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Chen C, Jost M, Outram MA, Friendship D, Chen J, Wang A, Periyannan S, Bartoš J, Holušová K, Doležel J, Zhang P, Bhatt D, Singh D, Lagudah E, Park RF, Dracatos PM. A pathogen-induced putative NAC transcription factor mediates leaf rust resistance in barley. Nat Commun 2023; 14:5468. [PMID: 37673864 PMCID: PMC10482968 DOI: 10.1038/s41467-023-41021-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/21/2023] [Indexed: 09/08/2023] Open
Abstract
Leaf rust, caused by Puccinia hordei, is one of the most widespread and damaging foliar diseases affecting barley. The barley leaf rust resistance locus Rph7 has been shown to have unusually high sequence and haplotype divergence. In this study, we isolate the Rph7 gene using a fine mapping and RNA-Seq approach that is confirmed by mutational analysis and transgenic complementation. Rph7 is a pathogen-induced, non-canonical resistance gene encoding a protein that is distinct from other known plant disease resistance proteins in the Triticeae. Structural analysis using an AlphaFold2 protein model suggests that Rph7 encodes a putative NAC transcription factor with a zinc-finger BED domain with structural similarity to the N-terminal DNA-binding domain of the NAC transcription factor (ANAC019) from Arabidopsis. A global gene expression analysis suggests Rph7 mediates the activation and strength of the basal defence response. The isolation of Rph7 highlights the diversification of resistance mechanisms available for engineering disease control in crops.
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Affiliation(s)
- Chunhong Chen
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Matthias Jost
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Megan A Outram
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Dorian Friendship
- The University of Sydney, Faculty of Science, Plant Breeding Institute, Cobbitty, NSW, 2570, Australia
| | - Jian Chen
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Aihua Wang
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Sambasivam Periyannan
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
- The University of Southern Queensland, School of Agriculture and Environmental Science, Centre for Crop Health, Toowoomba, QLD, 4350, Australia
| | - Jan Bartoš
- Institute of Experimental Botany, Centre of Plant Structural and Functional Genomics, Olomouc, CZ-77900, Czech Republic
| | - Kateřina Holušová
- Institute of Experimental Botany, Centre of Plant Structural and Functional Genomics, Olomouc, CZ-77900, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of Plant Structural and Functional Genomics, Olomouc, CZ-77900, Czech Republic
| | - Peng Zhang
- The University of Sydney, Faculty of Science, Plant Breeding Institute, Cobbitty, NSW, 2570, Australia
| | - Dhara Bhatt
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Davinder Singh
- The University of Sydney, Faculty of Science, Plant Breeding Institute, Cobbitty, NSW, 2570, Australia
| | - Evans Lagudah
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia.
| | - Robert F Park
- The University of Sydney, Faculty of Science, Plant Breeding Institute, Cobbitty, NSW, 2570, Australia.
| | - Peter M Dracatos
- The University of Sydney, Faculty of Science, Plant Breeding Institute, Cobbitty, NSW, 2570, Australia.
- La Trobe Institute for Sustainable Agriculture & Food (LISAF), Department of Animal, Plant and Soil Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.
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Dinh HX, Singh D, Periyannan S, Park RF, Pourkheirandish M. Molecular genetics of leaf rust resistance in wheat and barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2035-2050. [PMID: 32128617 DOI: 10.1007/s00122-020-03570-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/18/2020] [Indexed: 06/10/2023]
Abstract
The demand for cereal grains as a main source of energy continues to increase due to the rapid increase in world population. The leaf rust diseases of cereals cause significant yield losses, posing challenges for global food security. The deployment of resistance genes has long been considered as the most effective and sustainable way to control cereal leaf rust diseases. While genetic resistance has reduced the impact of these diseases in agriculture, losses still occur due to the ability of the respective rust pathogens to change and render resistance genes ineffective plus the slow pace at which resistance genes are discovered and characterized. This article highlights novel recently developed strategies based on advances in genome sequencing that have accelerated gene isolation by overcoming the complexity of cereal genomes. The leaf rust resistance genes cloned so far from wheat and barley belong to various protein families, including nucleotide binding site/leucine-rich repeat receptors and transporters. We review recent studies that are beginning to reveal the defense mechanisms conferred by the leaf rust resistance genes identified to date in cereals and their roles in either pattern-triggered immunity or effector-triggered immunity.
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Affiliation(s)
- Hoan X Dinh
- Plant Breeding Institute, Faculty of Science, The University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Davinder Singh
- Plant Breeding Institute, Faculty of Science, The University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Sambasivam Periyannan
- CSIRO Agriculture and Food, Box 1700, Clunies Ross Street, Canberra, 2601, Australia
| | - Robert F Park
- Plant Breeding Institute, Faculty of Science, The University of Sydney, Cobbitty, NSW, 2570, Australia.
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Fazlikhani L, Keilwagen J, Kopahnke D, Deising H, Ordon F, Perovic D. High Resolution Mapping of Rph MBR1012 Conferring Resistance to Puccinia hordei in Barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2019; 10:640. [PMID: 31191570 PMCID: PMC6541035 DOI: 10.3389/fpls.2019.00640] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/29/2019] [Indexed: 06/01/2023]
Abstract
Isolation of disease resistance genes in barley was hampered by the large genome size, but has become easy due to the availability of the reference genome sequence. During the last years, many genomic resources, e.g., the Illumina 9K iSelect, the 50K Infinium arrays, the Barley Genome Zipper, POPSEQ, and genotyping by sequencing (GBS), were developed that enable enhanced gene isolation in combination with the barley genome sequence. In the present study, we developed a fine map of the barley leaf rust resistance gene Rph MBR1012. 537 segmental homozygous recombinant inbred lines (RILs) derived from 4775 F2-plants were used to construct a high-resolution mapping population (HRMP). The Barley Genome Zipper, the 9K iSelect chip, the 50K Infinium chip and GBS were used to develop 56 molecular markers located in the target interval of 8 cM. This interval was narrowed down to about 0.07 cM corresponding to 0.44 Mb of the barley reference genome. Eleven low-confidence and 18 high-confidence genes were identified in this interval. Five of these are putative disease resistance genes and were subjected to allele-specific sequencing. In addition, comparison of the genetic map and the reference genome revealed an inversion of 1.34 Mb located distally to the resistance locus. In conclusion, the barley reference sequence and the respective gene annotation delivered detailed information about the physical size of the target interval, the genes located in the target interval and facilitated the efficient development of molecular markers for marker-assisted selection for RphMBR1012.
