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Li R, Zheng W, Jiang M, Zhang H. A review of starch biosynthesis in cereal crops and its potential breeding applications in rice ( Oryza Sativa L.). PeerJ 2022; 9:e12678. [PMID: 35036154 PMCID: PMC8710062 DOI: 10.7717/peerj.12678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/02/2021] [Indexed: 11/20/2022] Open
Abstract
Starch provides primary storage of carbohydrates, accounting for approximately 85% of the dry weight of cereal endosperm. Cereal seeds contribute to maximum annual starch production and provide the primary food for humans and livestock worldwide. However, the growing demand for starch in food and industry and the increasing loss of arable land with urbanization emphasizes the urgency to understand starch biosynthesis and its regulation. Here, we first summarized the regulatory signaling pathways about leaf starch biosynthesis. Subsequently, we paid more attention to how transcriptional factors (TFs) systematically respond to various stimulants via the regulation of the enzymes during starch biosynthesis. Finally, some strategies to improve cereal yield and quality were put forward based on the previous reports. This review would collectively help to design future studies on starch biosynthesis in cereal crops.
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Affiliation(s)
- Ruiqing Li
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China.,College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Wenyin Zheng
- College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Meng Jiang
- State Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou, China
| | - Huali Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
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2
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Lavania UC, Yamamoto M, Mukai Y. Extended Chromatin and DNA Fibers from Active Plant Nuclei for High-resolution FISH. J Histochem Cytochem 2016; 51:1249-53. [PMID: 14500692 DOI: 10.1177/002215540305101001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The conventional protocol for isolation of cell wall free nuclei for release of DNA fibers for plants involves mechanical removal of the cell wall and separation of debris by sieve filtration. The mechanical grinding pressure applied during the process leaves only the more tolerant G(1) nuclei intact, and all other states of active nuclei that may be present in the target tissues (e.g., leaf) are simply crushed/disrupted during the isolation process. Here we describe an alternative enzymatic protocol for isolation of nuclei from root tip tissue. Cell wall free nuclei at a given stage of cell cycle, free of any cell debris, could be realized in suspension that are fit for preparation of extended fibers suitable for fiber FISH applications. The protocol utilizes selective harvest of active nuclei from root tip tissue in liquid suspension under the influence of cell wall-degrading enzymes, and provides opportunities to target cell cycle-specific nuclei from interphase through division phase for the release of extended DNA fibers. Availability of cell cycle-specific fibers may have added value in transcriptional analysis, DNA:RNA hybridization, visualization of DNA replication and replication forks, and improved FISH efficiency.
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Affiliation(s)
- U C Lavania
- Cytogenetics Division, Central Institute of Medicinal and Aromatic Plants, Lucknow, India.
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3
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Sharma AK, Lavania UC. Chromosome identification—evolving technology from elucidating condensed chromatin to DNA molecules. THE NUCLEUS 2015. [DOI: 10.1007/s13237-016-0160-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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4
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Genes involved in the accumulation of starch and lipids in wheat and rice: characterization using molecular and cytogenetic techniques. THE NUCLEUS 2015. [DOI: 10.1007/s13237-015-0149-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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5
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Characterization of genes encoding Starch Branching Enzyme I from Triticum monococcum and its diploid wheat relatives. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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6
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Wang XY, Ma J, Wang CS, Zhang LL, Wang JR, Liu YX, Qi PF, Wei YM, Zheng YL, Jiang QT. Characterization of starch branching enzyme I (SBE I) gene in twoTriticum monococcumaccessions with different starch content. STARCH-STARKE 2015. [DOI: 10.1002/star.201500027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Xiu-Ying Wang
- Triticeae Research Institute; Sichuan Agricultural University; Chengdu Sichuan P.R. China
| | - Jian Ma
- Triticeae Research Institute; Sichuan Agricultural University; Chengdu Sichuan P.R. China
| | - Chang-Shui Wang
- Triticeae Research Institute; Sichuan Agricultural University; Chengdu Sichuan P.R. China
| | - Ling-Ling Zhang
- Triticeae Research Institute; Sichuan Agricultural University; Chengdu Sichuan P.R. China
| | - Ji-Rui Wang
- Triticeae Research Institute; Sichuan Agricultural University; Chengdu Sichuan P.R. China
| | - Ya-Xi Liu
- Triticeae Research Institute; Sichuan Agricultural University; Chengdu Sichuan P.R. China
| | - Peng-Fei Qi
- Triticeae Research Institute; Sichuan Agricultural University; Chengdu Sichuan P.R. China
| | - Yu-Ming Wei
- Triticeae Research Institute; Sichuan Agricultural University; Chengdu Sichuan P.R. China
| | - You-Liang Zheng
- Key Laboratory of Southwestern Crop Germplasm Utilization, Ministry of Agriculture; Sichuan Agricultural University; Ya'an Sichuan P.R. China
| | - Qian-Tao Jiang
- Triticeae Research Institute; Sichuan Agricultural University; Chengdu Sichuan P.R. China
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7
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Butardo VM, Fitzgerald MA, Bird AR, Gidley MJ, Flanagan BM, Larroque O, Resurreccion AP, Laidlaw HKC, Jobling SA, Morell MK, Rahman S. Impact of down-regulation of starch branching enzyme IIb in rice by artificial microRNA- and hairpin RNA-mediated RNA silencing. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:4927-41. [PMID: 21791436 PMCID: PMC3193005 DOI: 10.1093/jxb/err188] [Citation(s) in RCA: 150] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2011] [Revised: 05/10/2011] [Accepted: 05/13/2011] [Indexed: 05/19/2023]
Abstract
The inactivation of starch branching IIb (SBEIIb) in rice is traditionally associated with elevated apparent amylose content, increased peak gelatinization temperature, and a decreased proportion of short amylopectin branches. To elucidate further the structural and functional role of this enzyme, the phenotypic effects of down-regulating SBEIIb expression in rice endosperm were characterized by artificial microRNA (amiRNA) and hairpin RNA (hp-RNA) gene silencing. The results showed that RNA silencing of SBEIIb expression in rice grains did not affect the expression of other major isoforms of starch branching enzymes or starch synthases. Structural analyses of debranched starch showed that the doubling of apparent amylose content was not due to an increase in the relative proportion of amylose chains but instead was due to significantly elevated levels of long amylopectin and intermediate chains. Rices altered by the amiRNA technique produced a more extreme starch phenotype than those modified using the hp-RNA technique, with a greater increase in the proportion of long amylopectin and intermediate chains. The more pronounced starch structural modifications produced in the amiRNA lines led to more severe alterations in starch granule morphology and crystallinity as well as digestibility of freshly cooked grains. The potential role of attenuating SBEIIb expression in generating starch with elevated levels of resistant starch and lower glycaemic index is discussed.
