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Mutti JS, Bhullar RK, Gill KS. Evolution of Gene Expression Balance Among Homeologs of Natural Polyploids. G3 (BETHESDA, MD.) 2017; 7:1225-1237. [PMID: 28193629 PMCID: PMC5386871 DOI: 10.1534/g3.116.038711] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 02/11/2017] [Indexed: 11/18/2022]
Abstract
Polyploidy is a major evolutionary process in eukaryotes, yet the expression balance of homeologs in natural polyploids is largely unknown. To study this expression balance, the expression patterns of 2180 structurally well-characterized genes of wheat were studied, of which 813 had the expected three copies and 375 had less than three. Copy numbers of the remaining 992 ranged from 4 to 14, including homeologs, orthologs, and paralogs. Of the genes with three structural copies corresponding to homeologs, 55% expressed from all three, 38% from two, and the remaining 7% expressed from only one of the three copies. Homeologs of 76-87% of the genes showed differential expression patterns in different tissues, thus have evolved different gene expression controls, possibly resulting in novel functions. Homeologs of 55% of the genes showed tissue-specific expression, with the largest percentage (14%) in the anthers and the smallest (7%) in the pistils. The highest number (1.72/3) of homeologs/gene expression was in the roots and the lowest (1.03/3) in the anthers. As the expression of homeologs changed with changes in structural copy number, about 30% of the genes showed dosage dependence. Chromosomal location also impacted expression pattern as a significantly higher proportion of genes in the proximal regions showed expression from all three copies compared to that present in the distal regions.
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Affiliation(s)
- Jasdeep S Mutti
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
| | - Ramanjot K Bhullar
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
| | - Kulvinder S Gill
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
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Rodríguez F, Cai D, Teng Y, Spooner D. Asymmetric single-strand conformation polymorphism: an accurate and cost-effective method to amplify and sequence allelic variants. AMERICAN JOURNAL OF BOTANY 2011; 98:1061-1067. [PMID: 21730333 DOI: 10.3732/ajb.1000251] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY An efficient alternative strategy to conventional cloning was needed to generate high-quality DNA sequences from a variety of nuclear orthologs for phylogenetic studies. This method would facilitate studies and minimize technical problems typically encountered in cloning methodologies. METHODS We tested a variety of single-strand conformation polymorphism (SSCP) protocols including purified and unpurified symmetric and asymmetric PCR, loading buffers, and electrophoresis conditions (buffers, matrix, running time, temperature). Results obtained from direct SSCP band sequencing were compared to those obtained from cloning. KEY RESULTS Our optimized protocol uses asymmetric PCR, with the majority of the samples run in polyacrylamide gel electrophoresis (PAGE). It consistently separated PCR products from 450 to 1200 bp. CONCLUSIONS Asymmetric PCR single-strand conformation polymorphism is an efficient alternative technique for isolating allelic variants of highly heterozygous individuals, with its greatest applications in sequencing allopolyploids. It eliminates two common problems encountered in cloning: PCR recombination and heteroduplex fixation. In addition, our protocol greatly lowers costs and time associated with procedures.
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Affiliation(s)
- Flor Rodríguez
- USDA, Agricultural Research Service, Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin 53706-1590, USA
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Dong S, Adams KL. Differential contributions to the transcriptome of duplicated genes in response to abiotic stresses in natural and synthetic polyploids. THE NEW PHYTOLOGIST 2011; 190:1045-1057. [PMID: 21361962 DOI: 10.1111/j.1469-8137.2011.03650.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Polyploidy has occurred throughout plant evolution and can result in considerable changes to gene expression when it takes place and over evolutionary time. Little is known about the effects of abiotic stress conditions on duplicate gene expression patterns in polyploid plants. We examined the expression patterns of 60 duplicated genes in leaves, roots and cotyledons of allotetraploid Gossypium hirsutum in response to five abiotic stress treatments (heat, cold, drought, high salt and water submersion) using single-strand conformation polymorphism assays, and 20 genes in a synthetic allotetraploid. Over 70% of the genes showed stress-induced changes in the relative expression levels of the duplicates under one or more stress treatments with frequent variability among treatments. Twelve pairs showed opposite changes in expression levels in response to different abiotic stress treatments. Stress-induced expression changes occurred in the synthetic allopolyploid, but there was little correspondence in patterns between the natural and synthetic polyploids. Our results indicate that abiotic stress conditions can have considerable effects on duplicate gene expression in a polyploid, with the effects varying by gene, stress and organ type. Differential expression in response to environmental stresses may be a factor in the preservation of some duplicated genes in polyploids.