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Affiliation(s)
- Leila Fazlikhani
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), Quedlinburg, Germany
- Department of Phytopathology and Plant Protection, Institute of Agricultural and Nutrition Sciences, Faculty of Natural Sciences III, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), Quedlinburg, Germany
| | - Doris Kopahnke
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), Quedlinburg, Germany
| | - Holger Deising
- Department of Phytopathology and Plant Protection, Institute of Agricultural and Nutrition Sciences, Faculty of Natural Sciences III, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), Quedlinburg, Germany
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), Quedlinburg, Germany
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Schweiger W, Steiner B, Vautrin S, Nussbaumer T, Siegwart G, Zamini M, Jungreithmeier F, Gratl V, Lemmens M, Mayer KFX, Bérgès H, Adam G, Buerstmayr H. Suppressed recombination and unique candidate genes in the divergent haplotype encoding Fhb1, a major Fusarium head blight resistance locus in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1607-23. [PMID: 27174222 PMCID: PMC4943984 DOI: 10.1007/s00122-016-2727-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 05/03/2016] [Indexed: 05/09/2023]
Abstract
Fine mapping and sequencing revealed 28 genes in the non-recombining haplotype containing Fhb1 . Of these, only a GDSL lipase gene shows a pathogen-dependent expression pattern. Fhb1 is a prominent Fusarium head blight resistance locus of wheat, which has been successfully introgressed in adapted breeding material, where it confers a significant increase in overall resistance to the causal pathogen Fusarium graminearum and the fungal virulence factor and mycotoxin deoxynivalenol. The Fhb1 region has been resolved for the susceptible wheat reference genotype Chinese Spring, yet the causal gene itself has not been identified in resistant cultivars. Here, we report the establishment of a 1 Mb contig embracing Fhb1 in the donor line CM-82036. Sequencing revealed that the region of Fhb1 deviates from the Chinese Spring reference in DNA size and gene content, which explains the repressed recombination at the locus in the performed fine mapping. Differences in genes expression between near-isogenic lines segregating for Fhb1 challenged with F. graminearum or treated with mock were investigated in a time-course experiment by RNA sequencing. Several candidate genes were identified, including a pathogen-responsive GDSL lipase absent in susceptible lines. The sequence of the Fhb1 region, the resulting list of candidate genes, and near-diagnostic KASP markers for Fhb1 constitute a valuable resource for breeding and further studies aiming to identify the gene(s) responsible for F. graminearum and deoxynivalenol resistance.
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Affiliation(s)
- W Schweiger
- Institute for Biotechnology in Plant Production (IFA-Tulln), BOKU-University of Natural Resources and Life Sciences, Konrad Lorenz Strasse 20, 3430, Tulln, Austria.
| | - B Steiner
- Institute for Biotechnology in Plant Production (IFA-Tulln), BOKU-University of Natural Resources and Life Sciences, Konrad Lorenz Strasse 20, 3430, Tulln, Austria
| | - S Vautrin
- French Plant Genomic Resource Centre, INRA-CNRGV, Chemin de Borde Rouge, CS 52627, 31326, Castanet Tolosan, France
| | - T Nussbaumer
- Plant Genome and Systems Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- Division of Computational System Biology, Department of Microbiology and Ecosystem Science, University of Vienna, 1090, Vienna, Austria
| | - G Siegwart
- Institute for Biotechnology in Plant Production (IFA-Tulln), BOKU-University of Natural Resources and Life Sciences, Konrad Lorenz Strasse 20, 3430, Tulln, Austria
- Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life Sciences, Konrad Lorenz Strasse 22, 3430, Tulln, Austria
| | - M Zamini
- Institute for Biotechnology in Plant Production (IFA-Tulln), BOKU-University of Natural Resources and Life Sciences, Konrad Lorenz Strasse 20, 3430, Tulln, Austria
| | - F Jungreithmeier
- Institute for Biotechnology in Plant Production (IFA-Tulln), BOKU-University of Natural Resources and Life Sciences, Konrad Lorenz Strasse 20, 3430, Tulln, Austria
| | - V Gratl
- Institute for Biotechnology in Plant Production (IFA-Tulln), BOKU-University of Natural Resources and Life Sciences, Konrad Lorenz Strasse 20, 3430, Tulln, Austria
| | - M Lemmens
- Institute for Biotechnology in Plant Production (IFA-Tulln), BOKU-University of Natural Resources and Life Sciences, Konrad Lorenz Strasse 20, 3430, Tulln, Austria
| | - K F X Mayer
- Plant Genome and Systems Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - H Bérgès
- French Plant Genomic Resource Centre, INRA-CNRGV, Chemin de Borde Rouge, CS 52627, 31326, Castanet Tolosan, France
| | - G Adam
- Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life Sciences, Konrad Lorenz Strasse 22, 3430, Tulln, Austria
| | - H Buerstmayr
- Institute for Biotechnology in Plant Production (IFA-Tulln), BOKU-University of Natural Resources and Life Sciences, Konrad Lorenz Strasse 20, 3430, Tulln, Austria
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5
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Yeo FKS, Wang Y, Vozabova T, Huneau C, Leroy P, Chalhoub B, Qi XQ, Niks RE, Marcel TC. Haplotype divergence and multiple candidate genes at Rphq2, a partial resistance QTL of barley to Puccinia hordei. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:289-304. [PMID: 26542283 PMCID: PMC4733143 DOI: 10.1007/s00122-015-2627-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 10/17/2015] [Indexed: 05/04/2023]
Abstract
KEY MESSAGE Rphq2, a minor gene for partial resistance to Puccinia hordei , was physically mapped in a 188 kbp introgression with suppressed recombination between haplotypes of rphq2 and Rphq2 barley cultivars. ABSTRACT Partial and non-host resistances to rust fungi in barley (Hordeum vulgare) may be based on pathogen-associated molecular pattern (PAMP)-triggered immunity. Understanding partial resistance may help to understand non-host resistance, and vice versa. We constructed two non-gridded BAC libraries from cultivar Vada and line SusPtrit. Vada is immune to non-adapted Puccinia rust fungi, and partially resistant to P. hordei. SusPtrit is susceptible to several non-adapted rust fungi, and has been used for mapping QTLs for non-host and partial resistance. The BAC libraries help to identify genes determining the natural variation for partial and non-host resistances of barley to rust fungi. A major-effect QTL, Rphq2, for partial resistance to P. hordei was mapped in a complete Vada and an incomplete SusPtrit contig. The physical distance between the markers flanking Rphq2 was 195 Kbp in Vada and at least 226 Kbp in SusPtrit. This marker interval was predicted to contain 12 genes in either accession, of which only five genes were in common. The haplotypes represented by Vada and SusPtrit were found in 57 and 43%, respectively, of a 194 barley accessions panel. The lack of homology between the two haplotypes probably explains the suppression of recombination in the Rphq2 area and limit further genetic resolution in fine mapping. The possible candidate genes for Rphq2 encode peroxidases, kinases and a member of seven-in-absentia protein family. This result suggests that Rphq2 does not belong to the NB-LRR gene family and does not resemble any of the partial resistance genes cloned previously.
