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A statistical framework for genome-wide scanning and testing of imprinted quantitative trait loci. J Theor Biol 2006; 244:115-26. [PMID: 16959270 DOI: 10.1016/j.jtbi.2006.07.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Revised: 06/28/2006] [Accepted: 07/11/2006] [Indexed: 10/24/2022]
Abstract
Non-equivalent expression of alleles at a locus results in genomic imprinting. In this article, a statistical framework for genome-wide scanning and testing of imprinted quantitative trait loci (iQTL) underlying complex traits is developed based on experimental crosses of inbred line species in backcross populations. The joint likelihood function is composed of four component likelihood functions with each of them derived from one of four backcross families. The proposed approach models genomic imprinting effect as a probability measure with which one can test the degree of imprinting. Simulation results show that the model is robust for identifying iQTL with various degree of imprinting ranging from no imprinting, partial imprinting to complete imprinting. Under various simulation scenarios, the proposed model shows consistent parameter estimation with reasonable precision and high power in testing iQTL. When a QTL shows Mendelian effect, the proposed model also outperforms traditional Mendelian model. Extension to incorporate maternal effect is also given. The developed model, built within the maximum likelihood framework and implemented with the EM algorithm, provides a quantitative framework for testing and estimating iQTL involved in the genetic control of complex traits.
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Radchuk V, Borisjuk L, Radchuk R, Steinbiss HH, Rolletschek H, Broeders S, Wobus U. Jekyll encodes a novel protein involved in the sexual reproduction of barley. THE PLANT CELL 2006; 18:1652-66. [PMID: 16766690 PMCID: PMC1488922 DOI: 10.1105/tpc.106.041335] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2006] [Revised: 04/10/2006] [Accepted: 05/10/2006] [Indexed: 05/10/2023]
Abstract
Cereal seed development depends on the intimate interaction of filial and maternal tissues, ensuring nourishment of the new generation. The gene jekyll, which was identified in barley (Hordeum vulgare), is preferentially expressed in the nurse tissues. JEKYLL shares partial similarity with the scorpion Cn4 toxin and is toxic when ectopically expressed in Escherichia coli and tobacco (Nicotiana tabacum). In barley, jekyll is upregulated in cells destined for autolysis. The gene generates a gradient of expression in the nucellar projection, which mediates the maternal-filial interaction during seed filling. Downregulation of jekyll by the RNA interference technique in barley decelerates autolysis and cell differentiation within the nurse tissues. Flower development and seed filling are thereby extended, and the nucellar projection no longer functions as the main transport route for assimilates. A slowing down in the proliferation of endosperm nuclei and a severely impaired ability to accumulate starch in the endosperm leads to the formation of irregular and small-sized seeds at maturity. Overall, JEKYLL plays a decisive role in the differentiation of the nucellar projection and drives the programmed cell death necessary for its proper function. We further suggest that cell autolysis during the differentiation of the nucellar projection allows the optimal provision of basic nutrients for biosynthesis in endosperm and embryo.
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Affiliation(s)
- Volodymyr Radchuk
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, D-06466 Gatersleben, Germany
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Normark BB. PERSPECTIVE: MATERNAL KIN GROUPS AND THE ORIGINS OF ASYMMETRIC GENETIC SYSTEMS?GENOMIC IMPRINTING, HAPLODIPLOIDY, AND PARTHENOGENESIS. Evolution 2006. [DOI: 10.1111/j.0014-3820.2006.tb01145.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Irish EE, McMurray D. Rejuvenation by shoot apex culture recapitulates the developmental increase of methylation at the maize gene Pl-Blotched. PLANT MOLECULAR BIOLOGY 2006; 60:747-58. [PMID: 16649110 DOI: 10.1007/s11103-005-5620-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2005] [Accepted: 12/02/2005] [Indexed: 05/08/2023]
Abstract
Cytosine methylation provides an attractive epigenetic modification for the global maintenance of phases in plant development; however, there are few known examples of specific genes whose methylation status changes in a developmentally regulated manner. Pl-Blotched, an allele of purple plant1 (pl1), which encodes a myb-like transcription factor that regulates anthocyanin production in maize, is one such gene: certain cytosines at the 3' end of this allele are hypomethylated in seedlings, become hypermethylated in organs formed in the adult phase, and are hypomethylated again in the next generation. We tested whether this developmental pattern of low juvenile cytosine methylation followed by higher methylation in adult tissues could also be observed in plants "rejuvenated" via shoot apex culture. We found that cytosine methylation patterns at Pl-Blotched were indeed recapitulated in culture-rejuvenated plants, showing hypomethylation in leaves with juvenile patterns of differentiation (even though they were made by an old meristem) followed by hypermethylation in later-formed leaves. Our results show that methylation status at that locus is determined by the developmental phase of the shoot, rather than by the age of the meristem forming it. These results support the hypothesis that DNA methylation is employed by the plant to maintain an epigenetic state.
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Affiliation(s)
- Erin E Irish
- Department of Biological Sciences, The University of Iowa, Iowa City, IA 52242, USA.
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56
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Normark BB. PERSPECTIVE: MATERNAL KIN GROUPS AND THE ORIGINS OF ASYMMETRIC GENETIC SYSTEMS—GENOMIC IMPRINTING, HAPLODIPLOIDY, AND PARTHENOGENESIS. Evolution 2006. [DOI: 10.1554/05-546.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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57
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Haberer G, Young S, Bharti AK, Gundlach H, Raymond C, Fuks G, Butler E, Wing RA, Rounsley S, Birren B, Nusbaum C, Mayer KFX, Messing J. Structure and architecture of the maize genome. PLANT PHYSIOLOGY 2005; 139:1612-24. [PMID: 16339807 PMCID: PMC1310546 DOI: 10.1104/pp.105.068718] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2005] [Revised: 09/11/2005] [Accepted: 10/05/2005] [Indexed: 05/05/2023]
Abstract
Maize (Zea mays or corn) plays many varied and important roles in society. It is not only an important experimental model plant, but also a major livestock feed crop and a significant source of industrial products such as sweeteners and ethanol. In this study we report the systematic analysis of contiguous sequences of the maize genome. We selected 100 random regions averaging 144 kb in size, representing about 0.6% of the genome, and generated a high-quality dataset for sequence analysis. This sampling contains 330 annotated genes, 91% of which are supported by expressed sequence tag data from maize and other cereal species. Genes averaged 4 kb in size with five exons, although the largest was over 59 kb with 31 exons. Gene density varied over a wide range from 0.5 to 10.7 genes per 100 kb and genes did not appear to cluster significantly. The total repetitive element content we observed (66%) was slightly higher than previous whole-genome estimates (58%-63%) and consisted almost exclusively of retroelements. The vast majority of genes can be aligned to at least one sequence read derived from gene-enrichment procedures, but only about 30% are fully covered. Our results indicate that much of the increase in genome size of maize relative to rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) is attributable to an increase in number of both repetitive elements and genes.