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Affiliation(s)
- Vito M. Butardo
- CSIRO Food Futures Flagship, GPO Box 93, North Ryde, NSW 1670, Australia
- CSIRO Plant Industry, GPO Box 1600, ACT 2601, Australia
- Grain Quality and Nutrition Centre, International Rice Research Institute, Los Baños, Laguna 4031, Philippines
- Centre for Nutrition and Food Sciences, University of Queensland, Brisbane, Qld 4072, Australia
| | - Melissa A. Fitzgerald
- Grain Quality and Nutrition Centre, International Rice Research Institute, Los Baños, Laguna 4031, Philippines
| | - Anthony R. Bird
- CSIRO Food Futures Flagship, GPO Box 93, North Ryde, NSW 1670, Australia
- CSIRO Food and Nutritional Sciences, PO Box 10041, Adelaide SA 5000, Australia
| | - Michael J. Gidley
- Centre for Nutrition and Food Sciences, University of Queensland, Brisbane, Qld 4072, Australia
| | - Bernadine M. Flanagan
- Centre for Nutrition and Food Sciences, University of Queensland, Brisbane, Qld 4072, Australia
| | - Oscar Larroque
- CSIRO Food Futures Flagship, GPO Box 93, North Ryde, NSW 1670, Australia
- CSIRO Plant Industry, GPO Box 1600, ACT 2601, Australia
| | - Adoracion P. Resurreccion
- Grain Quality and Nutrition Centre, International Rice Research Institute, Los Baños, Laguna 4031, Philippines
| | - Hunter K. C. Laidlaw
- CSIRO Food Futures Flagship, GPO Box 93, North Ryde, NSW 1670, Australia
- CSIRO Plant Industry, GPO Box 1600, ACT 2601, Australia
| | - Stephen A. Jobling
- CSIRO Food Futures Flagship, GPO Box 93, North Ryde, NSW 1670, Australia
- CSIRO Plant Industry, GPO Box 1600, ACT 2601, Australia
| | - Matthew K. Morell
- CSIRO Food Futures Flagship, GPO Box 93, North Ryde, NSW 1670, Australia
- CSIRO Plant Industry, GPO Box 1600, ACT 2601, Australia
| | - Sadequr Rahman
- CSIRO Food Futures Flagship, GPO Box 93, North Ryde, NSW 1670, Australia
- CSIRO Plant Industry, GPO Box 1600, ACT 2601, Australia
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8
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Bresolin NS, Li Z, Kosar-Hashemi B, Tetlow IJ, Chatterjee M, Rahman S, Morell MK, Howitt CA. Characterisation of disproportionating enzyme from wheat endosperm. PLANTA 2006; 224:20-31. [PMID: 16333636 DOI: 10.1007/s00425-005-0187-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2005] [Accepted: 11/15/2005] [Indexed: 05/05/2023]
Abstract
Disproportionating enzyme or D-enzyme (EC 2.4.1.25) is an alpha-1,4 glucanotransferase which catalyses cleavage and transfer reactions involving alpha-1,4 linked glucans altering (disproportionating) the chain length distribution of pools of oligosaccharides. While D-enzyme has been well characterised in some plants, e.g. potato and Arabidopsis, very little is known about its abundance and function in cereals which constitute the major source of starch worldwide. To address this we have investigated D-enzyme in wheat (Triticum aestivum). Two putative D-enzyme cDNA clones have been isolated from tissue-specific cDNA libraries. TaDPE1-e, from an endosperm cDNA library, encodes a putative polypeptide of 575 amino acid residues including a predicted transit peptide of 41 amino acids. The second cDNA clone, TaDPE1-l, from an Aegilops taushii leaf cDNA library, encodes a putative polypeptide of 579 amino acids including a predicted transit peptide of 45 amino acids. The mature polypeptides TaDPE1-e and TaDPE1-l were calculated to be 59 and 60 kDa, respectively, and had 96% identity. The putative polypeptides had significant identity with deduced D-enzyme sequences from corn and rice, and all the expected conserved residues were present. Protein analysis revealed that D-enzyme is present in the amyloplast of developing endosperm and in the germinating seeds. D-enzyme was partially purified from wheat endosperm and shown to exhibit disproportionating activity in vitro by cleaving maltotriose to produce glucose as well as being able to use maltoheptaose as the donor for the addition of glucans to the outer chains of glycogen and amylopectin.
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9
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Hayashi A, Saito T, Mukai Y, Kurita S, Hori TA. Genetic variations in Lycoris radiata var. radiata in Japan. Genes Genet Syst 2006; 80:199-212. [PMID: 16172532 DOI: 10.1266/ggs.80.199] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The genetic variations of Lycoris radiata var. radiata, a completely sterile triploid from Japan, were examined by comparing the nucleotide sequences of genomic DNA regions in 11 triploid strains sampled from Japan and four triploid strains sampled from China, and in two diploid strains of Lycoris radiata var. pumila, which is endemic to China and fertile. For this purpose, two genes were analyzed, the lectin gene in the nuclear genome and the maturase gene in the chloroplast genome. A clear genetic constancy was observed in their DNA nucleotide sequences. For both genes, completely identical nucleotide sequences were detected in the 11 Japanese and four Chinese triploid strains and also between the two Chinese diploid strains. However, some genetic variations were observed between the Japanese and Chinese triploid strains, and between the triploid and diploid strains. These results are consistent with the findings obtained from previous chromosome karyotype analyses and allozyme analyses. In addition, in our preliminary FISH analysis of the physical mapping of the rRNA gene family, the 18S-5.8S-26S rRNA and 5S rRNA loci were localized on six and four chromosomes, respectively. Regarding the 18S-5.8S-26S rRNA loci, two were associated with two SAT chromosomes. The remaining four were distinguished by having no secondary constriction. Localization of 5S rRNA loci to chromosome spreads revealed three sites on the proximal part of the long arm of three acrocentric chromosomes and one site on the distal part of the long arm of the SAT chromosome; the latter site was juxtaposed to the 18S-5.8S-26S rRNA loci. These findings indicate that L. radiata var. radiata is not a typical autotriploid. The present paper discusses the possible origin of L. radiata var. radiata from a diploid variety of L. radiata var. pumila, based on the molecular cytogenetic analysis and DNA sequence analysis.