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Affiliation(s)
- F K S Yeo
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708PB, 6700 AJ, Wageningen, The Netherlands
- Department of Plant Science and Environmental Ecology, Faculty of Resource Science and Technology, University Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Y Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - T Vozabova
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708PB, 6700 AJ, Wageningen, The Netherlands
- The Institute of Botany of the Academy of Science of the Czech Republic, Zámek 1, 252 43, Průhonice, Czech Republic
| | - C Huneau
- INRA, UMR1165, Unité de Recherche en Génomique Végétale, 91057, Evry, France
- Université d'Evry Val d'Essonne, UMR1165, Unité de Recherche en Génomique Végétale, 91057, Evry, France
| | - P Leroy
- INRA, UMR1095, Genetics Diversity and Ecophysiology of Cereals, 63039, Clermont-Ferrand, France
- Université Blaise Pascal, UMR1095, Genetics Diversity and Ecophysiology of Cereals, 63039, Clermont-Ferrand, France
| | - B Chalhoub
- INRA, UMR1165, Unité de Recherche en Génomique Végétale, 91057, Evry, France
- Université d'Evry Val d'Essonne, UMR1165, Unité de Recherche en Génomique Végétale, 91057, Evry, France
| | - X Q Qi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - R E Niks
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708PB, 6700 AJ, Wageningen, The Netherlands.
| | - T C Marcel
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708PB, 6700 AJ, Wageningen, The Netherlands
- INRA, UMR1290, BIOGER, 78850, Thiverval-Grignon, France
- AgroParisTech, UMR1290, BIOGER, 78850, Thiverval-Grignon, France
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Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe. PLoS One 2014; 9:e85761. [PMID: 24614886 PMCID: PMC3948623 DOI: 10.1371/journal.pone.0085761] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 12/06/2013] [Indexed: 01/08/2023] Open
Abstract
Using Roche/454 technology, we sequenced the chloroplast genomes of 12 Triticeae species, including bread wheat, barley and rye, as well as the diploid progenitors and relatives of bread wheat Triticum urartu, Aegilops speltoides and Ae. tauschii. Two wild tetraploid taxa, Ae. cylindrica and Ae. geniculata, were also included. Additionally, we incorporated wild Einkorn wheat Triticum boeoticum and its domesticated form T. monococcum and two Hordeum spontaneum (wild barley) genotypes. Chloroplast genomes were used for overall sequence comparison, phylogenetic analysis and dating of divergence times. We estimate that barley diverged from rye and wheat approximately 8–9 million years ago (MYA). The genome donors of hexaploid wheat diverged between 2.1–2.9 MYA, while rye diverged from Triticum aestivum approximately 3–4 MYA, more recently than previously estimated. Interestingly, the A genome taxa T. boeoticum and T. urartu were estimated to have diverged approximately 570,000 years ago. As these two have a reproductive barrier, the divergence time estimate also provides an upper limit for the time required for the formation of a species boundary between the two. Furthermore, we conclusively show that the chloroplast genome of hexaploid wheat was contributed by the B genome donor and that this unknown species diverged from Ae. speltoides about 980,000 years ago. Additionally, sequence alignments identified a translocation of a chloroplast segment to the nuclear genome which is specific to the rye/wheat lineage. We propose the presented phylogeny and divergence time estimates as a reference framework for future studies on Triticeae.
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Abstract
Two meiotic processes have a major influence on the plant breeding, namely, the independent assortment of chromosomes, and recombination. The major chromosome pairing locus in hexaploid and tetraploid wheat, Ph1, has a significant effect on both these processes. This chapter reviews our current understanding of this locus and how mutants of it can be exploited for breeding purposes.
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Affiliation(s)
- Graham Moore
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK,
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8
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Biselli C, Urso S, Tacconi G, Steuernagel B, Schulte D, Gianinetti A, Bagnaresi P, Stein N, Cattivelli L, Valè G. Haplotype variability and identification of new functional alleles at the Rdg2a leaf stripe resistance gene locus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1575-1586. [PMID: 23494394 DOI: 10.1007/s00122-013-2075-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 02/23/2013] [Indexed: 06/01/2023]
Abstract
The barley Rdg2a locus confers resistance to the leaf stripe pathogen Pyrenophora graminea and, in the barley genotype Thibaut, it is composed of a gene family with three highly similar paralogs. Only one member of the gene family (called as Rdg2a) encoding for a CC-NB-LRR protein is able to confer resistance to the leaf stripe isolate Dg2. To study the genome evolution and diversity at the Rdg2a locus, sequences spanning the Rdg2a gene were compared in two barley cultivars, Thibaut and Morex, respectively, resistant and susceptible to leaf stripe. An overall high level of sequence conservation interrupted by several rearrangements that included three main deletions was observed in the Morex contig. The main deletion of 13,692 bp was most likely derived from unequal crossing over between Rdg2a paralogs leading to the generation of a chimeric Morex rdg2a gene which was not associated to detectable level of resistance toward leaf stripe. PCR-based analyses of genic and intergenic regions at the Rdg2a locus in 29 H. vulgare lines and one H. vulgare ssp. spontaneum accession indicated large haplotype variability in the cultivated barley gene pool suggesting rapid and recent divergence at this locus. Barley genotypes showing the same haplotype as Thibaut at the Rdg2a locus were selected for a Rdg2a allele mining through allele re-sequencing and two lines with polymorphic nucleotides leading to amino acid changes in the CC-NB and LRR encoding domains, respectively, were identified. Analysis of nucleotide diversity of the Rdg2a alleles revealed that the polymorphic sites were subjected to positive selection. Moreover, strong positively selected sites were located in the LRR encoding domain suggesting that both positive selection and divergence at homologous loci are possibly representing the molecular mechanism for the generation of high diversity at the Rdg2a locus in the barley gene pool.
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Affiliation(s)
- Chiara Biselli
- Genomics Research Centre, CRA-Consiglio per la ricerca e la sperimentazione in agricoltura, Via S Protaso 302, 29017 Fiorenzuola d'Arda, Piacenza, Italy
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9
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Oh SA, Allen T, Kim GJ, Sidorova A, Borg M, Park SK, Twell D. Arabidopsis Fused kinase and the Kinesin-12 subfamily constitute a signalling module required for phragmoplast expansion. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 71:550-63. [PMID: 22448600 DOI: 10.1111/j.1365-313x.2012.05007.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The conserved Fused kinase plays vital but divergent roles in many organisms from Hedgehog signalling in Drosophila to polarization and chemotaxis in Dictyostelium. Previously we have shown that Arabidopsis Fused kinase termed TWO-IN-ONE (TIO) is essential for cytokinesis in both sporophytic and gametophytic cell types. Here using in vivo imaging of GFP-tagged microtubules in dividing microspores we show that TIO is required for expansion of the phragmoplast. We identify the phragmoplast-associated kinesins, PAKRP1/Kinesin-12A and PAKRP1L/Kinesin-12B, as TIO-interacting proteins and determine TIO-Kinesin-12 interaction domains and their requirement in male gametophytic cytokinesis. Our results support the role of TIO as a functional protein kinase that interacts with Kinesin-12 subfamily members mainly through the C-terminal ARM repeat domain, but with a contribution from the N-terminal kinase domain. The interaction of TIO with Kinesin proteins and the functional requirement of their interaction domains support the operation of a Fused kinase signalling module in phragmoplast expansion that depends upon conserved structural features in diverse Fused kinases.