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Affiliation(s)
- Shaowei Dong
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, 2357 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Plant Science Graduate Program, University of British Columbia, 2357 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Keith L Adams
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, 2357 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, 2357 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Plant Science Graduate Program, University of British Columbia, 2357 Main Mall, Vancouver, BC, V6T 1Z4, Canada
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Lebel S, Schellenbaum P, Walter B, Maillot P. Characterisation of the Vitis vinifera PR10 multigene family. BMC PLANT BIOLOGY 2010; 10:184. [PMID: 20727162 PMCID: PMC3095314 DOI: 10.1186/1471-2229-10-184] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 08/20/2010] [Indexed: 05/21/2023]
Abstract
BACKGROUND Genes belonging to the pathogenesis related 10 (PR10) group have been studied in several plant species, where they form multigene families. Until now, such an analysis has not been performed in Vitis vinifera, although three different PR10 genes were found to be expressed under pathogen attack or abiotic stress, and during somatic embryogenesis induction. We used the complete genome sequence for characterising the whole V. vinifera PR10 gene family. The expression of candidate genes was studied in various non-treated tissues and following somatic embryogenesis induction by the auxin 2,4-D. RESULTS In addition to the three V. vinifera PR10 genes already described, namely VvPR10.1, VvPR10.2 and VvPR10.3, fourteen different PR10 related sequences were identified. Showing high similarity, they form a single cluster on the chromosome 5 comprising three pseudogenes. The expression of nine different genes was detected in various tissues. Although differentially expressed in non-treated plant organs, several genes were up-regulated in tissues treated with 2,4-D, as expected for PR genes. CONCLUSIONS PR10 genes form a multigene family in V. vinifera, as found in birch, apple or peach. Seventeen closely related PR10 sequences are arranged in a tandem array on the chromosome 5, probably reflecting small-scale duplications during evolution. Various expression patterns were found for nine studied genes, highlighting functional diversification. A phylogenetic comparison of deduced proteins with PR10 proteins of other plants showed a characteristic low intraspecific variability. Particularly, a group of seven close tandem duplicates including VvPR10.1, VvPR10.2 and VvPR10.3 showed a very high similarity, suggesting concerted evolution or/and recent duplications.
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Affiliation(s)
- Sylvain Lebel
- Université de Haute Alsace, Laboratoire Vigne, Biotechnologies & Environnement, 33 rue de Herrlisheim, BP 50568, 68 008, Colmar Cedex, France
| | - Paul Schellenbaum
- Université de Haute Alsace, Laboratoire Vigne, Biotechnologies & Environnement, 33 rue de Herrlisheim, BP 50568, 68 008, Colmar Cedex, France
| | - Bernard Walter
- Université de Haute Alsace, Laboratoire Vigne, Biotechnologies & Environnement, 33 rue de Herrlisheim, BP 50568, 68 008, Colmar Cedex, France
| | - Pascale Maillot
- Université de Haute Alsace, Laboratoire Vigne, Biotechnologies & Environnement, 33 rue de Herrlisheim, BP 50568, 68 008, Colmar Cedex, France
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Ge XH, Wang J, Li ZY. Different genome-specific chromosome stabilities in synthetic Brassica allohexaploids revealed by wide crosses with Orychophragmus. ANNALS OF BOTANY 2009; 104:19-31. [PMID: 19403626 PMCID: PMC2706731 DOI: 10.1093/aob/mcp099] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2008] [Revised: 02/12/2009] [Accepted: 03/17/2009] [Indexed: 05/21/2023]
Abstract
BACKGROUND AND AIMS In sexual hybrids between cultivated Brassica species and another crucifer, Orychophragmus violaceus (2n = 24), parental genome separation during mitosis and meiosis is under genetic control but this phenomenon varies depending upon the Brassica species. To further investigate the mechanisms involved in parental genome separation, complex hybrids between synthetic Brassica allohexaploids (2n = 54, AABBCC) from three sources and O. violaceus were obtained and characterized. METHODS Genomic in situ hybridization, amplified fragment length polymorphism (AFLP) and single-strand conformation polymorphism (SSCP) were used to explore chromosomal/genomic components and rRNA gene expression of the complex hybrids and their progenies. KEY RESULTS Complex hybrids with variable fertility exhibited phenotypes that were different from the female allohexaploids and expressed some traits from O. violaceus. These hybrids were