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Affiliation(s)
- Georg Haberer
- Munich Information Center for Protein Sequences, Institute for Bioinformatics, Gesellschaft für Strahlenforschung Research Center for Environment and Health, D-85764 Neuherberg, Germany
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58
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GRANT-DOWNTON RT, DICKINSON HG. Epigenetics and its implications for plant biology. 1. The epigenetic network in plants. ANNALS OF BOTANY 2005; 96:1143-64. [PMID: 16254022 PMCID: PMC4247072 DOI: 10.1093/aob/mci273] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
BACKGROUND Epigenetics has rapidly evolved in the past decade to form an exciting new branch of biology. In modern terms, 'epigenetics' studies molecular pathways regulating how the genes are packaged in the chromosome and expressed, with effects that are heritable between cell divisions and even across generations. CONTEXT Epigenetic mechanisms often conflict with Mendelian models of genetics, and many components of the epigenetic systems in plants appeared anomalous. However, it is now clear that these systems govern how the entire genome operates and evolves. SCOPE In the first part of a two-part review, how epigenetic systems in plants were elucidated is addressed. Also there is a discussion on how the different components of the epigenetic system--regulating DNA methylation, histones and their post-translational modification, and pathways recognizing aberrant transcripts--may work together.
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59
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Bonduriansky R, Rowe L. INTRALOCUS SEXUAL CONFLICT AND THE GENETIC ARCHITECTURE OF SEXUALLY DIMORPHIC TRAITS IN PROCHYLIZA XANTHOSTOMA (DIPTERA: PIOPHILIDAE). Evolution 2005. [DOI: 10.1111/j.0014-3820.2005.tb01066.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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60
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Hegarty MJ, Jones JM, Wilson ID, Barker GL, Coghill JA, Sanchez-Baracaldo P, Liu G, Buggs RJA, Abbott RJ, Edwards KJ, Hiscock SJ. Development of anonymous cDNA microarrays to study changes to the Senecio floral transcriptome during hybrid speciation. Mol Ecol 2005; 14:2493-510. [PMID: 15969730 DOI: 10.1111/j.1365-294x.2005.02608.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Interspecific hybridization is an important process through which abrupt speciation can occur. In recent years, genetic changes associated with hybrid speciation have been identified through a variety of techniques, including AFLP/SSR mapping, GISH/FISH and cDNA-AFLP differential display. However, progress in using microarray technology to analyse whole genome/transcriptome changes associated with hybrid speciation has been limited due to the lack of extensive sequence data for many hybrid species and the difficulties in extrapolating results from commercially available microarrays for model species onto nonmodel hybrid taxa. Increasingly therefore researchers studying nonmodel systems are turning to the development of 'anonymous' cDNA microarrays, where the time and cost of producing microarrays is reduced by printing unsequenced cDNA clones, and sequencing only those clones that display interesting expression patterns. Here we describe the creation, testing and preliminary use of anonymous cDNA microarrays to study changes in floral transcriptome associated with allopolyploid speciation in the genus Senecio. We report a comparison of gene expression between the allohexaploid hybrid, Senecio cambrensis, its parental taxa Senecio squalidus (diploid) and Senecio vulgaris (tetraploid), and the intermediate triploid (sterile) hybrid Senecioxbaxteri. Anonymous microarray analysis revealed dramatic differences in floral gene expression between these four taxa and demonstrates the power of this technique for studies of the genetic impact of hybridization in nonmodel flowering plants.
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Affiliation(s)
- Matthew J Hegarty
- School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK.
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61
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Köhler C, Grossniklaus U. Seed development and genomic imprinting in plants. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2005; 38:237-62. [PMID: 15881898 DOI: 10.1007/3-540-27310-7_10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Genomic imprinting refers to an epigenetic phenomenon where the activity of an allele depends on its parental origin. Imprinting at individual genes has only been described in mammals and seed plants. We will discuss the role imprinted genes play in seed development and compare the situation in plants with that in mammals. Interestingly, many imprinted genes appear to control cell proliferation and growth in both groups of organisms although imprinting in plants may also be involved in the cellular differentiation of the two pairs of gametes involved in double fertilization. DNA methylation plays some role in the control of parent-of-origin-specific expression in both mammals and plants. Thus, although imprinting evolved independently in mammals and plants, there are striking similarities at the phenotypic and possibly also mechanistic level.
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Affiliation(s)
- Claudia Köhler
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland
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62
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Sha K, Fire A. Imprinting capacity of gamete lineages in Caenorhabditis elegans. Genetics 2005; 170:1633-52. [PMID: 15944356 PMCID: PMC1449763 DOI: 10.1534/genetics.104.040303] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2004] [Accepted: 04/20/2005] [Indexed: 01/05/2023] Open
Abstract
We have observed a gamete-of-origin imprinting effect in C. elegans using a set of GFP reporter transgenes. From a single progenitor line carrying an extrachromosomal unc-54::gfp transgene array, we generated three independent autosomal integrations of the unc-54::gfp transgene. The progenitor line, two of its three integrated derivatives, and a nonrelated unc-119:gfp transgene exhibit an imprinting effect: single-generation transmission of these transgenes through the male germline results in approximately 1.5- to 2.0-fold greater expression than transmission through the female germline. There is a detectable resetting of the imprint after passage through the opposite germline for a single generation, indicating that the imprinted status of the transgenes is reversible. In cases where the transgene is maintained in either the oocyte lineage or sperm lineage for multiple, consecutive generations, a full reset requires passage through the opposite germline for several generations. Taken together, our results indicate that C. elegans has the ability to imprint chromosomes and that differences in the cell and/or molecular biology of oogenesis and spermatogenesis are manifest in an imprint that can persist in both somatic and germline gene expression for multiple generations.