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Affiliation(s)
- Sung Aeong Oh
- Department of Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
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11
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Barabaschi D, Guerra D, Lacrima K, Laino P, Michelotti V, Urso S, Valè G, Cattivelli L. Emerging knowledge from genome sequencing of crop species. Mol Biotechnol 2012; 50:250-66. [PMID: 21822975 DOI: 10.1007/s12033-011-9443-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Extensive insights into the genome composition, organization, and evolution have been gained from the plant genome sequencing and annotation ongoing projects. The analysis of crop genomes provided surprising evidences with important implications in plant origin and evolution: genome duplication, ancestral re-arrangements and unexpected polyploidization events opened new doors to address fundamental questions related to species proliferation, adaptation, and functional modulations. Detailed paleogenomic analysis led to many speculation on how chromosomes have been shaped over time in terms of gene content and order. The completion of the genome sequences of several major crops, prompted to a detailed identification and annotation of transposable elements: new hypothesis related to their composition, chromosomal distribution, insertion models, amplification rate, and evolution patterns are coming up. Availability of full genome sequence of several crop species as well as from many accessions within species is providing new keys for biodiversity exploitation and interpretation. Re-sequencing is enabling high-throughput genotyping to identify a wealth of SNP and afterward to produce haplotype maps necessary to accurately associate molecular variation to phenotype. Conservation genomics is emerging as a powerful tool to explain adaptation, genetic drift, natural selection, hybridization and to estimate genetic variation, fitness and population's viability.
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Affiliation(s)
- Delfina Barabaschi
- CRA, Viticolture Research Centre, Via Casoni 13/A, 31058 Susegana, TV, Italy
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12
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Buti M, Giordani T, Cattonaro F, Cossu RM, Pistelli L, Vukich M, Morgante M, Cavallini A, Natali L. Temporal dynamics in the evolution of the sunflower genome as revealed by sequencing and annotation of three large genomic regions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:779-91. [PMID: 21647740 DOI: 10.1007/s00122-011-1626-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Accepted: 05/09/2011] [Indexed: 05/02/2023]
Abstract
Improved knowledge of genome composition, especially of its repetitive component, generates important informations in both theoretical and applied research. In this study, we provide the first insight into the local organization of the sunflower genome by sequencing and annotating 349,380 bp from 3 BAC clones, each including one single-copy gene. These analyses resulted in the identification of 11 putative gene sequences, 18 full-length LTR retrotransposons, 6 incomplete LTR retrotransposons, 2 non-autonomous LTR-retroelements (LINEs), 2 putative DNA transposons fragments and one putative helitron. Among LTR-retrotransposons, non-autonomous elements (the so-called LARDs), which do not carry any protein-encoding sequence, were discovered for the first time in the sunflower. The insertion time of intact retroelements was measured, based on sister LTRs divergence. All isolated elements were inserted relatively recently, especially those belonging to the Gypsy superfamily. Retrotransposon families related to those identified in the BAC clones are present also in other species of Helianthus, both annual and perennial, and even in other Asteraceae. In one of the three BAC clones, we found five copies of a lipid transfer protein (LTP) encoding gene within less than 100,000 bp, four of which are potentially functional. Two of these are interrupted by LTR retrotransposons, in the intron and in the coding sequence, respectively. The divergence between sister LTRs of the retrotransposons inserted within the genes indicates that LTP gene duplication started earlier than 1.749 MYRS ago. On the whole, the results reported in this study confirm that the sunflower is an excellent system to study transposons dynamics and evolution.
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Affiliation(s)
- M Buti
- Department of Crop Plant Biology, University of Pisa, Pisa, Italy
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Baurens FC, Bocs S, Rouard M, Matsumoto T, Miller RNG, Rodier-Goud M, MBéguié-A-MBéguié D, Yahiaoui N. Mechanisms of haplotype divergence at the RGA08 nucleotide-binding leucine-rich repeat gene locus in wild banana (Musa balbisiana). BMC PLANT BIOLOGY 2010; 10:149. [PMID: 20637079 PMCID: PMC3017797 DOI: 10.1186/1471-2229-10-149] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Accepted: 07/16/2010] [Indexed: 05/09/2023]
Abstract
BACKGROUND Comparative sequence analysis of complex loci such as resistance gene analog clusters allows estimating the degree of sequence conservation and mechanisms of divergence at the intraspecies level. In banana (Musa sp.), two diploid wild species Musa acuminata (A genome) and Musa balbisiana (B genome) contribute to the polyploid genome of many cultivars. The M. balbisiana species is associated with vigour and tolerance to pests and disease and little is known on the genome structure and haplotype diversity within this species. Here, we compare two genomic sequences of 253 and 223 kb corresponding to two haplotypes of the RGA08 resistance gene analog locus in M. balbisiana "Pisang Klutuk Wulung" (PKW). RESULTS Sequence comparison revealed two regions of contrasting features. The first is a highly colinear gene-rich region where the two haplotypes diverge only by single nucleotide polymorphisms and two repetitive element insertions. The second corresponds to a large cluster of RGA08 genes, with 13 and 18 predicted RGA genes and pseudogenes spread over 131 and 152 kb respectively on each haplotype. The RGA08 cluster is enriched in repetitive element insertions, in duplicated non-coding intergenic sequences including low complexity regions and shows structural variations between haplotypes. Although some allelic relationships are retained, a large diversity of RGA08 genes occurs in this single M. balbisiana genotype, with several RGA08 paralogs specific to each haplotype. The RGA08 gene family has evolved by mechanisms of unequal recombination, intragenic sequence exchange and diversifying selection. An unequal recombination event taking place between duplicated non-coding intergenic sequences resulted in a different RGA08 gene content between haplotypes pointing out the role of such duplicated regions in the evolution of RGA clusters. Based on the synonymous substitution rate in coding sequences, we estimated a 1 million year divergence time for these M. balbisiana haplotypes. CONCLUSIONS A large RGA08 gene cluster identified in wild banana corresponds to a highly variable genomic region between haplotypes surrounded by conserved flanking regions. High level of sequence identity (70 to 99%) of the genic and intergenic regions suggests a recent and rapid evolution of this cluster in M. balbisiana.