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Affiliation(s)
- Akiko Hayashi
- Transcriptome Profiling Group, National Institute of Radiological Sciences, Chiba, Japan
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10
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Regina A, Kosar-Hashemi B, Li Z, Pedler A, Mukai Y, Yamamoto M, Gale K, Sharp PJ, Morell MK, Rahman S. Starch branching enzyme IIb in wheat is expressed at low levels in the endosperm compared to other cereals and encoded at a non-syntenic locus. PLANTA 2005; 222:899-909. [PMID: 16172866 DOI: 10.1007/s00425-005-0032-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2005] [Accepted: 06/02/2005] [Indexed: 05/04/2023]
Abstract
Studies of maize starch branching enzyme mutants suggest that the amylose extender high amylose starch phenotype is a consequence of the lack of expression of the predominant starch branching enzyme II isoform expressed in the endosperm, SBEIIb. However, in wheat, the ratio of SBEIIb and SBEIIa expression are inversely related to the expression levels observed in maize and rice. Analysis of RNA at 15 days post anthesis suggests that there are about 4-fold more RNA for SBE IIa than for SBE IIb. The genes for SBE IIa and SBE IIb from wheat are distinguished in the size of the first three exons, allowing isoform-specific antibodies to be produced. These antibodies were used to demonstrate that in the soluble fraction, the amount of SBE IIa protein is two to three fold higher than SBIIb, whereas in the starch granule, there is two to three fold more SBE IIb protein amount than SBE IIa. In a further difference to maize and rice, the genes for SBE IIa and SBE IIb are both located on the long arm of chromosome 2 in wheat, in a position not expected from rice-maize-wheat synteny.
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MESH Headings
- 1,4-alpha-Glucan Branching Enzyme/genetics
- 1,4-alpha-Glucan Branching Enzyme/metabolism
- Amino Acid Sequence
- Base Sequence
- Chromosome Mapping
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- DNA, Plant/genetics
- DNA, Plant/isolation & purification
- Edible Grain/enzymology
- Edible Grain/genetics
- Gene Expression
- Genes, Plant
- In Situ Hybridization, Fluorescence
- Isoenzymes/genetics
- Isoenzymes/metabolism
- Molecular Sequence Data
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Sequence Homology, Amino Acid
- Species Specificity
- Triticum/enzymology
- Triticum/genetics
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Affiliation(s)
- Ahmed Regina
- Commonwealth Scientific and Industrial Research Organisation, Plant Industry, P.O. Box 1600, Australian Capital Territory, 2601, Australia
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11
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Vitte C, Panaud O. LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model. Cytogenet Genome Res 2005; 110:91-107. [PMID: 16093661 DOI: 10.1159/000084941] [Citation(s) in RCA: 180] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2003] [Accepted: 04/14/2004] [Indexed: 12/11/2022] Open
Abstract
Long Terminal Repeat (LTR) retrotransposons are ubiquitous components of plant genomes. Because of their copy-and-paste mode of transposition, these elements tend to increase their copy number while they are active. In addition, it is now well established that the differences in genome size observed in the plant kingdom are accompanied by variations in LTR retrotransposon content, suggesting that LTR retrotransposons might be important players in the evolution of plant genome size, along with polyploidy. The recent availability of large genomic sequences for many crop species has made it possible to examine in detail how LTR retrotransposons actually drive genomic changes in plants. In the present paper, we provide a review of the recent publications that have contributed to the knowledge of plant LTR retrotransposons, as structural components of the genomes, as well as from an evolutionary genomic perspective. These studies have shown that plant genomes undergo genome size increases through bursts of retrotransposition, while there is a counteracting process that tends to eliminate the transposed copies from the genomes. This process involves recombination mechanisms that occur either between the LTRs of the elements, leading to the formation of solo-LTRs, or between direct repeats anywhere in the sequence of the element, leading to internal deletions. All these studies have led to the emergence of a new model for plant genome evolution that takes into account both genome size increases (through retrotransposition) and decreases (through solo-LTR and deletion formation). In the conclusion, we discuss this new model and present the future prospects in the study of plant genome evolution in relation to the activity of transposable elements.
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Affiliation(s)
- C Vitte
- Laboratoire Ecologie, Systématique et Evolution, Université Paris-Sud, Orsay, France
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12
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Yamamoto M, Mukai Y. High-resolution physical mapping of the secalin-1 locus of rye on extended DNA fibers. Cytogenet Genome Res 2005; 109:79-82. [PMID: 15753562 DOI: 10.1159/000082385] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2003] [Accepted: 01/22/2004] [Indexed: 11/19/2022] Open
Abstract
High-resolution mapping of secalin-1 (Sec-1) locus has been performed by fluorescence in situ hybridization to extended DNA fibers of rye (Secale cereale, 2n = 14), employing DNA probes of lambda phage clones containing the omega-secalin gene. The fluorescent signals to rye extended DNA fibers revealed continuous strings of 45 microm, corresponding to the size of 147 kb DNA. To determine the copy number of Sec-1 locus on DNA fibers, a 1.2-kb fragment including the entire coding region of the omega-secalin gene and a 1.0-kb fragment of the promoter region were amplified by PCR as probes for another fiber FISH. The physical position of these sequences was visualized as alternating fluorescent spots by multicolor in situ hybridization. Alternating signals of two DNA probes reflected the tandem repeated organization of the Sec-1 locus having 15 copies of the gene. The present findings based on fiber FISH analysis support the contention that the omega-secalin genes are arranged in a head-to-tail fashion separated by 8 kb of spacer sequences with a total length of 145 kb.
