes in DNA sequence. In eukaryotes these phenomena are common and control important processes, such as development, imprinting, viral and transposon sequence silencing, as well as transgene silencing. Among the epigenetic events, paramutation occurs when a silenced allele (named paramutagenic) is able to silence another allele (paramutable) in trans and this change is heritable. The silenced paramutable allele acquires paramutagenic capacity in the next generations. In the 1950s, Alexander Brink described for the first time the phenomenon of paramutation, occurring in maize at the colored1 (r1) gene, a complex locus (encoding myc-homologous transcription factors) that regulates the anthocyanin biosynthetic pathway. Since then, paramutation and paramutation-like interactions have been discovered in other plants and animals, suggesting that they may underlie important mechanisms for gene expression. The molecular bases of these phenomena are unknown. However in some cases, the event of paramutation has been correlated with changes in DNA methylation, chromatin structure and recently several studies suggest that RNA could play a fundamental role. This last consideration is greatly supported by genetic screening for mutants inhibiting paramutation, which allowed the identification of genes involved in RNA-directed transcriptional silencing, although it is possible that proteins are also required for paramutation.The meaning of paramutation in the life cycle and in evolution remains to be determined even though we might conjecture that this phenomenon could be involved in a fast heritability of favourable epigenetic states across generations in a non-Mendelian way.
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Affiliation(s)
- Roberto Pilu
- Dipartimento di Produzione Vegetale, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
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Creasey KM, Martienssen RA. Germline reprogramming of heterochromatin in plants. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2011; 75:269-74. [PMID: 21502413 DOI: 10.1101/sqb.2010.75.064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Heterochromatin is composed of transposable elements (TEs) and other repeats and was once considered to be a wasteland of redundant genetic material and potentially harmful TE. Therefore, the reprogramming of heterochromatin and subsequent reactivation of TE in the immature seed and pollen is paradoxical in plants. Recent studies have shown that reactivation of TE occurs specifically in germline companion cells, the vegetative nucleus (VN) in pollen (Slotkin et al. 2009) and the endosperm in seed (Gehring et al. 2009). In the ovule, ARGONAUTE 9 (AGO9) not only has a role in silencing TE in the egg cell but also in preventing the formation of multiple asexual gametophytes (Olmedo-Monfil et al. 2010). We propose that reprogramming of heterochromatin in germline companion cells reveals TE in a controlled manner to expose them within the germline and, by the production of small interfering RNA (siRNA), ensures TE silencing in the next generation. We also propose that the mechanisms evolved to silence TE may actually promote sexual reproduction by inhibiting the formation of asexual gametes.
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Affiliation(s)
- K M Creasey
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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A paramutation phenomenon is involved in the genetics of maize low phytic acid1-241 (lpa1-241) trait. Heredity (Edinb) 2008; 102:236-45. [PMID: 18781168 DOI: 10.1038/hdy.2008.96] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
So far, in maize, three classes of mutants involved in phytic acid biosynthesis have been isolated: lpa1, lpa2 and lpa3. In 2007, a gene tagging experiment performed by Shi et al. found that mutations in ZmMRP4 (multidrug resistance-associated proteins 4) gene cause lpa1 phenotype. In previous studies, we isolated and described a single recessive lpa mutation (originally named lpa241), which was allelic to the lpa1-1 mutant, and was consequently renamed lpa1-241. It showed a decrease in the expression of the myo-inositol (Ins)-3-phosphate synthase gene (mips1S). In this study, we present genetic and molecular analyses of the lpa1-241 mutation that indicate an epigenetic origin of this trait, that is, a paramutagenic interaction that results in meiotically heritable changes in ZmMRP4 gene expression, causing a strong pleiotropic effect on the whole plant. The use of a 5-Azacytidine treatment provided data suggesting an association between gene methylation and the lpa1-241 phenotype. To our knowledge, this is the first report of a paramutagenic activity not involving flavonoid biosynthesis in maize, but regarding a key enzyme of an important metabolic pathway in plants.