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Affiliation(s)
| | - Stéphanie Bocs
- CIRAD, UMR DAP, TA A-96/03, Avenue Agropolis, F-34398 Montpellier Cedex 5, France
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, F-34397 Montpellier Cedex 5, France
| | - Takashi Matsumoto
- Rice Genome Research Program (RGP), National Institute of Agrobiological Sciences (NIAS)/Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-8602, Japan
| | - Robert NG Miller
- Postgraduate program in Genomic Science and Biotechnology, Universidade Católica de Brasília, SGAN 916, Módulo B, CEP 70.790-160, Brasília, DF, Brazil
- Universidade de Brasília, Campus Universitário Darcy Ribeiro, Instituto de Ciências Biológicas, Departamento de Biologia Celular, Asa Norte, Brasília, Brazil
| | | | | | - Nabila Yahiaoui
- CIRAD, UMR DAP, TA A-96/03, Avenue Agropolis, F-34398 Montpellier Cedex 5, France
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Vukich M, Giordani T, Natali L, Cavallini A. Copia and Gypsy retrotransposons activity in sunflower (Helianthus annuus L.). BMC PLANT BIOLOGY 2009; 9:150. [PMID: 20030800 PMCID: PMC2805666 DOI: 10.1186/1471-2229-9-150] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 12/23/2009] [Indexed: 05/02/2023]
Abstract
BACKGROUND Retrotransposons are heterogeneous sequences, widespread in eukaryotic genomes, which refer to the so-called mobile DNA. They resemble retroviruses, both in their structure and for their ability to transpose within the host genome, of which they make up a considerable portion. Copia- and Gypsy-like retrotransposons are the two main classes of retroelements shown to be ubiquitous in plant genomes. Ideally, the retrotransposons life cycle results in the synthesis of a messenger RNA and then self-encoded proteins to process retrotransposon mRNA in double stranded extra-chromosomal cDNA copies which may integrate in new chromosomal locations. RESULTS The RT-PCR and IRAP protocol were applied to detect the presence of Copia and Gypsy retrotransposon transcripts and of new events of integration in unstressed plants of a sunflower (Helianthus annuus L.) selfed line. Results show that in sunflower retrotransposons transcription occurs in all analyzed organs (embryos, leaves, roots, and flowers). In one out of sixty-four individuals analyzed, retrotransposons transcription resulted in the integration of a new element into the genome. CONCLUSION These results indicate that the retrotransposon life cycle is firmly controlled at a post transcriptional level. A possible silencing mechanism is discussed.
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Affiliation(s)
- Marco Vukich
- Dipartimento di Biologia delle Piante Agrarie, Università di Pisa, Via del Borghetto 80, I-56124 Pisa, Italy
| | - Tommaso Giordani
- Dipartimento di Biologia delle Piante Agrarie, Università di Pisa, Via del Borghetto 80, I-56124 Pisa, Italy
| | - Lucia Natali
- Dipartimento di Biologia delle Piante Agrarie, Università di Pisa, Via del Borghetto 80, I-56124 Pisa, Italy
| | - Andrea Cavallini
- Dipartimento di Biologia delle Piante Agrarie, Università di Pisa, Via del Borghetto 80, I-56124 Pisa, Italy
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Shi BJ, Gustafson JP, Button J, Miyazaki J, Pallotta M, Gustafson N, Zhou H, Langridge P, Collins NC. Physical analysis of the complex rye (Secale cereale L.) Alt4 aluminium (aluminum) tolerance locus using a whole-genome BAC library of rye cv. Blanco. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:695-704. [PMID: 19529908 DOI: 10.1007/s00122-009-1080-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Accepted: 05/21/2009] [Indexed: 05/27/2023]
Abstract
Rye is a diploid crop species with many outstanding qualities, and is important as a source of new traits for wheat and triticale improvement. Rye is highly tolerant of aluminum (Al) toxicity, and possesses a complex structure at the Alt4 Al tolerance locus not found at the corresponding locus in wheat. Here we describe a BAC library of rye cv. Blanco, representing a valuable resource for rye molecular genetic studies, and assess the library's suitability for investigating Al tolerance genes. The library provides 6 x genome coverage of the 8.1 Gb rye genome, has an average insert size of 131 kb, and contains only ~2% of empty or organelle-derived clones. Genetic analysis attributed the Al tolerance of Blanco to the Alt4 locus on the short arm of chromosome 7R, and revealed the presence of multiple allelic variants (haplotypes) of the Alt4 locus in the BAC library. BAC clones containing ALMT1 gene clusters from several Alt4 haplotypes were identified, and will provide useful starting points for exploring the basis for the structural variability and functional specialization of ALMT1 genes at this locus.
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Affiliation(s)
- B-J Shi
- Australian Centre for Plant Functional Genomics (ACPFG), School of Agriculture, Food and Wine, University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
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16
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von Korff M, Radovic S, Choumane W, Stamati K, Udupa SM, Grando S, Ceccarelli S, Mackay I, Powell W, Baum M, Morgante M. Asymmetric allele-specific expression in relation to developmental variation and drought stress in barley hybrids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 59:14-26. [PMID: 19309461 DOI: 10.1111/j.1365-313x.2009.03848.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In the present study, we analysed allele-specific expression (ASE) in the selfing species barley to assess the frequency of cis-acting regulatory variation and the effects of genetic background, developmental differences and drought stress on allelic expression levels. We measured ASE ratios in 30 genes putatively involved in stress responses in five hybrids and their reciprocals, namely Hordeum spontaneum 41-1/Alexis (HAl), Hordeum spontaneum 41-1/Arta (HAr), Sloop/WI3408 (SW), Tadmor/Sloop (TS) and Tadmor/WI3408 (TW). In order to detect cis-acting variation related to drought and developmental changes, the barley hybrids were grown under control and water-limited conditions, and leaf tissue was harvested at two developmental stages. The analysis demonstrated that more than half of the genes measured (63%) showed allelic differences in expression of up to 19-fold due to cis-regulatory variation in at least one cross by treatment/stage combination. Drought stress induced changes in allelic expression ratios, indicating differences between drought responsive cis-elements. In addition, ASE differences between developmental stages suggested the presence of cis-acting elements interacting with developmental cues. We were also able to demonstrate that the levels and frequency of allelic imbalance and hence differences in cis-regulatory elements are correlated with the genetic divergence between the parental lines, but may also arise as an adaptation to diverse habitats. Our findings suggest that cis-regulatory variation is a common phenomenon in barley, and may provide a molecular basis of transgression. Differential expression of near-isogenic members of the same gene family could potentially result in hybrid lines out performing their parents in terms of expression level, timing and response to developmental and environmental cues. Identification and targeted manipulation of cis-regulatory elements will assist in breeding improved crops with a better adaptation to changing environments.