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Affiliation(s)
- M Yamamoto
- Kansai University of Welfare Sciences, Osaka, Japan
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13
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Sabot F, Guyot R, Wicker T, Chantret N, Laubin B, Chalhoub B, Leroy P, Sourdille P, Bernard M. Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations. Mol Genet Genomics 2005; 274:119-30. [PMID: 16034625 DOI: 10.1007/s00438-005-0012-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2005] [Accepted: 05/07/2005] [Indexed: 11/29/2022]
Abstract
Triticeae species (including wheat, barley and rye) have huge and complex genomes due to polyploidization and a high content of transposable elements (TEs). TEs are known to play a major role in the structure and evolutionary dynamics of Triticeae genomes. During the last 5 years, substantial stretches of contiguous genomic sequence from various species of Triticeae have been generated, making it necessary to update and standardize TE annotations and nomenclature. In this study we propose standard procedures for these tasks, based on structure, nucleic acid and protein sequence homologies. We report statistical analyses of TE composition and distribution in large blocks of genomic sequences from wheat and barley. Altogether, 3.8 Mb of wheat sequence available in the databases was analyzed or re-analyzed, and compared with 1.3 Mb of re-annotated genomic sequences from barley. The wheat sequences were relatively gene-rich (one gene per 23.9 kb), although wheat gene-derived sequences represented only 7.8% (159 elements) of the total, while the remainder mainly comprised coding sequences found in TEs (54.7%, 751 elements). Class I elements [mainly long terminal repeat (LTR) retrotransposons] accounted for the major proportion of TEs, in terms of sequence length as well as element number (83.6% and 498, respectively). In addition, we show that the gene-rich sequences of wheat genome A seem to have a higher TE content than those of genomes B and D, or of barley gene-rich sequences. Moreover, among the various TE groups, MITEs were most often associated with genes: 43.1% of MITEs fell into this category. Finally, the TRIM and copia elements were shown to be the most active TEs in the wheat genome. The implications of these results for the evolution of diploid and polyploid wheat species are discussed.
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Affiliation(s)
- François Sabot
- UMR 1095 INRA/UBP Amélioration et Santé des Plantes, 234 Avenue du Brézet, 63100 Clermont-Ferrand Cedex, France
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14
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Suzuki G, Tanaka S, Yamamoto M, Tomita RN, Kowyama Y, Mukai Y. Visualization of the S-locus region in Ipomoea trifida: toward positional cloning of self-incompatibility genes. Chromosome Res 2005; 12:475-81. [PMID: 15252243 DOI: 10.1023/b:chro.0000034749.58877.b7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Self-incompatibility (SI) in Ipomoea trifida is regulated by a single S locus with multiple alleles. Identification of SI genes in the S -locus region by positional cloning is one of the most important goals for understanding sexual reproduction in this species. Despite our intensive efforts to construct bacterial artificial chromosome (BAC) contigs covering the S -locus region, a gap was observed in the core region of the potential S locus. In order to confirm the physical linkage of two non-overlapping BAC contigs in the S -locus region and to determine the size of the gap between them, fluorescence in-situ hybridization (FISH) was performed on mitotic chromosomes and extended DNA fibres using previously isolated S -linked BAC clones as probes. The information obtained from this work would be useful for molecular cloning of the SI genes by a chromosome walking approach. In addition, we showed that strong suppression of recombination in the S locus was not related to the centromere because the S locus was mapped to one end of a chromosome.
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Affiliation(s)
- Go Suzuki
- Division of Natural Science, Osaka Kyoiku University, 4-698-1 Asahigaoka, Kashiwara, Osaka 582-8582, Japan
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15
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Kellogg EA, Bennetzen JL. The evolution of nuclear genome structure in seed plants. AMERICAN JOURNAL OF BOTANY 2004; 91:1709-25. [PMID: 21652319 DOI: 10.3732/ajb.91.10.1709] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Plant nuclear genomes exhibit extensive structural variation in size, chromosome number, number and arrangement of genes, and number of genome copies per nucleus. This variation is the outcome of a set of highly active processes, including gene duplication and deletion, chromosomal duplication followed by gene loss, amplification of retrotransposons separating genes, and genome rearrangement, the latter often following hybridization and/or polyploidy. While these changes occur continuously, it is not surprising that some of them should be fixed evolutionarily and come to mark major clades. Large-scale duplications pre-date the radiation of Brassicaceae and Poaceae and correlate with the origin of many smaller clades as well. Nuclear genomes are largely colinear among closely related species, but more rearrangements are observed with increasing phylogenetic distance; however, the correlation between amount of rearrangement and time since divergence is not perfect. By changing patterns of gene expression and triggering genome rearrangements, novel combinations of genomes (hybrids) may be a driving force in evolution.
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Affiliation(s)
- Elizabeth A Kellogg
- Department of Biology, University of Missouri-St. Louis, One University Boulevard, St. Louis, Missouri 63121 USA
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16
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Regina A, Kosar-Hashemi B, Li Z, Rampling L, Cmiel M, Gianibelli MC, Konik-Rose C, Larroque O, Rahman S, Morell MK. Multiple isoforms of starch branching enzyme-I in wheat: lack of the major SBE-I isoform does not alter starch phenotype. FUNCTIONAL PLANT BIOLOGY : FPB 2004; 31:591-601. [PMID: 32688931 DOI: 10.1071/fp03193] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2003] [Accepted: 03/17/2004] [Indexed: 05/27/2023]
Abstract
The role of starch branching enzyme-I (SBE-I) in determining starch structure in the endosperm has been investigated. Null mutations of SBE-I at the A, B and D genomes of wheat were identified in Australian wheat varieties by immunoblotting. By combining individual null mutations at the B and D genomes through hybridisation, a double-null mutant wheat, which lacks the B and D isoforms of SBE-I, was developed. Wheat mutants lacking all the three isoforms of SBE-I were generated from a doubled haploid progeny of a cross between the BD double-null mutant line and a Chinese Spring (CS) deletion line lacking the A genome isoform. Comparison of starch from this mutant wheat to that from wild type revealed no substantial alteration in any of the structural or functional properties analysed. Further analysis of this triple-null mutant line revealed the presence of another residual peak of SBE-I activity, referred to as SBE-Ir, in wheat endosperm representing < 3% of the activity of SBE-I in wild type endosperm.