mixoploids (2n = 34-46) and retained partial complements of allohexaploids, including whole chromosomes of the A and B genomes and some of the C genome but no intact O. violaceus chromosomes; AFLP bands specific for O. violaceus, novel for two parents and absent in hexaploids were detected. The complex hybrids produced progenies with chromosomes/genomic complements biased to B. juncea (2n = 36, AABB) and novel B. juncea lines with two genomes of different origins. The expression of rRNA genes from B. nigra was revealed in all allohexaploids and complex hybrids, showing that the hierarchy of nucleolar dominance (B. nigra, BB > B. rapa, AA > B. oleracea, CC) in Brassica allotetraploids was still valid in these plants. CONCLUSIONS The chromosomes of three genomes in these synthetic Brassica allohexaploids showed different genome-specific stabilities (B > A > C) under induction of alien chromosome elimination in crosses with O. violaceus, which was possibly affected by nucleolar dominance.
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Nonadditive expression of homoeologous genes is established upon polyploidization in hexaploid wheat. Genetics 2008; 181:1147-57. [PMID: 19104075 DOI: 10.1534/genetics.108.096941] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Effects of polyploidy in allohexaploid wheat (Triticum aestivum L.) have primarily been ascribed to increases in coding sequence variation and potential to acquire new gene functions through mutation of redundant loci. However, regulatory variation that arises through new promoter and transcription factor combinations or epigenetic events may also contribute to the effects of polyploidization. In this study, gene expression was characterized in a synthetic T. aestivum line and the T. turgidum and Aegilops tauschii parents to establish a timeline for such regulatory changes and estimate the frequency of nonadditive expression of homoeologous transcripts in newly formed T. aestivum. Large-scale analysis of nonadditive gene expression was assayed by microarray expression experiments, where synthetic T. aestivum gene expression was compared to additive model values (mid-parent) calculated from parental T. turgidum and Ae. tauschii expression levels. Approximately 16% of genes were estimated to display nonadditive expression in synthetic T. aestivum. A certain fraction of the genes (2.9%) showed overdominance or underdominance. cDNA-single strand conformation polymorphism analysis was applied to measure expression of homoeologous transcripts and further verify microarray data. The results demonstrate that allopolyploidization, per se, results in rapid initiation of differential expression of homoeologous loci and nonadditive gene expression in T. aestivum.
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Agarwal M, Shrivastava N, Padh H. Advances in molecular marker techniques and their applications in plant sciences. PLANT CELL REPORTS 2008; 27:617-31. [PMID: 18246355 DOI: 10.1007/s00299-008-0507-z] [Citation(s) in RCA: 220] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Revised: 12/16/2007] [Accepted: 01/11/2008] [Indexed: 05/20/2023]
Abstract
Detection and analysis of genetic variation can help us to understand the molecular basis of various biological phenomena in plants. Since the entire plant kingdom cannot be covered under sequencing projects, molecular markers and their correlation to phenotypes provide us with requisite landmarks for elucidation of genetic variation. Genetic or DNA based marker techniques such as RFLP (restriction fragment length polymorphism), RAPD (random amplified polymorphic DNA), SSR (simple sequence repeats) and AFLP (amplified fragment length polymorphism) are routinely being used in ecological, evolutionary, taxonomical, phylogenic and genetic studies of plant sciences. These techniques are well established and their advantages as well as limitations have been realized. In recent years, a new class of advanced techniques has emerged, primarily derived from combination of earlier basic techniques. Advanced marker techniques tend to amalgamate advantageous features of several basic techniques. The newer methods also incorporate modifications in the methodology of basic techniques to increase the sensitivity and resolution to detect genetic discontinuity and distinctiveness. The advanced marker techniques also utilize newer class of DNA elements such as retrotransposons, mitochondrial and chloroplast based microsatellites, thereby revealing genetic variation through increased genome coverage. Techniques such as RAPD and AFLP are also being applied to cDNA-based templates to study patterns of gene expression and uncover the genetic basis of biological responses. The review details account of techniques used in identification of markers and their applicability in plant sciences.