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Affiliation(s)
- Maria von Korff
- International Center for Agricultural Research in the Dry Areas, PO Box 5466, Aleppo, Syria
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17
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Wicker T, Krattinger SG, Lagudah ES, Komatsuda T, Pourkheirandish M, Matsumoto T, Cloutier S, Reiser L, Kanamori H, Sato K, Perovic D, Stein N, Keller B. Analysis of intraspecies diversity in wheat and barley genomes identifies breakpoints of ancient haplotypes and provides insight into the structure of diploid and hexaploid triticeae gene pools. PLANT PHYSIOLOGY 2009; 149:258-70. [PMID: 19011002 PMCID: PMC2613701 DOI: 10.1104/pp.108.129734] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Accepted: 11/12/2008] [Indexed: 05/19/2023]
Abstract
A large number of wheat (Triticum aestivum) and barley (Hordeum vulgare) varieties have evolved in agricultural ecosystems since domestication. Because of the large, repetitive genomes of these Triticeae crops, sequence information is limited and molecular differences between modern varieties are poorly understood. To study intraspecies genomic diversity, we compared large genomic sequences at the Lr34 locus of the wheat varieties Chinese Spring, Renan, and Glenlea, and diploid wheat Aegilops tauschii. Additionally, we compared the barley loci Vrs1 and Rym4 of the varieties Morex, Cebada Capa, and Haruna Nijo. Molecular dating showed that the wheat D genome haplotypes diverged only a few thousand years ago, while some barley and Ae. tauschii haplotypes diverged more than 500,000 years ago. This suggests gene flow from wild barley relatives after domestication, whereas this was rare or absent in the D genome of hexaploid wheat. In some segments, the compared haplotypes were very similar to each other, but for two varieties each at the Rym4 and Lr34 loci, sequence conservation showed a breakpoint that separates a highly conserved from a less conserved segment. We interpret this as recombination breakpoints of two ancient haplotypes, indicating that the Triticeae genomes are a heterogeneous and variable mosaic of haplotype fragments. Analysis of insertions and deletions showed that large events caused by transposable element insertions, illegitimate recombination, or unequal crossing over were relatively rare. Most insertions and deletions were small and caused by template slippage in short homopolymers of only a few base pairs in size. Such frequent polymorphisms could be exploited for future molecular marker development.
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Affiliation(s)
- Thomas Wicker
- Institute of Plant Biology, University of Zurich, 8008 Zurich, Switzerland
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Molecular analysis of a large subtelomeric nucleotide-binding-site-leucine-rich-repeat family in two representative genotypes of the major gene pools of Phaseolus vulgaris. Genetics 2008; 181:405-19. [PMID: 19087965 DOI: 10.1534/genetics.108.093583] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In common bean, the B4 disease resistance gene cluster is a complex cluster localized at the end of linkage group (LG) B4, containing at least three R specificities to the fungus Colletotrichum lindemuthianum. To investigate the evolution of this R cluster since the divergence of Andean and Mesoamerican gene pools, DNA sequences were characterized from two representative genotypes of the two major gene pools of common bean (BAT93: Mesoamerican; JaloEEP558: Andean). Sequences encoding 29 B4-CC nucleotide-binding-site-leucine-rich-repeat (B4-CNL) genes were determined-12 from JaloEEP558 and 17 from BAT93. Although sequence exchange events were identified, phylogenetic analyses revealed that they were not frequent enough to lead to homogenization of B4-CNL sequences within a haplotype. Genetic mapping based on pulsed-field gel electrophoresis separation confirmed that the B4-CNL family is a large family specific to one end of LG B4 and is present at two distinct blocks separated by 26 cM. Fluorescent in situ hybridization on meiotic pachytene chromosomes revealed that two B4-CNL blocks are located in the subtelomeric region of the short arm of chromosome 4 on both sides of a heterochromatic block (knob), suggesting that this peculiar genomic environment may favor the proliferation of a large R gene cluster.
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Wicker T, Narechania A, Sabot F, Stein J, Vu GTH, Graner A, Ware D, Stein N. Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats. BMC Genomics 2008; 9:518. [PMID: 18976483 PMCID: PMC2584661 DOI: 10.1186/1471-2164-9-518] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Accepted: 10/31/2008] [Indexed: 11/10/2022] Open
Abstract
Background Barley has one of the largest and most complex genomes of all economically important food crops. The rise of new short read sequencing technologies such as Illumina/Solexa permits such large genomes to be effectively sampled at relatively low cost. Based on the corresponding sequence reads a Mathematically Defined Repeat (MDR) index can be generated to map repetitive regions in genomic sequences. Results We have generated 574 Mbp of Illumina/Solexa sequences from barley total genomic DNA, representing about 10% of a genome equivalent. From these sequences we generated an MDR index which was then used to identify and mark repetitive regions in the barley genome. Comparison of the MDR plots with expert repeat annotation drawing on the information already available for known repetitive elements revealed a significant correspondence between the two methods. MDR-based annotation allowed for the identification of dozens of novel repeat sequences, though, which were not recognised by hand-annotation. The MDR data was also used to identify gene-containing regions by masking of repetitive sequences in eight de-novo sequenced bacterial artificial chromosome (BAC) clones. For half of the identified candidate gene islands indeed gene sequences could be identified. MDR data were only of limited use, when mapped on genomic sequences from the closely related species Triticum monococcum as only a fraction of the repetitive sequences was recognised. Conclusion An MDR index for barley, which was obtained by whole-genome Illumina/Solexa sequencing, proved as efficient in repeat identification as manual expert annotation. Circumventing the labour-intensive step of producing a specific repeat library for expert annotation, an MDR index provides an elegant and efficient resource for the identification of repetitive and low-copy (i.e. potentially gene-containing sequences) regions in uncharacterised genomic sequences. The restriction that a particular MDR index can not be used across species is outweighed by the low costs of Illumina/Solexa sequencing which makes any chosen genome accessible for whole-genome sequence sampling.
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Affiliation(s)
- Thomas Wicker
- Institute of Plant Biology, University Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.