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Affiliation(s)
- Ahmed Regina
- CSIRO Division of Plant Industry, PO Box 1600, Canberra, ACT 2601, Australia
| | | | - Zhongyi Li
- CSIRO Division of Plant Industry, PO Box 1600, Canberra, ACT 2601, Australia
| | - Lynette Rampling
- CSIRO Division of Plant Industry, PO Box 1600, Canberra, ACT 2601, Australia
| | - Mark Cmiel
- CSIRO Division of Plant Industry, PO Box 1600, Canberra, ACT 2601, Australia
| | - Maria C Gianibelli
- CSIRO Division of Plant Industry, PO Box 1600, Canberra, ACT 2601, Australia
| | | | - Oscar Larroque
- CSIRO Division of Plant Industry, PO Box 1600, Canberra, ACT 2601, Australia
| | - Sadequr Rahman
- CSIRO Division of Plant Industry, PO Box 1600, Canberra, ACT 2601, Australia
| | - Matthew K Morell
- CSIRO Division of Plant Industry, PO Box 1600, Canberra, ACT 2601, Australia
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17
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Cenci A, Chantret N, Kong X, Gu Y, Anderson OD, Fahima T, Distelfeld A, Dubcovsky J. Construction and characterization of a half million clone BAC library of durum wheat ( Triticum turgidum ssp. durum). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2003; 107:931-9. [PMID: 12830387 DOI: 10.1007/s00122-003-1331-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2002] [Accepted: 03/14/2003] [Indexed: 05/21/2023]
Abstract
Durum wheat ( Triticum turgidum ssp. durum, 2 n = 4 x = 28, genomes AB) is an economically important cereal used as the raw material to make pasta and semolina. In this paper we present the construction and characterization of a bacterial artificial chromosome (BAC) library of tetraploid durum wheat cv. Langdon. This variety was selected because of the availability of substitution lines that facilitate the assignment of BACs to the A and B genome. The selected Langdon line has a 30-cM segment of chromosome 6BS from T. turgidum ssp. dicoccoides carrying a gene for high grain protein content, the target of a positional cloning effort in our laboratory. A total of 516,096 clones were organized in 1,344 384-well plates and blotted on 28 high-density filters. Ninety-eight percent of these clones had wheat DNA inserts (0.3% chloroplast DNA, 1.4% empty clones and 0.3% empty wells). The average insert size of 500 randomly selected BAC clones was 131 kb, resulting in a coverage of 5.1-fold genome equivalents for each of the two genomes, and a 99.4% probability of recovering any gene from each of the two genomes of durum wheat. Six known copy-number probes were used to validate this theoretical coverage and gave an estimated coverage of 5.8-fold genome equivalents. Screening of the library with 11 probes related to grain storage proteins and starch biosynthesis showed that the library contains several clones for each of these genes, confirming the value of the library in characterizing the organization of these important gene families. In addition, characterization of fingerprints from colinear BACs from the A and B genomes showed a large differentiation between the A and B genomes. This library will be a useful tool for evolutionary studies in one of the best characterized polyploid systems and a source of valuable genes for wheat. Clones and high-density filters can be requested at http://agronomy.ucdavis.edu/Dubcovsky/BAC-library/BAC_Langdon.htm
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Affiliation(s)
- A Cenci
- Department of Agronomy and Range Science, University of California, One Shields Avenue, Davis, CA 95616-8515, USA
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18
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Rahman S, Nakamura Y, Li Z, Clarke B, Fujita N, Mukai Y, Yamamoto M, Regina A, Tan Z, Kawasaki S, Morell M. The sugary-type isoamylase gene from rice and Aegilops tauschii: characterization and comparison with maize and arabidopsis. Genome 2003; 46:496-506. [PMID: 12834068 DOI: 10.1139/g02-130] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genes for an isoamylase-like debranching enzyme have been isolated from rice and Aegilops tauschii, the donor of the D genome to wheat. The structures of the genes are very similar to each other and to the maize SU1 isoamylase gene and consist of 18 exons spread over approximately 7.5 kb. Southern analysis and fluorescent in situ hybridization showed the Ae. tauschii gene to be located in the proximal region of the short arm of chromosome 7D, thus showing synteny with the localization of the rice isoamylase gene on rice chromosome 8. Analysis of the expression pattern of wheat sugary isoamylase genes indicates that they are strongly expressed in the developing endosperm 6 days after flowering. Three distinct Sugary-type cDNA sequences were isolated from the wheat endosperm that are likely to correspond to the products of the three genomes. The deduced amino acid sequence of rice and wheat Sugary-type isoamylase is compared with other sequences available in the database and the results demonstrate that there are three types of isoamylase sequences in plants: those containing 18 exons (the Sugary-type isoamylase gene), those containing 21 exons, and those containing only 1 exon. It is possible that different combinations of isoamylase genes are expressed in different tissues.
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Affiliation(s)
- S Rahman
- CSIRO Plant Industry, PO Box 1600, ACT 2601, Australia.
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19
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Turnbull KM, Turner M, Mukai Y, Yamamoto M, Morell MK, Appels R, Rahman S. The organization of genes tightly linked to the Ha locus in Aegilops tauschii, the D-genome donor to wheat. Genome 2003; 46:330-8. [PMID: 12723049 DOI: 10.1139/g02-124] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The grain hardness locus, Ha, is located at the distal end of the short arm of chromosome 5D in wheat. Three polypeptides, puroindoline-a, puroindoline-b, and grain softness protein (GSP-1), have been identified as components of friabilin, a biochemical marker for grain softness, and the genes for these polypeptides are known to be tightly linked to the Ha locus. However, this region of the chromosome 5D has not been well characterized and the physical distance between the markers is not known. Separate lambda clones containing the puroindoline-a gene and the puroindoline-b gene have been isolated from an Aegilops tauschii (the donor of the D genome to wheat) genomic lambda library and investigated. Considerable variation appears to exist in the organization of the region upstream of the gene for puroindoline-b among species closely related to wheat. Using in situ hybridization the genes for puroindoline-a, -b, and GSP-1 were demonstrated to be physically located at the tip of the short arm of chromosome 5 of A. tauschii. Four overlapping clones were isolated from a large-insert BAC library constructed from A. tauschii and of these one contained genes for all of puroindoline-a, puroindoline-b, and GSP-1. The gene for puroindoline-a is located between the other two genes at a distance no greater than approximately 30 kb from either gene. The BAC clone containing all three known genes was used to screen a cDNA library constructed from hexaploid wheat and cDNAs that could encode novel polypeptides were isolated.
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Affiliation(s)
- K M Turnbull
- CSIRO Plant Industry, P.O. Box 1600, ACT 2601, Australia
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20
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Abstract
Comparison of partially sequenced cereal genomes suggests a mosaic structure consisting of recombinationally active gene-rich islands that are separated by blocks of high-copy DNA. Annotation of the whole rice genome suggests that most, but not all, cereal genes are present within the rice genome and that the high number of reported genes in this genome is probably due to duplications. Within the cereals, macrocolinearity is conserved but, at the level of individual genes, microcolinearity is frequently disrupted. Preliminary evidence from limited comparative analysis of sequenced orthologous genomic segments suggests that local gene amplification and translocation within a plant genome may be linked in some cases.
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Affiliation(s)
- Doreen Ware
- Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.