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Affiliation(s)
- Milee Agarwal
- B. V. Patel Pharmaceutical Education Research and Development Centre, Thaltej-Gandhinagar Highway, Ahmadabad, 380054, India
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de Bustos A, Pérez R, Jouve N. Characterization of the gene Mre11 and evidence of silencing after polyploidization in Triticum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:985-99. [PMID: 17262197 DOI: 10.1007/s00122-006-0493-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2006] [Accepted: 12/21/2006] [Indexed: 05/13/2023]
Abstract
The MRE11 protein is a component of the highly conserved MRN complex, along with RAD50 and NBS1. This complex is crucial in the repair of breaks in double stranded DNA, and is involved in many other cell processes. The present paper reports the molecular characterization of Mre11 gene in all three genomes of wheat, making use of the diploid species Triticum monococcum (genome A) and Aegilops Tauschii (genome D), the tetraploid T. turgidum (genomes A and B), and the hexaploid T. aestivum (genomes A, B and D). The genomic sequences characterized ranged from 4,662 to 4,766 bp in length; the cDNA corresponding to the processed mRNA was 2,440-2,510 bp long. In all cases, Mre11 coded for a highly conserved protein of 699 amino acids with a structure involving 22 exons. Mre11 expression was determined by real-time PCR in all the species analysed. The tetraploid species showed an expression similar to that of the diploid Ae. tauschii and lower than that of T. monococcum. Stronger expression was detected in the hexaploid T. aestivum. The SSCP technique was modified by introducing fluorescent labelling to the procedure in order to analyse the expression of the different Mre11 genes (i.e., those belonging to the different genomes) in the polyploid species. In both polyploids, the Mre11 gene belonging to the B genome was the least expressed. This probably reflects a first step in the process of silencing duplicate genes after polyploidization.
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MESH Headings
- Amino Acid Sequence
- Base Pairing
- Base Sequence
- Blotting, Southern
- DNA, Complementary
- DNA, Plant/genetics
- DNA, Plant/isolation & purification
- Exons
- Gene Expression Regulation, Plant
- Gene Silencing
- Genes, Plant
- Genetic Variation
- Genome, Plant
- Molecular Sequence Data
- Phylogeny
- Plant Proteins/analysis
- Plant Proteins/chemistry
- Plant Proteins/genetics
- Polymerase Chain Reaction
- Polymorphism, Single-Stranded Conformational
- Polyploidy
- RNA, Messenger/chemistry
- RNA, Plant/chemistry
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Species Specificity
- Triticum/classification
- Triticum/genetics
- Triticum/metabolism
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Affiliation(s)
- Alfredo de Bustos
- Department of Cell Biology and Genetics, University of Alcalá, Campus Universidad de Alcalá, 28871 Alcalá de Henares (Madrid), Spain
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Federico ML, Iñiguez-Luy FL, Skadsen RW, Kaeppler HF. Spatial and temporal divergence of expression in duplicated barley germin-like protein-encoding genes. Genetics 2006; 174:179-90. [PMID: 16751662 PMCID: PMC1569785 DOI: 10.1534/genetics.106.058156] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2006] [Accepted: 05/28/2006] [Indexed: 02/06/2023] Open
Abstract
Subfunctionalization is the process by which a pair of duplicated genes, or paralogs, experiences a reduction of individual expression patterns or function while still reproducing the complete expression pattern and function of the ancestral gene. Two germin-like protein (GLP)-encoding genes, GerB and GerF, are paralogs that belong to a small gene family in barley (Hordeum vulgare). Both genes share high nucleotide sequence similarity in coding and noncoding regions and encode identical apoplastic proteins. The use of RNA gel blots, coupled with single-stranded conformation polymorphism (SSCP) analysis of RT-PCR products, elucidated the developmental and tissue-specific expression patterns of each gene. Individual expression patterns provided evidence of both overlapping redundancy and early subfunctionalization. GerB is predominantly expressed in developing shoots, while GerF is predominantly expressed in seedling roots, developing spikes, and pericarp/testa. GerF promoter deletion studies located a region (-356/-97) responsible for high promoter activity and showed the ability of GerB and GerF upstream regions to drive gfp expression in coleoptiles, epicarps, and lemma/palea of developing spikes. The observed expression patterns are consistent with proposed roles in plant development and defense mechanisms for this gene family. These roles may explain why redundancy has been selectively maintained in this duplicate gene pair.