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20
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BAC end sequences corresponding to the B4 resistance gene cluster in common bean: a resource for markers and synteny analyses. Mol Genet Genomics 2008; 280:521-33. [PMID: 18813956 DOI: 10.1007/s00438-008-0384-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Accepted: 09/06/2008] [Indexed: 10/21/2022]
Abstract
In common bean, a complex disease resistance (R) gene cluster, harboring many specific R genes against various pathogens, is located at the end of the linkage group B4. A BAC library of the Meso-american bean genotype BAT93 was screened with PRLJ1, a probe previously shown to be specific to the B4 R gene cluster, leading to the identification of 73 positive BAC clones. BAC-end sequencing (BES) of the 73 positive BACs generated 75 kb of sequence. These BACs were organized into 6 contigs, all mapped at the B4 R gene cluster. To evaluate the potential of BES for marker development, BES-derived specific primers were used to check for linkage with two allelic anthracnose R specificities Co-3 and Co-3 ( 2 ), through the analysis of pairs of Near Isogenic Lines (NILs). Out of 32 primer pairs tested, two revealed polymorphisms between the NILs, confirming the suspected location of Co-3 and Co-3 ( 2 ) at the B4 cluster. In order to identify the orthologous region of the B4 R gene cluster in the two model legume genomes, bean BESs were used as queries in TBLASTX searches of Medicago truncatula and Lotus japonicus BAC clones. Putative orthologous regions were identified on chromosome Mt6 and Lj2, in agreement with the colinearity observed between Mt and Lj for these regions.
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21
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Li X, Tian F, Huang H, Tan L, Zhu Z, Hu S, Sun C. Construction of the physical map of the gpa7 locus reveals that a large segment was deleted during rice domestication. PLANT CELL REPORTS 2008; 27:1087-1092. [PMID: 18317774 DOI: 10.1007/s00299-008-0529-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2007] [Revised: 02/06/2008] [Accepted: 02/20/2008] [Indexed: 05/26/2023]
Abstract
To facilitate cloning gene(s) underlying gpa7, a deep-coverage BAC library was constructed for an isolate of common wild rice (Oryza rufipogon Griff.) collected from Dongxiang, Jiangxi Province, China (DXCWR). gpa7, a quantitative trait locus corresponding to grain number per panicle, is positioned in the short arm of chromosome 7. The BAC library containing 96,768 clones represents approximate 18 haploid genome equivalents. The contig spanning DXCWR gpa7 was constructed with a series of ordered markers. The putative physical map near the gpa7 locus of another accession of O. rufipogon (Accession: IRGC 105491) was also isolated in silico. Analysis of the physical maps of gpa7 indicated that a segment of about 150 kb was deleted during domestication of common wild rice.
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Affiliation(s)
- Xianran Li
- Department of Plant Genetics and Breeding and State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, 100094 Beijing, China
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22
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Martinez-Perez E, Moore G. To check or not to check? The application of meiotic studies to plant breeding. CURRENT OPINION IN PLANT BIOLOGY 2008; 11:222-7. [PMID: 18294901 DOI: 10.1016/j.pbi.2008.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2007] [Revised: 01/02/2008] [Accepted: 01/03/2008] [Indexed: 05/08/2023]
Abstract
Understanding the barriers that prevent pairing and recombination of the chromosomes from two parental species is important for crop improvement strategies. It had been generally thought that plants do not possess checkpoint mechanisms during meiosis. However, recent data may question this assumption and suggest that exploitation of such mechanisms could be crucial to breeding.
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Affiliation(s)
- Enrique Martinez-Perez
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
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Feuillet C, Langridge P, Waugh R. Cereal breeding takes a walk on the wild side. Trends Genet 2008; 24:24-32. [DOI: 10.1016/j.tig.2007.11.001] [Citation(s) in RCA: 216] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2007] [Revised: 11/06/2007] [Accepted: 11/06/2007] [Indexed: 01/08/2023]
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Xing Y, Frei U, Schejbel B, Asp T, Lübberstedt T. Nucleotide diversity and linkage disequilibrium in 11 expressed resistance candidate genes in Lolium perenne. BMC PLANT BIOLOGY 2007; 7:43. [PMID: 17683574 PMCID: PMC1978496 DOI: 10.1186/1471-2229-7-43] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Accepted: 08/04/2007] [Indexed: 05/16/2023]
Abstract
BACKGROUND Association analysis is an alternative way for QTL mapping in ryegrass. So far, knowledge on nucleotide diversity and linkage disequilibrium in ryegrass is lacking, which is essential for the efficiency of association analyses. RESULTS 11 expressed disease resistance candidate (R) genes including 6 nucleotide binding site and leucine rich repeat (NBS-LRR) like genes and 5 non-NBS-LRR genes were analyzed for nucleotide diversity. For each of the genes about 1 kb genomic fragments were isolated from 20 heterozygous genotypes in ryegrass. The number of haplotypes per gene ranged from 9 to 27. On average, one single nucleotide polymorphism (SNP) was present per 33 bp between two randomly sampled sequences for the 11 genes. NBS-LRR like gene fragments showed a high degree of nucleotide diversity, with one SNP every 22 bp between two randomly sampled sequences. NBS-LRR like gene fragments showed very high non-synonymous mutation rates, leading to altered amino acid sequences. Particularly LRR regions showed very high diversity with on average one SNP every 10 bp between two sequences. In contrast, non-NBS LRR resistance candidate genes showed a lower degree of nucleotide diversity, with one SNP every 112 bp. 78% of haplotypes occurred at low frequency (<5%) within the collection of 20 genotypes. Low intragenic LD was detected for most R genes, and rapid LD decay within 500 bp was detected. CONCLUSION Substantial LD decay was found within a distance of 500 bp for most resistance candidate genes in this study. Hence, LD based association analysis is feasible and promising for QTL fine mapping of resistance traits in ryegrass.
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Affiliation(s)
- Yongzhong Xing
- University of Århus, Faculty of Agricultural Sciences, Department of Genetics and Biotechnology, Research Centre Flakkebjerg, Slagelse DK-4200, Denmark
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Uschi Frei
- University of Århus, Faculty of Agricultural Sciences, Department of Genetics and Biotechnology, Research Centre Flakkebjerg, Slagelse DK-4200, Denmark
| | - Britt Schejbel
- University of Århus, Faculty of Agricultural Sciences, Department of Genetics and Biotechnology, Research Centre Flakkebjerg, Slagelse DK-4200, Denmark
| | - Torben Asp
- University of Århus, Faculty of Agricultural Sciences, Department of Genetics and Biotechnology, Research Centre Flakkebjerg, Slagelse DK-4200, Denmark
| | - Thomas Lübberstedt
- University of Århus, Faculty of Agricultural Sciences, Department of Genetics and Biotechnology, Research Centre Flakkebjerg, Slagelse DK-4200, Denmark
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Zhang S, Gu YQ, Singh J, Coleman-Derr D, Brar DS, Jiang N, Lemaux PG. New insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification. PLANT MOLECULAR BIOLOGY 2007; 64:589-600. [PMID: 17534720 DOI: 10.1007/s11103-007-9178-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Accepted: 04/26/2007] [Indexed: 05/15/2023]
Abstract
An approximately 247-kb genomic region from FF genome of wild rice Oryza brachyantha, possessing the smallest Oryza genome, was compared to the orthologous approximately 450-kb region from AA genome, O. sativa L. ssp. japonica. 37 of 38 genes in the orthologous regions are shared between japonica and O. brachyantha. Analyses of nucleotide substitution in coding regions suggest the two genomes diverged approximately 10 million years ago. Comparisons of transposable elements (TEs) reveal that the density of DNA TEs in O. brachyantha is comparable to O. sativa; however, the density of RNA TEs is dramatically lower. The genomic fraction of RNA TEs in japonica is two times greater than in O. brachyantha. Differences, particularly in RNA TEs, in this region and in BAC end sequences from five wild and two cultivated Oryza species explain major genome size differences between sativa and brachyantha. Gene expression analyses of three ObDREB1 genes in the sequenced region indicate orthologous genes retain similar expression patterns following cold stress. Our results demonstrate that size and number of RNA TEs play a major role in genomic differentiation and evolution in Oryza. Additionally, distantly related O. brachyantha shares colinearity with O. sativa, offering opportunities to use comparative genomics to explore the genetic diversity of wild species to improve cultivated rice.