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21
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Suzuki G, Ura A, Saito N, Do GS, Seo BB, Yamamoto M, Mukai Y. BAC FISH analysis in Allium cepa. Genes Genet Syst 2001; 76:251-5. [PMID: 11732634 DOI: 10.1266/ggs.76.251] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Onion (Allium cepa L.; 1C=15,000 Mb) is an agriculturally important plant. The genome of onion has been extensively studied at the conventional cytogenetic level, but molecular analyses have lagged behind due to its large genome size. To overcome this bottleneck, a partial bacterial artificial chromosome (BAC) library of onion was constructed. The average insert size of the BAC library was about 100 kb. A total of 48,000 clones, corresponding to 0.32 genome equivalent, were obtained. Fluorescent in situ hybridization (FISH) screening resulted in identification of BAC clones localized on centromeric, telomeric, or several limited interstitial chromosomal regions, although most of the clones hybridized with entire chromosomes. The partial BAC library proved to be a useful resource for molecular cytogenetic studies of onion, and should be useful for further mapping and sequencing studies of important genes of this plant. BAC FISH screening is a powerful method for identification of molecular cytogenetic markers in large-genome plants.
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Affiliation(s)
- G Suzuki
- Division of Natural Science, Osaka Kyoiku University, Kashiwara, Japan.
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22
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Rahman S, Regina A, Li Z, Mukai Y, Yamamoto M, Kosar-Hashemi B, Abrahams S, Morell MK. Comparison of starch-branching enzyme genes reveals evolutionary relationships among isoforms. Characterization of a gene for starch-branching enzyme IIa from the wheat genome donor Aegilops tauschii. PLANT PHYSIOLOGY 2001; 125:1314-24. [PMID: 11244112 PMCID: PMC65611 DOI: 10.1104/pp.125.3.1314] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2000] [Accepted: 12/20/2000] [Indexed: 05/20/2023]
Abstract
Genes and cDNAs for starch-branching enzyme II (SBEII) have been isolated from libraries constructed from Aegilops tauschii and wheat (Triticum aestivum) endosperm, respectively. One class of genes has been termed wSBEII-DA1 and encodes the N terminus reported for an SBEII from wheat endosperm. On the basis of phylogenetic comparisons with other branching enzyme sequences, wSBEII-DA1 is considered to be a member of the SBEIIa class. The wSBEII-DA1 gene consists of 22 exons with exons 4 to 21 being identical in length to the maize (Zea mays) SBEIIb gene, and the gene is located in the proximal region of the long arm of chromosome 2 at a locus designated sbe2a. RNA encoding SBEIIa can be detected in the endosperm from 6 d after flowering and is at its maximum level from 15 to 18 d after anthesis. Use of antibodies specific for SBEIIa demonstrated that this protein was present in both the soluble and granule bound fractions in developing wheat endosperm. We also report a cDNA sequence for SBEIIa that could arise by variant transcription/splicing. A second gene, termed wSBEII-DB1, was isolated and encodes an SBEII, which shows greater sequence identity with SBEIIb-type sequences than with SBEIIa-type sequences. Comparisons of SBEII gene structures among wheat, maize, and Arabidopsis indicate the lineage of the SBEII genes.
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Affiliation(s)
- S Rahman
- Commonwealth Scientific and Industrial Research Organization Plant Industry, P.O. Box 1600, Australian Capital Territory 2601, Australia.
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23
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Fukui KN, Suzuki G, Lagudah ES, Rahman S, Appels R, Yamamoto M, Mukai Y. Physical arrangement of retrotransposon-related repeats in centromeric regions of wheat. PLANT & CELL PHYSIOLOGY 2001; 42:189-96. [PMID: 11230573 DOI: 10.1093/pcp/pce026] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cereal centromeres commonly contain many repetitive sequences that are derived from Ty3/gypsy retrotransposon. FISH analysis using a large DNA insert library of wheat identified a 67-kb clone (R11H) that showed strong hybridization signals on the centromeres. The R11H clone contains Ty3/gypsy retrotransposon-related sequences; both integrase and CCS1 family sequences were identified. Subsequently, we isolated additional 23 large-insert clones which also contained the integrase and CCS1 sequences. Based on the number of the integrase repeats in the clones determined by DNA gel blot analysis, we concluded that the retrotransposon-like sequences are tandemly repeated in wheat centromeres in ca. 55-kb interval on average. This conclusion is consistent with the results of FISH analysis on the extended DNA fibers.
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Affiliation(s)
- K N Fukui
- Division of Natural Science, Osaka Kyoiku University, Kashiwara, 582-8582 Japan
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24
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Båga M, Nair RB, Repellin A, Scoles GJ, Chibbar RN. Isolation of a cDNA encoding a granule-bound 152-kilodalton starch-branching enzyme in wheat. PLANT PHYSIOLOGY 2000; 124:253-63. [PMID: 10982440 PMCID: PMC59140 DOI: 10.1104/pp.124.1.253] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2000] [Accepted: 05/17/2000] [Indexed: 05/21/2023]
Abstract
Screening of a wheat (Triticum aestivum) cDNA library for starch-branching enzyme I (SBEI) genes combined with 5'-rapid amplification of cDNA ends resulted in isolation of a 4,563-bp composite cDNA, Sbe1c. Based on sequence alignment to characterized SBEI cDNA clones isolated from plants, the SBEIc predicted from the cDNA sequence was produced with a transit peptide directing the polypeptide into plastids. Furthermore, the predicted mature form of SBEIc was much larger (152 kD) than previously characterized plant SBEI (80-100 kD) and contained a partial duplication of SBEI sequences. The first SBEI domain showed high amino acid similarity to a 74-kD wheat SBEI-like protein that is inactive as a branching enzyme when expressed in Escherichia coli. The second SBEI domain on SBEIc was identical in sequence to a functional 87-kD SBEI produced in the wheat endosperm. Immunoblot analysis of proteins produced in developing wheat kernels demonstrated that the 152-kD SBEIc was, in contrast to the 87- to 88-kD SBEI, preferentially associated with the starch granules. Proteins similar in size and recognized by wheat SBEI antibodies were also present in Triticum monococcum, Triticum tauschii, and Triticum turgidum subsp. durum.