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Paramutation-Like Effects at the Mouse scapinin (Phactr3) Locus. J Mol Biol 2008; 377:605-8. [DOI: 10.1016/j.jmb.2008.01.062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Revised: 01/14/2008] [Accepted: 01/16/2008] [Indexed: 10/22/2022]
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Dominant suppression of repeat-induced point mutation in Neurospora crassa by a variant catalytic subunit of DNA polymerase zeta. Genetics 2008; 178:1169-76. [PMID: 18245848 DOI: 10.1534/genetics.107.079483] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Crosses involving the Adiopodoumé strain of Neurospora crassa are defective for repeat-induced point mutation (RIP), a genome defense mechanism of fungi. We show here that the Adiopodoumé strain possesses an incompletely penetrant and variably expressive dominant suppressor of RIP (Srp) that maps to an approximately 34-kbp genome segment that is approximately 26 kbp proximal to mat on linkage group IL. Gene disruption experiments revealed that Srp is the upr-1 allele of Adiopodoumé (upr-1(Ad)) that is contained within this segment. The upr-1 gene codes for the catalytic subunit of the translesion DNA polymerase-zeta (Pol-zeta) and it is unusually polymorphic in Neurospora. That the upr-1 gene contains upstream ORFs that overlap with the main ORF is potentially relevant to the incomplete penetrance and variable expressivity of the suppressor. Crosses between heterokaryons that contain upr-1(Ad) and strains that prevent mating events involving nuclei that contain upr-1(Ad) yielded no progeny in which RIP had occurred, consistent with the idea that the suppressor encoded by upr-1(Ad) is diffusible. The potential involvement of the Pol-zeta subunit in two functions, translesion DNA synthesis and RIP regulation, might account for the rapid evolution of its gene in Neurospora.
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Della Vedova CB, Lorbiecke R, Kirsch H, Schulte MB, Scheets K, Borchert LM, Scheffler BE, Wienand U, Cone KC, Birchler JA. The dominant inhibitory chalcone synthase allele C2-Idf (inhibitor diffuse) from Zea mays (L.) acts via an endogenous RNA silencing mechanism. Genetics 2005; 170:1989-2002. [PMID: 15956664 PMCID: PMC1449766 DOI: 10.1534/genetics.105.043406] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2005] [Accepted: 05/09/2005] [Indexed: 11/18/2022] Open
Abstract
The flavonoid pigment pathway in plants has been used as a model system for studying gene regulatory mechanisms. C2-Idf is a stable dominant mutation of the chalcone synthase gene, c2, which encodes the first dedicated enzyme in this biosynthetic pathway of maize. Homozygous C2-Idf plants show no pigmentation. This allele also inhibits expression of functional C2 alleles in heterozygotes, producing a less pigmented condition instead of the normal deeply pigmented phenotype. To explore the nature of this effect, the C2-Idf allele was cloned. The gene structure of the C2-Idf haplotype differs substantially from that of the normal c2 gene in that three copies are present. Two of these are located in close proximity to each other in a head-to-head orientation and the third is closely linked. Previous experiments showed that the lower level of pigmentation in heterozygotes is correlated with reduced enzyme activity and low steady-state mRNA levels. We found that c2 transcription occurs in nuclei of C2-Idf/C2 heterozygotes, but mRNA does not accumulate, suggesting that the inhibition is mediated by RNA silencing. Infection of C2-Idf/C2 heterozygotes with viruses that carry suppressors of RNA silencing relieved the phenotypic inhibition, restoring pigment production and mRNA levels. Finally, we detected small interfering RNAs (siRNAs) in plants carrying C2-Idf, but not in plants homozygous for the wild-type C2 allele. Together, our results indicate that the inhibitory effect of C2-Idf occurs through RNA silencing.