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Affiliation(s)
- Maria L Federico
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706, USA
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Adams KL, Wendel JF. Allele-specific, bidirectional silencing of an alcohol dehydrogenase gene in different organs of interspecific diploid cotton hybrids. Genetics 2005; 171:2139-42. [PMID: 16143609 PMCID: PMC1456131 DOI: 10.1534/genetics.105.047357] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Interspecific hybridization is a common and important process that generates phenotypic novelty and can lead to hybrid speciation as well as to changes in gene expression. Using two different interspecific cotton (Gossypium) diploid hybrids, we show organ-specific, bidirectional allelic silencing at a heterozygous Adh locus, with alternate alleles being silenced in leaves and many floral organs, respectively. These results show that developmental regulation of gene expression is changed immediately upon hybridization between diploid species, possibly due to epigenetic factors or regulatory mismatch.
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Affiliation(s)
- Keith L Adams
- UBC Botanical Garden, Centre for Plant Research and Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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Kwade Z, Swiatek A, Azmi A, Goossens A, Inzé D, Van Onckelen H, Roef L. Identification of four adenosine kinase isoforms in tobacco By-2 cells and their putative role in the cell cycle-regulated cytokinin metabolism. J Biol Chem 2005; 280:17512-9. [PMID: 15731114 DOI: 10.1074/jbc.m411428200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Adenosine kinase (ADK), a key enzyme in the regulation of the intracellular level of adenosine is also speculated to be responsible for the conversion of cytokinin ribosides to their respective nucleotides. To elucidate the role of ADK in the cytokinin metabolism of tobacco BY-2 cells (Nicotiana tabacum cv. "Bright Yellow-2"; TBY-2), we have identified and characterized the full-length cDNAs encoding four ADK isoforms of N. tabacum and determined their catalytic properties. The four TBY-2 ADK isoforms (designated 1S, 2S, 1T, and 2T) display a high affinity for both adenosine (Km 1.88-7.30 microm) and three distinct types of cytokinin ribosides: isopentenyladenosine; zeatin riboside; and dihydrozeatin riboside (Km 0.30-8.71 microm). The Vmax/Km values suggest that ADK2S exhibits in vitro an overall higher efficiency in the metabolism of cytokinin ribosides than the other three isoforms. The expression pattern of NtADK genes is modulated significantly during the cell cycle. We suggest that the increased transcript accumulation of NtADK coupled to an increased ADK activity just prior to mitosis is associated with a very active cytokinin metabolism at that phase of the cell cycle of synchronized TBY-2 cells.
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Affiliation(s)
- Zuzanna Kwade
- Laboratory of Plant Biochemistry and Physiology, Department of Biology, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
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PIRES JCHRIS, ZHAO JIANWEI, SCHRANZ MERIC, LEON ENRIQUEJ, QUIJADA PABLOA, LUKENS LEWISN, OSBORN THOMASC. Flowering time divergence and genomic rearrangements in resynthesized Brassica polyploids (Brassicaceae). Biol J Linn Soc Lond 2004. [DOI: 10.1111/j.1095-8312.2004.00350.x] [Citation(s) in RCA: 263] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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