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Affiliation(s)
- M Båga
- Plant Biotechnology Institute, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, Saskatchewan, Canada S7N 0W9
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25
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Peng M, Gao M, Båga M, Hucl P, Chibbar RN. Starch-branching enzymes preferentially associated with A-type starch granules in wheat endosperm. PLANT PHYSIOLOGY 2000; 124:265-72. [PMID: 10982441 PMCID: PMC59141 DOI: 10.1104/pp.124.1.265] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2000] [Accepted: 05/17/2000] [Indexed: 05/21/2023]
Abstract
Two starch granule-bound proteins (SGP), SGP-140 and SGP-145, were preferentially associated with A-type starch granules (>10 microm) in developing and mature wheat (Triticum aestivum) kernels. Immunoblotting and N-terminal sequencing suggested that the two proteins were different variants of SBEIc, a 152-kD isoform of wheat starch-branching enzyme. Both SGP-140 and SGP-145 were localized to the endosperm starch granules but were not found in the endosperm soluble fraction or pericarp starch granules younger than 15 d post anthesis (DPA). Small-size starch granules (<10 microm) initiated before 15 DPA incorporated SGP-140 and SGP-145 throughout endosperm development and grew into full-size A-type starch granules (>10 microm). In contrast, small-size starch granules harvested after 15 DPA contained only low amounts of SGP-140 and SGP-145 and developed mainly into B-type starch granules (<10 microm). Polypeptides of similar mass and immunologically related to SGP-140 and/or SGP-145 were also preferentially incorporated into A-type starch granules of barley (Hordeum vulgare), rye (Secale cereale), and triticale (x Triticosecale Wittmack) endosperm, which like wheat endosperm have a bimodal starch granule size distribution.
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Affiliation(s)
- M Peng
- Plant Biotechnology Institute, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, Saskatchewan, Canada S7N 0W9
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26
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Abstract
Grasses are the single most important plant family in agriculture. In the past years, comparative genetic mapping has revealed conserved gene order (colinearity) among many grass species. Recently, the first studies at gene level have demonstrated that microcolinearity of genes is less conserved: small scale rearrangements and deletions complicate the microcolinearity between closely related species, such as sorghum and maize, but also between rice and other crop plants. In spite of these problems, rice remains the model plant for grasses as there is limited useful colinearity between Arabidopsis and grasses. However, studies in rice have to be complemented by more intensive genetic work on grass species with large genomes (maize, Triticeae). Gene-rich chromosomal regions in species with large genomes, such as wheat, have a high gene density and are ideal targets for partial genome sequencing.
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Affiliation(s)
- B Keller
- Dept of Plant Molecular Biology, University of Zürich, Switzerland.
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27
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Li Z, Mouille G, Kosar-Hashemi B, Rahman S, Clarke B, Gale KR, Appels R, Morell MK. The structure and expression of the wheat starch synthase III gene. Motifs in the expressed gene define the lineage of the starch synthase III gene family. PLANT PHYSIOLOGY 2000; 123:613-24. [PMID: 10859191 PMCID: PMC59029 DOI: 10.1104/pp.123.2.613] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/1999] [Accepted: 02/21/2000] [Indexed: 05/18/2023]
Abstract
The endosperm of hexaploid wheat (Triticum aestivum [L.]) was shown to contain a high molecular weight starch synthase (SS) analogous to the product of the maize du1 gene, starch synthase III (SSIII; DU1). cDNA and genomic DNA sequences encoding wheat SSIII were isolated and characterized. The wheat SSIII cDNA is 5,346 bp long and contains an open reading frame that encodes a 1,628-amino acid polypeptide. A putative N-terminal transit peptide, a 436-amino acid C-terminal catalytic domain, and a central 470-amino acid SSIII-specific domain containing three regions of repeated amino acid similarity were identified in the wheat gene. A fourth region between the transit peptide and the SSIII-specific domain contains repeat motifs that are variable with respect to motif sequence and repeat number between wheat and maize. In dicots, this N-terminal region does not contain repeat motifs and is truncated. The gene encoding wheat SSIII, designated ss3, consists of 16 exons extending over 10 kb, and is located on wheat chromosome I. Expression of ss3 mRNA in wheat was detected in leaves, pre-anthesis florets, and from very early to middle stage of endosperm development. The entire N-terminal variable repeat region and the majority of the SSIII-specific domain are encoded on a single 2,703-bp exon. A gene encoding a class III SS from the Arabidopsis genome sequencing project shows a strongly conserved exon structure to the wheat ss3 gene, with the exception of the N-terminal region. The evolutionary relationships of the genes encoding monocot and dicot class III SSs are discussed.
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Affiliation(s)
- Z Li
- Commonwealth Scientific and Industrial Research Organization, Division of Plant Industry, Canberra, Australian Capital Territory
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28
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Yan L, Bhave M, Fairclough R, Konik C, Rahman S, Appels R. The genes encoding granule-bound starch synthases at the waxy loci of the A, B, and D progenitors of common wheat. Genome 2000; 43:264-72. [PMID: 10791814 DOI: 10.1139/g99-117] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Three genes encoding granule-bound starch synthase (wx-TmA, wx-TsB, and wx-TtD) have been isolated from Triticum monococcum (AA), and Triticum speltoides (BB), by the polymerase chain reaction (PCR) approach, and from Triticum tauschii (DD), by screening a genomic DNA library. Multiple sequence alignment indicated that the wx-TmA, wx-TsB, and wx-TtD genes had the same extron and (or) intron structure as the previously reported waxy gene from barley. The lengths of the three wx-TmA, wx-TsB, and wx-TtD genes were 2834 bp, 2826 bp, and 2893 bp, respectively, each covering 31 bp in the untranslated leader and the entire coding region consisting of 11 exons and 10 introns. The three genes had identical lengths of exons, except exonl, and shared over 95% identity with each other within the exon regions. The majority of introns were significantly variable in length and sequence, differing mainly in length (1-57 bp) as a result of insertion and (or) deletion events. The deduced amino acid sequence from these three genes indicated that the mature WX-TMA, -TSB, and -TTD proteins contained the same number of amino acids, but differed in predicted molecular weight and isoelectric point (pI) due to amino acid substitutions (13-18). The predicted physical characteristics of the WX proteins matched the respective proteins in wheat very closely, but the match was not perfect. Furthermore the exon5 sequences of the wx-TmA, wx-TsB, and wx-TtD genes were different from a cDNA encoding a waxy gene of common wheat previously reported. The striking difference was that an insertion of 11 amino acids occurred in the cDNA sequence that could not be observed in the exons of the A, B, and D genes. It was noted, however, that the 3' end of intron4 of these genes could account for the additional 11 amino acids. The sequence information from the available waxy genes identified the intron4-exon5-intron5 region as being diagnostic for sequence variation in waxy. The sequence variation in the waxy genes provides the basis for primer design to distinguish the respective genes in common wheat, and its progenitors, using PCR.