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Affiliation(s)
- Ky Sha
- Carnegie Institution of Washington, Department of Embryology, Baltimore, Maryland 21210, USA
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63
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Fieldes MA, Schaeffer SM, Krech MJ, Brown JCL. DNA hypomethylation in 5-azacytidine-induced early-flowering lines of flax. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:136-149. [PMID: 15864524 DOI: 10.1007/s00122-005-2005-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2004] [Accepted: 03/13/2005] [Indexed: 05/24/2023]
Abstract
HPLC analysis was used to examine the cytosine methylation of total DNA extracted from four early-flowering lines that were induced by treating germinating seeds of flax (Linum usitatissimum) with the DNA demethylating agent 5-azacytidine. In the normal lines that gave rise to the induced early-flowering lines, flowering usually begins approximately 50 days after sowing. The early-flowering lines flower 7-13 days earlier than normal. The normal level of cytosine methylation was approximately 14% of the cytosines and 2.7% of the nucleosides. In the early-flowering lines, these levels were 6.2% lower than normal in DNA from the terminal leaf clusters of 14-day-old seedlings and 9.7% lower than normal in DNA from the cotyledons and immature shoot buds of 4-day-old seedlings. This hypomethylation was seen in lines that were five to nine generations beyond the treatment generation. The level of hypomethylation was similar in three of the four early-flowering lines, but was not as low in the fourth line, which flowers early but not quite as early as the other three lines. Unexpectedly, the degree of hypomethylation seen in segregant lines, derived by selecting for the early-flowering phenotype in the F(2) and F(3) generations of out-crosses, was similar to that seen in the early-flowering lines. Analysis of the methylation levels in segregating generations of out-crosses between early-flowering and normal lines demonstrated a decrease in methylation level during the selection of early-flowering segregants. The results suggest an association between hypomethylation and the early-flowering phenotype, and that the hypomethylated regions may not be randomly distributed throughout the genome of the early-flowering lines.
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Affiliation(s)
- M A Fieldes
- Department of Biology, Wilfrid Laurier University, 75 University Ave. West, Waterloo, ON N2L 3C5, Canada.
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64
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Spillane C, Curtis MD, Grossniklaus U. Apomixis technology development-virgin births in farmers' fields? Nat Biotechnol 2005; 22:687-91. [PMID: 15175691 DOI: 10.1038/nbt976] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Apomixis is the process of asexual reproduction through seed, in the absence of meiosis and fertilization, generating clonal progeny of maternal origin. Major benefits to agriculture could result from harnessing apomixis in crop plants. Although >400 apomictic plant species are known, apomixis is rare among crop plants, and the transfer of apomixis to crop varieties by conventional breeding has been largely unsuccessful. Because apomictic and sexual pathways are closely related, de novo engineering of apomixis might be achieved in sexually reproducing crops. Early consideration of issues relating to biosafety and intellectual property (IP) management can facilitate the acceptance and deployment of apomixis technology in agriculture.
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Affiliation(s)
- Charles Spillane
- Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, CH-8008 Zürich, Switzerland
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65
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De Jong TJ, Van Dijk H, Klinkhamer PGL. Hamilton's rule, imprinting and parent-offspring conflict over seed mass in partially selfing plants. J Evol Biol 2005; 18:676-82. [PMID: 15842497 DOI: 10.1111/j.1420-9101.2004.00856.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
When genes in the offspring control the provisioning of the seed, the optimal seed size can be calculated exactly by applying Hamilton's rule. When seed size is a compromise between mother and offspring, we predict that outcrossing plant species produce larger seeds than selfers. This trend was found in the British flora and in a number of well-studied plant families. The analysis was extended to imprinting, a conditional strategy in which a gene in the offspring takes more resources when derived from the father than from the mother. The conditions for imprinting to be selected were rather restrictive. The analysis is relevant for the current debate about the evolution of imprinting in Arabidopsis thaliana.
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Affiliation(s)
- T J De Jong
- Institute of Biology, University of Leiden, PO Box 9516, 2300 RA Leiden, The Netherlands.
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66
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Autran D, Huanca-Mamani W, Vielle-Calzada JP. Genomic imprinting in plants: the epigenetic version of an Oedipus complex. CURRENT OPINION IN PLANT BIOLOGY 2005; 8:19-25. [PMID: 15653395 DOI: 10.1016/j.pbi.2004.11.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Genomic imprinting is a mitotically stable epigenetic modification that results in the functional non-equivalency of both parental genomes following fertilization. In flowering plants, studies of parent-of-origin effects have mostly identified genes that are only transcribed from a maternally inherited allele. In Arabidopsis, the Polycomb group protein MEDEA regulates seed development through the expression of the MADS-box gene PHERES1. Activation of the maternal MEDEA allele requires the function of DEMETER, a plant DNA glycosylase that also controls the transcriptional activity of the maternally inherited allele of the late-flowering gene FWA. Current studies of parent-of-origin effects have mostly identified genes that are only transcribed from a maternally inherited allele. Our current understanding of parent-of-origin effects could represent a new form of an Oedipus complex in which flowering plants prefer to rely transcriptionally on their maternal rather than their paternal chromosomes to ensure normal initiation of seed development.
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Affiliation(s)
- Daphné Autran
- Laboratory of Reproductive Development and Apomixis, Department of Genetic Engineering, CINVESTAV--Unidad Irapuato, Apartado Postal 629, CP 36 500, Irapuato, Gto. México.
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67
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Hegarty MJ, Hiscock SJ. Hybrid speciation in plants: new insights from molecular studies. THE NEW PHYTOLOGIST 2005; 165:411-23. [PMID: 15720652 DOI: 10.1111/j.1469-8137.2004.01253.x] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Abrupt speciation through interspecific hybridisation is an important mechanism in angiosperm evolution. Flowering plants therefore offer excellent opportunities for studying genetic processes associated with hybrid speciation. Novel molecular approaches are now available to examine these processes at the level of both genome organization and gene expression - transcriptomics. Here, we present an overview of the molecular technologies currently used to study hybrid speciation and how they are providing new insights into this mode of speciation in flowering plants. We begin with an introduction to hybrid speciation in plants, followed by a review of techniques, such as isozymes and other markers, which have been used to study hybrid species in the past. We then review advances in molecular techniques that have the potential to be applied to studies of hybrid species, followed by an overview of the main genomic and transcriptomic changes suspected, or known, to occur in newly formed hybrids, together with commentary on the application of advanced molecular tools to studying these changes.
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Affiliation(s)
- Matthew J Hegarty
- School of Biological Sciences, University of Bristol, Woodland Road, Bristol, BS8 1UG, UK
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68
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Bonduriansky R, Rowe L. INTRALOCUS SEXUAL CONFLICT AND THE GENETIC ARCHITECTURE OF SEXUALLY DIMORPHIC TRAITS IN PROCHYLIZA XANTHOSTOMA (DIPTERA: PIOPHILIDAE). Evolution 2005. [DOI: 10.1554/05-236.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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69
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Spencer HG, Feldman MW, Clark AG, Weisstein AE. The effect of genetic conflict on genomic imprinting and modification of expression at a sex-linked locus. Genetics 2004; 166:565-79. [PMID: 15020445 PMCID: PMC1470692 DOI: 10.1534/genetics.166.1.565] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We examine how genomic imprinting may have evolved at an X-linked locus, using six diallelic models of selection in which one allele is imprintable and the other is not. Selection pressures are generated by genetic conflict between mothers and their offspring. The various models describe cases of maternal and paternal inactivation, in which females may be monogamous or bigamous. When inactivation is maternal, we examine the situations in which only female offspring exhibit imprinting as well as when both sexes do. We compare our results to those previously obtained for an autosomal locus and to four models in which a dominant modifier of biallelic expression is subjected to the same selection pressures. We find that, in accord with verbal predictions, maternal inactivation of growth enhancers and paternal inactivation of growth inhibitors are more likely than imprinting in the respective opposite directions, although these latter outcomes are possible for certain parameter combinations. The expected outcomes are easier to evolve than the same outcomes for autosomal loci, contradicting the available evidence concerning the direction of imprinting on mammalian sex chromosomes. In most of our models stable polymorphism of imprinting status is possible, a behavior not predicted by verbal accounts.