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MESH Headings
- Acyltransferases/genetics
- Alleles
- Cell Nucleus/genetics
- Cloning, Molecular
- DNA Methylation
- DNA, Plant/analysis
- Gene Dosage
- Genes, Dominant
- Genes, Plant
- Genome, Plant
- Haplotypes
- Heterozygote
- Homozygote
- Molecular Sequence Data
- Mutation
- Promoter Regions, Genetic
- RNA Interference
- RNA, Messenger/metabolism
- RNA, Small Interfering/analysis
- Sequence Analysis, DNA
- Transcription, Genetic
- Zea mays/genetics
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Peterhänsel C, Lahaye T. Be fruitful and multiply: gene amplification inducing pathogen resistance. TRENDS IN PLANT SCIENCE 2005; 10:257-60. [PMID: 15949756 DOI: 10.1016/j.tplants.2005.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2005] [Revised: 03/07/2005] [Accepted: 04/25/2005] [Indexed: 05/02/2023]
Abstract
The majority of European spring barley cultivars have broad-spectrum powdery mildew resistance conditioned by a naturally occurring recessive resistance allele at the Mlo locus that originates from Ethiopian landraces. A recent publication by Pietro Piffanelli et al. describes an unusual amplification of gene segments upstream of the Mlo promoter that probably interferes with transcription and is responsible for gene inactivation. Their findings provide insights into the breeding events during the domestication of wild barley.
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Masclaux FG, Pont-Lezica R, Galaud JP. Relationship between allelic state of T-DNA and DNA methylation of chromosomal integration region in transformed Arabidopsis thaliana plants. PLANT MOLECULAR BIOLOGY 2005; 58:295-303. [PMID: 16021396 DOI: 10.1007/s11103-005-4808-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Accepted: 03/31/2005] [Indexed: 05/03/2023]
Abstract
T-DNA insertions are currently used as a tool to introduce, or knock out, specific genes. The expression of the inserted gene is frequently haphazard and up to now, it was proposed that transgene expression depends on the site of insertion within the genome, as well as the number of copies of the transgene. In this paper, we show that the allelic state of a T-DNA insertion can be at the origin of epigenetic silencing. A T-DNA insertional mutant was characterized to explore the function of AtBP80a', a vacuolar sorting receptor previously associated with germination. Seeds homozygous for the T-DNA do not germinate, but this can be overcome by a cold treatment and maintained by the following generations. The non-germinating phenotype is only observed in homozygous seed produced by heterozygous plants indicating that it is correlated with the allelic state of the T-DNA in parental lines. Analysis of the region between the T-DNA insertion and the ATG codon of atbp80a' showed that cytosine methylation is highly enhanced in chromatin containing the T-DNA. Data presented here show that an unpaired DNA region during meiosis could be at the origin of a de novo cytosine methylation mechanism.
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Affiliation(s)
- Frédéric G Masclaux
- UMR 5546 CNRS-Université Paul Sabatier, Pôle de Biotechnologie végétale, 24 chemin de Borde-Rouge, BP42617, 31326 Castanet-Tolosan, France
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Abstract
During the development of a multicellular organism, cell differentiation involves activation and repression of transcription programs that must be stably maintained during subsequent cell divisions. Chromatin remodeling plays a crucial role in regulating chromatin states that conserve transcription programs and provide a mechanism for chromatin states to be maintained as cells proliferate, a process referred to as epigenetic inheritance. A large number of factors and protein complexes are now known to be involved in regulating the dynamic states of chromatin structure. Their biological functions and molecular mechanisms are beginning to be revealed.
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Affiliation(s)
- Tzung-Fu Hsieh
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102, USA.
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Spillane C, Baroux C, Escobar-Restrepo JM, Page DR, Laoueille S, Grossniklaus U. Transposons and tandem repeats are not involved in the control of genomic imprinting at the MEDEA locus in Arabidopsis. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2004; 69:465-75. [PMID: 16117682 DOI: 10.1101/sqb.2004.69.465] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- C Spillane
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zürich, Switzerland
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