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Affiliation(s)
- L Yan
- School of Life Sciences and Technology, Victoria University of Technology, Melbourne, Australia
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29
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Vrinten PL, Nakamura T. Wheat granule-bound starch synthase I and II are encoded by separate genes that are expressed in different tissues. PLANT PHYSIOLOGY 2000; 122:255-64. [PMID: 10631269 PMCID: PMC58864 DOI: 10.1104/pp.122.1.255] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/1999] [Accepted: 10/06/1999] [Indexed: 05/18/2023]
Abstract
Studies of waxy mutations in wheat and other cereals have shown that null mutations in genes encoding granule-bound starch synthase I (GBSSI) result in amylose-free starch in endosperm and pollen grains, whereas starch in other tissues may contain amylose. We have isolated a cDNA from waxy wheat that encodes GBSSII, which is thought to be responsible for the elongation of amylose chains in non-storage tissues. The deduced amino acid sequences of wheat GBSSI and GBSSII were almost 66% identical, while those of wheat GBSSII and potato GBSSI were 72% identical. GBSSII was expressed in leaf, culm, and pericarp tissue, but transcripts were not detected in endosperm tissue. In contrast, GBSSI expression was high in endosperm tissue. The expression of GBSSII mRNA in pericarp tissue was similar at the midpoints of the day and night periods. The GBSSII genes were mapped to chromosomes 2AL, 2B, and 2D, whereas GBSSI genes are located on group 7 chromosomes. Gel-blot analysis indicated that genes related to GBSSII also occur in barley, rice, and maize. The possible role of GBSSII in starch synthesis is discussed.
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Affiliation(s)
- P L Vrinten
- Tohoku National Agricultural Experiment Station, Akahira 4, Morioka 020-0198, Japan
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30
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31
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Turner M, Mukai Y, Leroy P, Charef B, Appels R, Rahman S. The Ha locus of wheat: Identification of a polymorphic region for tracing grain hardness in crosses. Genome 1999. [DOI: 10.1139/g99-075] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The grain softness proteins or friabilins are known to be composed of three main components: puroindoline a, puroindoline b, and GSP-1. cDNAs for GSP-1 have previously been mapped to group-5 chromosomes and their location on chromosome 5D is closely linked to the grain hardness (Ha) locus of hexaploid wheat. A genomic DNA clone containing the GSP-1 gene (wGSP1-A1) from hexaploid wheat has been identified by fluorescent in situ hybridization as having originated from the distal end of the short arm of chromosome 5A. A genomic clone containing the gene (wGSP1-D1) was also isolated from Aegilops tauschii, the donor of the D genome to bread wheat. There are no introns in the GSP-1 genes, and there is high sequence identity between wGSP1-A1 and wGSP1-D1 up to 1 kb 5' and 300 bp 3' to wGSP1-D1. However, regions further upstream and downstream of wGSP1-D1 share no significant sequence identity to corresponding sequences in wGSP1-A1. These regions therefore identified potentially valuable sequences for tracing the Ha locus through assaying polymorphic DNA sequences. The sequence from 300 to 500 bp 3' to wGSP1-D1 (wGSP1-D13) was mapped to the Ha locus in a mapping population. wGSP1-D13 was also tightly linked to genes for puroindoline a and puroindoline b which have been previously mapped to be at the Ha locus. In addition wGSP1-D13 was used to detect RFLPs between near isogenic soft and hard Falcon lines and in a random selection of soft and hard wheats.Key words: wheat, grain hardness, chromosome 5, puroindoline, GSP-1.
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32
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Li Z, Chu X, Mouille G, Yan L, Kosar-Hashemi B, Hey S, Napier J, Shewry P, Clarke B, Appels R, Morell MK, Rahman S. The localization and expression of the class II starch synthases of wheat. PLANT PHYSIOLOGY 1999; 120:1147-56. [PMID: 10444098 PMCID: PMC59348 DOI: 10.1104/pp.120.4.1147] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/1999] [Accepted: 05/04/1999] [Indexed: 05/21/2023]
Abstract
The starch granules of hexaploid wheat (Triticum aestivum) contain a group of three proteins known as SGP-1 (starch granule protein-1) proteins, which have apparent molecular masses of 100, 108, and 115 kD. The nature and role of these proteins has not been defined previously. We demonstrate that these polypeptides are starch synthases that are present in both the starch granule and the soluble fraction at the early stages of wheat endosperm development, but that are exclusively granule bound at mid and late endosperm development. A partial cDNA clone encoding a fragment of the 100-kD protein was obtained by screening a wheat endosperm cDNA expression library using monoclonal antibodies. Three classes of cDNA were subsequently isolated from a wheat endosperm cDNA library by nucleic acid hybridization and were shown to encode the 100-, 108-, and 115-kD proteins. The cDNA sequences are highly homologous to class II starch synthases and have the highest homology with the maize SSIIa (starch synthase IIa) gene. mRNA for the SGP-1 proteins was detected in the leaf, pre-anthesis florets, and endosperm of wheat and is highly expressed in the leaf and in the grain during the early to mid stages of development. We discuss the roles of the SGP-1 proteins in starch biosynthesis in wheat.
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Affiliation(s)
- Z Li
- Commonwealth Scientific and Industrial Research Organization, Plant Industry, G.P.O. Box 1600, Canberra, Australian Capital Territory 2601, Australia
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33
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Feuillet C, Keller B. High gene density is conserved at syntenic loci of small and large grass genomes. Proc Natl Acad Sci U S A 1999; 96:8265-70. [PMID: 10393983 PMCID: PMC22223 DOI: 10.1073/pnas.96.14.8265] [Citation(s) in RCA: 174] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Comparative genomic analysis at the genetic-map level has shown extensive conservation of the gene order between the different grass genomes in many chromosomal regions. However, little is known about the gene organization in grass genomes at the microlevel. Comparison of gene-coding regions between maize, rice, and sorghum showed that the distance between the genes is correlated with the genome size. We have investigated the microcolinearity at Lrk gene loci in the genomes of four grass species: wheat, barley, maize, and rice. The Lrk genes, which encode receptor-like kinases, were found to be consistently associated with another type of receptor-like kinase (Tak) on chromosome groups 1 and 3 in Triticeae and on chromosomes homoeologous to Triticeae group 3 in the other grass genomes. On Triticeae chromosome group 1, Tak and Lrk together with genes putatively encoding NBS/LRR proteins form a cluster of genes possibly involved in signal transduction. Comparison of the gene composition at orthologous Lrk loci in wheat, barley, and rice revealed a maximal gene density of one gene per 4-5 kb, very similar to the gene density in Arabidopsis thaliana. We conclude that small and large grass genomes contain regions that are highly enriched in genes with very little or no repetitive DNA. The comparison of the gene organization suggested various genome rearrangements during the evolution of the different grass species.
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Affiliation(s)
- C Feuillet
- Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
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