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Affiliation(s)
- Hamish G Spencer
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, Dunedin, New Zealand.
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70
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Costa LM, Gutièrrez-Marcos JF, Dickinson HG. More than a yolk: the short life and complex times of the plant endosperm. TRENDS IN PLANT SCIENCE 2004; 9:507-14. [PMID: 15465686 DOI: 10.1016/j.tplants.2004.08.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Affiliation(s)
- Liliana M Costa
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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71
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Chandler VL, Stam M. Chromatin conversations: mechanisms and implications of paramutation. Nat Rev Genet 2004; 5:532-44. [PMID: 15211355 DOI: 10.1038/nrg1378] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Vicki L Chandler
- Department of Plant Sciences, 303 Forbes Building, University of Arizona, Tucson, Arizona 85721, USA.
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72
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Abstract
Plants and animals both exhibit parental imprinting, but do they control it the same way? Recent studies show that in Arabidopsis, as in mammals, imprinted alleles are subject to DNA methylation--but, surprisingly, the default state is silence rather than activity.
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Affiliation(s)
- Rod J Scott
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK.
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73
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Avivi Y, Morad V, Ben-Meir H, Zhao J, Kashkush K, Tzfira T, Citovsky V, Grafi G. Reorganization of specific chromosomal domains and activation of silent genes in plant cells acquiring pluripotentiality. Dev Dyn 2004; 230:12-22. [PMID: 15108305 DOI: 10.1002/dvdy.20006] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The transition from leaf cells to protoplasts (plant cells devoid of cell walls) confers pluripotentiality coupled with chromatin reorganization. Here, we sought to identify remodeled chromosomal domains in Arabidopsis protoplasts by tracking DNA sequences undergoing changes in DNA methylation and by identifying up-regulated genes. We observed a reduction in DNA methylation at a pericentromeric region of chromosome 1, and up-regulation of several members of the NAC (NAM/ATAF1/CUC2) domain family, two of which are located near the telomeric region of chromosome 1. Fluorescence in situ hybridization (FISH) analysis demonstrated that both pericentromeric and telomeric subdomains underwent chromatin decondensation. This decondensation is subdomain-specific inasmuch as centromeric repeats remained largely unchanged, whereas the 18S rDNA underwent condensation. Within the pericentromeric subdomain, VIP1, a gene encoding a b-Zip nuclear protein required for Agrobacterium infectivity, was transcriptionally activated. Overexpression of this gene in tobacco resulted in growth retardation and inhibition of differentiation and shoot formation. Altogether, our data indicate that acquisition of pluripotentiality involves changes in DNA methylation pattern and reorganization of specific chromosomal subdomains. This change leads to activation of silent genes whose products are involved in acquisition or maintenance of pluripotentiality and/or the ensuing fate of the cell.
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Affiliation(s)
- Yigal Avivi
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel
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74
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Gutiérrez-Marcos JF, Costa LM, Biderre-Petit C, Khbaya B, O'Sullivan DM, Wormald M, Perez P, Dickinson HG. maternally expressed gene1 Is a novel maize endosperm transfer cell-specific gene with a maternal parent-of-origin pattern of expression. THE PLANT CELL 2004; 16:1288-301. [PMID: 15105441 PMCID: PMC423216 DOI: 10.1105/tpc.019778] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2003] [Accepted: 02/04/2004] [Indexed: 05/18/2023]
Abstract
Growth of the maize (Zea mays) endosperm is tightly regulated by maternal zygotic and sporophytic genes, some of which are subject to a parent-of-origin effect. We report here a novel gene, maternally expressed gene1 (meg1), which shows a maternal parent-of-origin expression pattern during early stages of endosperm development but biallelic expression at later stages. Interestingly, a stable reporter fusion containing the meg1 promoter exhibits a similar pattern of expression. meg1 is exclusively expressed in the basal transfer region of the endosperm. Further, we show that the putatively processed MEG1 protein is glycosylated and subsequently localized to the labyrinthine ingrowths of the transfer cell walls. Hence, the discovery of a parent-of-origin gene expressed solely in the basal transfer region opens the door to epigenetic mechanisms operating in the endosperm to regulate certain aspects of nutrient trafficking from the maternal tissue into the developing seed.
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75
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Abstract
Armored scale insects are unusual in that a part of their bodies is genetically distinct from the rest. This extraordinary phenomenon challenges the notion of identity
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Affiliation(s)
- Benjamin B Normark
- Department of Entomology and Graduate Program in Organismic and Evolutionary Biology at the University of Massachusetts, Amherst, Massachusetts, USA.
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76
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Martienssen R, Lippman Z, May B, Ronemus M, Vaughn M. Transposons, tandem repeats, and the silencing of imprinted genes. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2004; 69:371-9. [PMID: 16117670 DOI: 10.1101/sqb.2004.69.371] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- R Martienssen
- Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA
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77
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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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78
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Isidore E, van Os H, Andrzejewski S, Bakker J, Barrena I, Bryan GJ, Caromel B, van Eck H, Ghareeb B, de Jong W, van Koert P, Lefebvre V, Milbourne D, Ritter E, van der Voort JR, Rousselle-Bourgeois F, van Vliet J, Waugh R. Toward a Marker-Dense Meiotic Map of the Potato Genome: Lessons From Linkage Group I. Genetics 2003; 165:2107-16. [PMID: 14704190 PMCID: PMC1462890 DOI: 10.1093/genetics/165.4.2107] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AbstractSegregation data were obtained for 1260 potato linkage group I-specific AFLP loci from a heterozygous diploid potato population. Analytical tools that identified potential typing errors and/or inconsistencies in the data and that assembled cosegregating markers into bins were applied. Bins contain multiple-marker data sets with an identical segregation pattern, which is defined as the bin signature. The bin signatures were used to construct a skeleton bin map that was based solely on observed recombination events. Markers that did not match any of the bin signatures exactly (and that were excluded from the calculation of the skeleton bin map) were placed on the map by maximum likelihood. The resulting maternal and paternal maps consisted of 95 and 101 bins, respectively. Markers derived from EcoRI/MseI, PstI/MseI, and SacI/MseI primer combinations showed different genetic distributions. Approximately three-fourths of the markers placed into a bin were considered to fit well on the basis of an estimated residual “error rate” of 0–3%. However, twice as many PstI-based markers fit badly, suggesting that parental PstI-site methylation patterns had changed in the population. Recombination frequencies were highly variable across the map. Inert, presumably centromeric, regions caused extensive marker clustering while recombination hotspots (or regions identical by descent) resulted in empty bins, despite the level of marker saturation.
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Affiliation(s)
- Edwige Isidore
- Genome Dynamics Programme, Scottish Crop Research Institute, Dundee DD2 5DA, United Kingdom
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79
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Guo M, Rupe MA, Danilevskaya ON, Yang X, Hu Z. Genome-wide mRNA profiling reveals heterochronic allelic variation and a new imprinted gene in hybrid maize endosperm. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 36:30-44. [PMID: 12974809 DOI: 10.1046/j.1365-313x.2003.01852.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We have taken a genomic approach to examine global gene expression in the maize endosperm in relation to dosage and parental effects. Endosperm of eight hybrids generated by reciprocal crosses and their seven inbred parents were sampled at three developmental stages: 10, 14, and 21 days after pollination (DAP). These samples were subjected to GeneCalling, an open-ended mRNA-profiling technology, which simultaneously analyzes thousands of genes. Results indicated that the overall level of gene expression in the maize endosperm was dosage-dependent, that is, the gene expression was proportional to the parental genome contribution of 2n maternal : 1n paternal. However, approximately 8% of the genes deviated from such allelic additive expression and exhibited differential expression in hybrids of reciprocal crosses, resembling either maternally or paternally expressed genes. There were more genes with maternal-like expression (MLE) than those with paternal-like expression (PLE). Allele-specific expression analysis of four selected genes using the WAVE denaturing HPLC (dHPLC) system revealed several mechanisms responsible for the deviation from the allelic additive expression in the hybrid endosperm: heterochronic allelic variation, allelic variation in the level of expression, and genomic imprinting. We discovered a novel imprinted gene no-apical-meristem (NAM) related protein1 (nrp1) that was expressed only in the endosperm and regulated by gene-specific imprinting. The nrp1 gene, a putative transcriptional factor, may play an important role in endosperm development.
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Affiliation(s)
- Mei Guo
- Pioneer Hi-Bred International, Inc., Johnston, IA 50131-0552, USA.
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80
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Abstract
The introduction of apomixis to crops would allow desirable genotypes to be propagated while preventing undesirable gene flow, but so far there has been little success in transferring this trait from a natural apomict to another species. One explanation is the sensitivity of endosperm to changes in relative maternal and paternal contribution owing to parental imprinting, an epigenetic system of transcriptional regulation by which some genes are expressed from only the maternally or paternally contributed allele. In sexual species, endosperm typically requires a ratio of two maternal genomes to one paternal genome for normal development, but this ratio is often altered in apomicts, suggesting that the imprinting system is altered as well. We present evidence that modification of DNA methylation is one mechanism by which the imprinting system could be altered to allow endosperm development in apomicts. Another feature of natural apomixis is the modification of the normal fertilization programme. Sexual reproduction uses both sperm from each pollen grain, but pseudogamous apomicts, which require a sexual endosperm to support the asexual embryo, often use just one. We present evidence that multiple fertilization of the central cell is possible in Arabidopsis thaliana, suggesting that pseudogamous apomicts may also need to acquire a mechanism for preventing more than one sperm from contributing to the endosperm. We conclude that strategies to transfer apomixis to crop species should take account of endosperm development and particularly its sensitivity to parental imprinting, as well as the mechanism of fertilization.
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Affiliation(s)
- Melissa Spielman
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
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81
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Zemach A, Grafi G. Characterization of Arabidopsis thaliana methyl-CpG-binding domain (MBD) proteins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 34:565-572. [PMID: 12787239 DOI: 10.1046/j.1365-313x.2003.01756.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cytosine methylation at symmetrical CpG and CpNpG sequences plays a key role in the epigenetic control of plant growth and development; yet, the way by which the methylation signal is interpreted into a functional state has not been elucidated. In animals, the methylation signal is recognized by methyl-CpG-binding domain (MBD) proteins that specifically bind methylated CpG dinucleotides. In Arabidopsis thaliana, 12 putative MBD proteins were identified and classified into seven subclasses. Here, we characterized six MBD proteins representing four subclasses (II, III, IV, and VI) of the Arabidopsis MBD family. We found that AtMBD7 (subclass VI), a unique protein containing a double MBD motif, as well as AtMBD5 and AtMBD6 (subclass IV), bind specifically symmetrically methylated CpG sites. The MBD motif derived from AtMBD6, but not from AtMBD2, was sufficient for binding methylated CpG dinucleotides. AtMBD6 precipitated histone deacetylase (HDAC) activity from the leaf nuclear extract. The examined AtMBD proteins neither bound methylated CpNpG sequences nor did they display DNA demethylase activity. Our results suggest that AtMBD5, AtMBD6, and AtMBD7 are likely to function in Arabidopsis plants as mediators of the CpG methylation, linking DNA methylation-induced gene silencing with histone deacetylation.
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Affiliation(s)
- Assaf Zemach
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
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82
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Abstract
Chromatin remodeling in plants has usually been discussed in relation to aspects of genome defense such as transgene silencing and the resetting of transposon activity. The role of remodeling in controlling development has been less emphasized, although well established in animal systems. This is because cell fate in plants is often held to be entirely specified on the basis of position, apparently excluding any significant role for cell ancestry and chromatin remodeling. We argue that chromatin remodeling is used to confer mitotically heritable cell fates at late stages in pattern formation. Several examples in which chromatin remodeling factors are used to confer a memory of transient events in plant development are discussed. Because the precise biochemical functions of most remodeling factors are obscure, and little is known of plant chromatin structure, the underlying mechanisms remain poorly understood.
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Affiliation(s)
- Justin Goodrich
- Institute of Cell and Molecular Biology, University of Edinburgh, King's Buildings, Mayfield Road, United Kingdom.
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83
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Abstract
Continuous development, the absence of a germline, flexible and reversible cellular differentiation, and the existence of haploid and diploid generations--both of which express genes--are characteristics that distinguish plants from animals. Because these differences alter the impact of mutations, animals and plants experience varied selection pressures. Despite different life-cycles, both flowering plants and multicellular animals have evolved complex sensing mechanisms that act after fertilization as 'quality checks' on reproduction, and that detect chromosome dosage and the parent of origin for specific genes. Although flowering plant embryos escape such surveillance in vitro, embryo success in the seed often depends on a healthy endosperm--a nutritive tissue that is produced by a second fertilization event in which maternal and paternal gene contributions can be monitored immediately after fertilization and throughout development.
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Affiliation(s)
- Virginia Walbot
- Department of Biological Sciences, Stanford University, Stanford, California 94305-5020, USA.
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84
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Reik W, Constância M, Fowden A, Anderson N, Dean W, Ferguson-Smith A, Tycko B, Sibley C. Regulation of supply and demand for maternal nutrients in mammals by imprinted genes. J Physiol 2003; 547:35-44. [PMID: 12562908 PMCID: PMC2342627 DOI: 10.1113/jphysiol.2002.033274] [Citation(s) in RCA: 281] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2002] [Accepted: 01/15/2003] [Indexed: 01/10/2023] Open
Abstract
The placenta has evolved in eutherian mammals primarily to provide nutrients for the developing fetus. The genetic control of the regulation of supply and demand for maternal nutrients is not understood. In this review we argue that imprinted genes have central roles in controlling both the fetal demand for, and the placental supply of, maternal nutrients. Recent studies on Igf2 (insulin-like growth factor 2) knockout mouse models provide experimental support for this hypothesis. These show effects on placental transport capacity consistent with a role of IGF-II in modulating both the placental supply and fetal demand for nutrients. Imprinting of genes with such functions may have coevolved with the placenta and new evidence suggests that transporter proteins, as well as the regulators themselves, may also be imprinted. These data and hypotheses are important, as deregulation of supply and demand affects fetal growth and has long term consequences for health in mammals both in the neonatal period and, as a result of fetal programming, in adulthood.
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Affiliation(s)
- Wolf Reik
- Laboratory of Developmental Genetics and Imprinting, Developmental Genetics Programme, The Babraham Institute, Cambridge CB2 4AT, UK.
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85
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Maggert KA, Golic KG. The Y chromosome of Drosophila melanogaster exhibits chromosome-wide imprinting. Genetics 2002; 162:1245-58. [PMID: 12454070 PMCID: PMC1462351 DOI: 10.1093/genetics/162.3.1245] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Genomic imprinting is well known as a regulatory property of a few specific chromosomal regions and leads to differential behavior of maternally and paternally inherited alleles. We surveyed the activity of two reporter genes in 23 independent P-element insertions on the heterochromatic Y chromosome of Drosophila melanogaster and found that all but one location showed differential expression of one or both genes according to the parental source of the chromosome. In contrast, genes inserted in autosomal heterochromatin generally did not show imprint-regulated expression. The imprints were established on Y-linked transgenes inserted into many different sequences and locations. We conclude that genomic imprinting affecting gene expression is a general property of the Drosophila Y chromosome and distinguishes the Y from the autosomal complement.
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Affiliation(s)
- Keith A Maggert
- The Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.
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86
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Stinard PS, Sachs MM. The identification and characterization of two dominant r1 haplotype-specific inhibitors of aleurone color in Zea mays. J Hered 2002; 93:421-8. [PMID: 12642642 DOI: 10.1093/jhered/93.6.421] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We report the identification and characterization of two novel dominant inhibitors of aleurone color in Zea mays that interact with specific haplotypes of the r1 locus. One inhibitor locus, inr1 (inhibitor of r1 aleurone color 1), maps to the long arm of chromosome 10, distal to the TB-10L19 breakpoint and tightly linked to dull1, and the second inhibitor locus, inr2 (inhibitor of r1 aleurone color 2), maps to the long arm of chromosome 9. Dominant inhibitory alleles of inr1 and inr2 act by suppressing aleurone color conditioned by certain r1 haplotypes. Two haplotypes, R1-ch:Stadler and R1-Randolph, exhibit nearly complete suppression of aleurone color in the presence of inhibitory alleles of inr1 or inr2. Two members of the R1-d class of haplotypes, R1-d:Catspaw and R1-d:Arapaho, show partial suppression. Other haplotypes tested were not visibly affected. The response of r1 haplotypes to inhibitory inr1 and inr2 alleles provides another means of analyzing the complex behavior of the seed color components of r1 haplotypes. Possible mechanisms of action of inr1 and inr2 are discussed.
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Affiliation(s)
- P S Stinard
- US Department of Agriculture/Agricultural Research Service, Soybean/Maize Germplasm, Pathology and Genetics Research Unit, Urbana, Illinois, USA
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87
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Scholten S, Lörz H, Kranz E. Paternal mRNA and protein synthesis coincides with male chromatin decondensation in maize zygotes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2002; 32:221-31. [PMID: 12383087 DOI: 10.1046/j.1365-313x.2002.01418.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Decondensation of the male genome after fertilization is a prerequisite for replication and transcription. Cytological analysis has revealed decondensation of the male chromatin to commence immediately after karyogamy and progress rapidly, pointing to an early start of transcription. To investigate early transcription from the paternal genome in maize zygotes, we generated transgenic plants containing green fluorescent protein (GFP) under control of the 35S promoter. Single transgenic sperm cells from these plants were used to fertilize isolated wild-type egg cells in vitro. These sperm cells did not contain gfp transcripts. Appearance of gfp mRNA, 4 h after fertilization, was coincident with decondensation of the male chromatin, and clearly demonstrates early accessibility to the transcriptional machinery of at least a part of the male genome. Translational activity in early zygotes was evident 6 h after fertilization, as demonstrated by measurable levels of GFP fluorescence signal. Using a similar strategy, we also demonstrated activity of the paternal genome early in endosperm development. These findings may exclude any global mechanism of silencing the entire paternal genome over this period, and make an almost immediate paternal contribution to zygote and early endosperm development conceivable. These data are also considered in the perspective of current views of genome activation in the zygotes and young embryos of animals.
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Affiliation(s)
- Stefan Scholten
- Institut für Allgemeine Botanik, Angewandte Molekularbiologie der Pflanzen II, Universität Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany
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88
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Dickinson H, Scott R. DEMETER, Goddess of the harvest, activates maternal MEDEA to produce the perfect seed. Mol Cell 2002; 10:5-7. [PMID: 12150899 DOI: 10.1016/s1097-2765(02)00582-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Parental imprinting regulates processes as diverse as mammalian development and seed size in crop plants. In Arabidopsis, the DNA glycosylase DEMETER regulates early seed development, through activation of the maternal copy of the imprinted MEDEA Polycomb gene. Paternal silencing of MEA appears to be a default condition.
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Affiliation(s)
- Hugh Dickinson
- Department of Plant Sciences, University of Oxford, South Parks Road, United Kingdom
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89
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Kollipara KP, Saab IN, Wych RD, Lauer MJ, Singletary GW. Expression profiling of reciprocal maize hybrids divergent for cold germination and desiccation tolerance. PLANT PHYSIOLOGY 2002; 129:974-92. [PMID: 12114554 PMCID: PMC166494 DOI: 10.1104/pp.000729] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2001] [Revised: 01/21/2002] [Accepted: 03/05/2002] [Indexed: 05/18/2023]
Abstract
Recombinant inbred lines (RILs) derived from B73 x M017 were screened for cold germination (CG) and desiccation tolerance (DT) phenotypes. Reciprocal F(1) hybrids were made between divergent RILs, and hybrids that showed differential phenotypes (parent-of-origin effect) for CG or DT were selected for profiling mRNA and protein expression. mRNA and proteins were extracted from embryo axes of seed germinated for 11 d at 12.5 degrees C in the dark and developing embryos at 40% seed moisture (R5 stage) for CG and DT, respectively. GeneCalling analysis, an open-ended mRNA profiling method, identified 336 of 32,496 and 656 of 32,940 cDNA fragments that showed >or=1.5-fold change in expression between the reciprocal F(1) hybrids for CG and DT, respectively. Protein expression map (PEM) analysis, an open-ended two-dimensional polyacrylamide gel electrophoresis, identified 117 of 2,641 and 205 of 1,876 detected proteins to be differentially expressed with >or=1.5-fold change between the reciprocal F(1) hybrids in CG and DT samples, respectively. A subset of these proteins was identified by tandem mass spectrometry followed by database query of the spectra. The differentially expressed genes/proteins were classified into various functional groups including carbohydrate and amino acid metabolism, ion transporters, stress and defense response, polyamine metabolism, chaperonins, cytoskeleton associated, etc. Phenotypic analysis of seed from self-pollinated ears of the reciprocal F(1) hybrids displayed small differences compared with the reciprocal hybrids themselves, suggesting a negligible effect of cytoplasmic factors on CG and DT traits. The results provide leads to improving our understanding of the genes involved in stress response during seed maturation and germination.
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90
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de Koning DJ, Bovenhuis H, van Arendonk JAM. On the detection of imprinted quantitative trait loci in experimental crosses of outbred species. Genetics 2002; 161:931-8. [PMID: 12072486 PMCID: PMC1462155 DOI: 10.1093/genetics/161.2.931] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this article, the quantitative genetic aspects of imprinted genes and statistical properties of methods to detect imprinted QTL are studied. Different models to detect imprinted QTL and to distinguish between imprinted and Mendelian QTL were compared in a simulation study. Mendelian and imprinted QTL were simulated in an F2 design and analyzed under Mendelian and imprinting models. Mode of expression was evaluated against the H(0) of a Mendelian QTL as well as the H(0) of an imprinted QTL. It was shown that imprinted QTL might remain undetected when analyzing the genome with Mendelian models only. Compared to testing against a Mendelian QTL, using the H(0) of an imprinted QTL gave a higher proportion of correctly identified imprinted QTL, but also gave a higher proportion of false inference of imprinting for Mendelian QTL. When QTL were segregating in the founder lines, spurious detection of imprinting became more prominent under both tests, especially for designs with a small number of F1 sires.
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Affiliation(s)
- Dirk-Jan de Koning
- Animal Breeding and Genetics Group, Wageningen Institute of Animal Sciences, Wageningen University, 6700 AH Wageningen, The Netherlands.
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91
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Dilkes BP, Dante RA, Coelho C, Larkins BA. Genetic analyses of endoreduplication in Zea mays endosperm: evidence of sporophytic and zygotic maternal control. Genetics 2002; 160:1163-77. [PMID: 11901131 PMCID: PMC1462025 DOI: 10.1093/genetics/160.3.1163] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Flow cytometry was used to assess the variability of endoreduplication in endosperms of maize inbred lines. Little variation was found between midwestern dent types, and high levels of endoreduplication were observed in popcorns. Endoreduplication is different between inbred lines by 13-18 days after pollination, and flow cytometric analysis of ploidy level was feasible until 20 DAP. To study the genetic regulation of endoreduplication, four inbreds were crossed to B73 and developing endosperms from both parental, reciprocal F(1), and backcross generations were subjected to flow cytometric analysis. Three measurements of endoreduplication were calculated from these data and analyzed as quantitative genetic traits. Multiple models of trait inheritance were considered including triploid, diploid, sporophytic maternal, and maternal and paternal zygotic nuclear inheritance. Maternal zygotic effects, often considered a form of parental imprinting, and maternal sporophytic effects were detected. To test the feasibility of introgressing a high endoreduplication phenotype into a midwestern dent inbred line, a backcross population was generated from B73 x Sg18. Parental and progeny endoreduplication levels were compared and heritabilities assessed. The heritabilities calculated from these data generally agree with the values calculated in the larger crossing experiments.
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Affiliation(s)
- Brian P Dilkes
- Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
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92
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Lohe AR, Chaudhury A. Genetic and epigenetic processes in seed development. CURRENT OPINION IN PLANT BIOLOGY 2002; 5:19-25. [PMID: 11788303 DOI: 10.1016/s1369-5266(01)00224-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Seed development has emerged as an important area of research in plant development. Recent research has highlighted the divergent reproductive strategies of the male and female genomes and interaction between genetic and epigenetic control mechanisms. Isolation of genes involved in embryo and endosperm development is leading to an understanding of the regulation of these processes at the molecular level. A thorough grasp of these processes will not only illuminate an important area of plant development but will also have an impact on agronomy by helping to facilitate food production. An understanding of seed development is also likely to clarify the molecular mechanisms of apomixis, a fascinating process of asexual seed production present in many plants.
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Affiliation(s)
- Allan R Lohe
- CSIRO Division of Plant Industry, PO Box 1600, Canberra, ACT 2601, Australia.
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93
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Spielman M, Vinkenoog R, Dickinson HG, Scott RJ. The epigenetic basis of gender in flowering plants and mammals. Trends Genet 2001; 17:705-11. [PMID: 11718924 DOI: 10.1016/s0168-9525(01)02519-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
What makes a sperm male or an egg female, and how can we tell? A gamete's gender could be defined in many ways, such as the sex of the individual or organ that produced it, its cellular morphology, or its behaviour at fertilization. In flowering plants and mammals, however, there is an extra dimension to the gender of a gamete--due to parental imprinting, some of the genes it contributes to the next generation will have different expression patterns depending on whether they were maternally or paternally transmitted. The non-equivalence of gamete genomes, along with natural and experimental modification of imprinting, reveal a level of sexual identity that we describe as 'epigender'. In this paper, we explore epigender in the life history of plants and animals, and its significance for reproduction and development.
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Affiliation(s)
- M Spielman
- Dept of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB, Oxford, UK
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94
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Li Y, Bernot JP, Illingworth C, Lison W, Bernot KM, Eggleston WB, Fogle KJ, DiPaola JE, Kermicle J, Alleman M. Gene conversion within regulatory sequences generates maize r alleles with altered gene expression. Genetics 2001; 159:1727-40. [PMID: 11779810 PMCID: PMC1461907 DOI: 10.1093/genetics/159.4.1727] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The maize r locus encodes a transcription factor that regulates the developmental expression of the plant pigment anthocyanin. In an unusual example of gene regulatory diversity, the R-sc (Sc, strong seed color) and the R-p (P, plant color) alleles of r have nonoverlapping tissue specificity and nonhomologous 5' flanking sequences. Heterozygotes between wild-type P and Sc mutants with Ds6 transposable element inserts (r-sc:m::Ds6 or sc:m) produce colored seed derivatives (Sc+) during meiotic recombination. The sc:m alleles with Ds6 insertion in 3' regions of r produce crossover Sc+ derivatives. sc:m alleles with Ds6 elements inserted in 5' regions produce rare Sc+ derivatives borne on nonrecombinant chromosomes. Among 52 such noncrossover Sc+ derivatives, 18 are indistinguishable from the Sc progenitor in phenotype and DNA sequence [Scp(+) alleles]. The remaining 34 derivatives have strong Sc+ expression, including darkly pigmented aleurone, scutellum, coleoptile, and scutellar node [Scp(e) alleles]. The coleoptile and scutellar node phenotypes are unique from either progenitor but are similar to those of some naturally occurring r alleles. Both classes of Sc+ derivatives are explained by gene conversion between the promoter region of Sc:124 and a homologous region located proximal to P. The recombinational intermediate formed between sc:m alleles and P results in deletion of the Ds6 element alone or both Ds6 and a nearby unrelated transposable element-like sequence.
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Affiliation(s)
- Y Li
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
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95
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Song R, Llaca V, Linton E, Messing J. Sequence, regulation, and evolution of the maize 22-kD alpha zein gene family. Genome Res 2001; 11:1817-25. [PMID: 11691845 PMCID: PMC311139 DOI: 10.1101/gr.197301] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2001] [Accepted: 08/07/2001] [Indexed: 12/20/2022]
Abstract
We have isolated and sequenced all 23 members of the 22-kD alpha zein (z1C) gene family of maize. This is one of the largest plant gene families that has been sequenced from a single genetic background and includes the largest contiguous genomic DNA from maize with 346,292 bp to date. Twenty-two of the z1C members are found in a roughly tandem array on chromosome 4S forming a dense gene cluster 168,489-bp long. The twenty-third copy of the gene family is also located on chromosome 4S at a site approximately 20 cM closer to the centromere and appears to be the wild-type allele of the floury-2 (fl2) mutation. On the basis of an analysis of maize cDNA databases, only seven of these genes appear to be expressed including the fl2 allele. The expressed genes in the cluster are interspersed with nonexpressed genes. Interestingly, some of the expressed genes differ in their transcriptional regulation. Gene amplification appears to be in blocks of genes explaining the rapid and compact expansion of the cluster during the evolution of maize.
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Affiliation(s)
- R Song
- Waksman Institute, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA
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96
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Abstract
While superficially simple, endosperm development is a complex, dynamic process. Cereal endosperms contain three major cell types: starchy endosperm, transfer cells and aleurone. The localized accumulation of the END1 transcript in the syncitial endosperm suggests that signals from the maternal placental tissue specify transfer cell type early. Aleurone fate is plastic and requires the continual input of positional cues to maintain cell identity. Starchy endosperm appears to be the default cell type. Mutant patterns suggest that a regulatory hierarchy integrates endosperm development. Requirements for gametic imprinting, maternal : paternal genome ratios and putative chromatin modeling factors indicate the importance of genomic control.
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Affiliation(s)
- P W Becraft
- Zoology and Genetics Department and Agronomy Department, Iowa State University, Ames, IA 50011, USA.
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97
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Habu Y, Kakutani T, Paszkowski J. Epigenetic developmental mechanisms in plants: molecules and targets of plant epigenetic regulation. Curr Opin Genet Dev 2001; 11:215-20. [PMID: 11250147 DOI: 10.1016/s0959-437x(00)00182-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genetic approaches to understanding the role of epigenetic regulation of gene expression in plants and its mechanisms have revealed several new components. Rapidly accumulating information from other eukaryotes provides complementary knowledge with important implications for plant research. Comparison of epigenetic events across species is proving critical for defining the mechanisms and functions of epigenetic modification, including those specific to plants.
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Affiliation(s)
- Y Habu
- Friedrich Miescher Institute, Novartis Research Foundation, Maulbeerstrasse 66, 4058, Basel, Switzerland.
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98
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Selinger DA, Chandler VL. B-Bolivia, an allele of the maize b1 gene with variable expression, contains a high copy retrotransposon-related sequence immediately upstream. PLANT PHYSIOLOGY 2001; 125:1363-79. [PMID: 11244116 PMCID: PMC65615 DOI: 10.1104/pp.125.3.1363] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2000] [Accepted: 12/21/2000] [Indexed: 05/18/2023]
Abstract
The maize (Zea mays) b1 gene encodes a transcription factor that regulates the anthocyanin pigment pathway. Of the b1 alleles with distinct tissue-specific expression, B-Peru and B-Bolivia are the only alleles that confer seed pigmentation. B-Bolivia produces variable and weaker seed expression but darker, more regular plant expression relative to B-Peru. Our experiments demonstrated that B-Bolivia is not expressed in the seed when transmitted through the male. When transmitted through the female the proportion of kernels pigmented and the intensity of pigment varied. Molecular characterization of B-Bolivia demonstrated that it shares the first 530 bp of the upstream region with B-Peru, a region sufficient for seed expression. Immediately upstream of 530 bp, B-Bolivia is completely divergent from B-Peru. These sequences share sequence similarity to retrotransposons. Transient expression assays of various promoter constructs identified a 33-bp region in B-Bolivia that can account for the reduced aleurone pigment amounts (40%) observed with B-Bolivia relative to B-Peru. Transgenic plants carrying the B-Bolivia promoter proximal region produced pigmented seeds. Similar to native B-Bolivia, some transgene loci are variably expressed in seeds. In contrast to native B-Bolivia, the transgene loci are expressed in seeds when transmitted through both the male and female. Some transgenic lines produced pigment in vegetative tissues, but the tissue-specificity was different from B-Bolivia, suggesting the introduced sequences do not contain the B-Bolivia plant-specific regulatory sequences. We hypothesize that the chromatin context of the B-Bolivia allele controls its epigenetic seed expression properties, which could be influenced by the adjacent highly repeated retrotransposon sequence.
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Affiliation(s)
- D A Selinger
- Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
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