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Affiliation(s)
- Shibo Zhang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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Abstract
Whole genome sequencing provides direct access to all genes of an organism and represents an essential step towards a systematic understanding of (crop) plant biology. Wheat and barley, two of the most important crop species worldwide, have two- to five-fold larger genomes than human - too large to be completely sequenced at current costs. Nevertheless, significant progress has been made to unlock the gene contents of these species by sequencing expressed sequence tags (EST) for high-density mapping and as a basis for elucidating gene function on a large scale. Several megabases of genomic (BAC) sequences have been obtained providing a first insight into the complexity of these huge cereal genomes. However, to fully exploit the information of the wheat and barley genomes for crop improvement, sequence analysis of a significantly larger portion of the Triticeae genomes is needed. In this review an overview of the current status of Triticeae genome sequencing and a perspective concerning future developments in cereal structural genomics is provided.
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Affiliation(s)
- Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany.
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Sherman-Broyles S, Boggs N, Farkas A, Liu P, Vrebalov J, Nasrallah ME, Nasrallah JB. S locus genes and the evolution of self-fertility in Arabidopsis thaliana. THE PLANT CELL 2007; 19:94-106. [PMID: 17237349 PMCID: PMC1820967 DOI: 10.1105/tpc.106.048199] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Loss of self-incompatibility (SI) in Arabidopsis thaliana was accompanied by inactivation of genes required for SI, including S-LOCUS RECEPTOR KINASE (SRK) and S-LOCUS CYSTEINE-RICH PROTEIN (SCR), coadapted genes that constitute the SI specificity-determining S haplotype. Arabidopsis accessions are polymorphic for PsiSRK and PsiSCR, but it is unknown if the species harbors structurally different S haplotypes, either representing relics of ancestral functional and structurally heteromorphic S haplotypes or resulting from decay concomitant with or subsequent to the switch to self-fertility. We cloned and sequenced the S haplotype from C24, in which self-fertility is due solely to S locus inactivation, and show that this haplotype was produced by interhaplotypic recombination. The highly divergent organization and sequence of the C24 and Columbia-0 (Col-0) S haplotypes demonstrate that the A. thaliana S locus underwent extensive structural remodeling in conjunction with a relaxation of selective pressures that once preserved the integrity and linkage of coadapted SRK and SCR alleles. Additional evidence for this process was obtained by assaying 70 accessions for the presence of C24- or Col-0-specific sequences. Furthermore, analysis of SRK and SCR polymorphisms in these accessions argues against the occurrence of a selective sweep of a particular allele of SCR, as previously proposed.
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Affiliation(s)
- Sue Sherman-Broyles
- Department of Plant Biology, Cornell University, Ithaca, New York 14853, USA
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Maize haplotype with a helitron-amplified cytidine deaminase gene copy. BMC Genet 2006; 7:52. [PMID: 17094807 PMCID: PMC1657028 DOI: 10.1186/1471-2156-7-52] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2006] [Accepted: 11/09/2006] [Indexed: 12/23/2022] Open
Abstract
Background Genetic maps are based on recombination of orthologous gene sequences between different strains of the same species. Therefore, it was unexpected to find extensive non-collinearity of genes between different inbred strains of maize. Interestingly, disruption of gene collinearity can be caused among others by a rolling circle-type copy and paste mechanism facilitated by Helitrons. However, understanding the role of this type of gene amplification has been hampered by the lack of finding intact gene sequences within Helitrons. Results By aligning two haplotypes of the z1C1 locus of maize we found a Helitron that contains two genes, one encoding a putative cytidine deaminase and one a hypothetical protein with part of a 40S ribosomal protein. The cytidine deaminase gene, called ZmCDA3, has been copied from the ZmCDA1 gene on maize chromosome 7 about 4.5 million years ago (mya) after maize was formed by whole-genome duplication from two progenitors. Inbred lines contain gene copies of both progenitors, the ZmCDA1 and ZmCDA2 genes. Both genes diverged when the progenitors of maize split and are derived from the same progenitor as the rice OsCDA1 gene. The ZmCDA1 and ZmCDA2 genes are both transcribed in leaf and seed tissue, but transcripts of the paralogous ZmCDA3 gene have not been found yet. Based on their protein structure the maize CDA genes encode a nucleoside deaminase that is found in bacterial systems and is distinct from the mammalian RNA and/or DNA modifying enzymes. Conclusion The conservation of a paralogous gene sequence encoding a cytidine deaminase gene over 4.5 million years suggests that Helitrons could add functional gene sequences to new chromosomal positions and thereby create new haplotypes. However, the function of such paralogous gene copies cannot be essential because they are not present in all maize strains. However, it is interesting to note that maize hybrids can outperform their inbred parents. Therefore, certain haplotypes may function only in combination with other haplotypes or under specialized environmental conditions.
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Gu YQ, Salse J, Coleman-Derr D, Dupin A, Crossman C, Lazo GR, Huo N, Belcram H, Ravel C, Charmet G, Charles M, Anderson OD, Chalhoub B. Types and rates of sequence evolution at the high-molecular-weight glutenin locus in hexaploid wheat and its ancestral genomes. Genetics 2006; 174:1493-504. [PMID: 17028342 PMCID: PMC1667099 DOI: 10.1534/genetics.106.060756] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The Glu-1 locus, encoding the high-molecular-weight glutenin protein subunits, controls bread-making quality in hexaploid wheat (Triticum aestivum) and represents a recently evolved region unique to Triticeae genomes. To understand the molecular evolution of this locus region, three orthologous Glu-1 regions from the three subgenomes of a single hexaploid wheat species were sequenced, totaling 729 kb of sequence. Comparing each Glu-1 region with its corresponding homologous region from the D genome of diploid wheat, Aegilops tauschii, and the A and B genomes of tetraploid wheat, Triticum turgidum, revealed that, in addition to the conservation of microsynteny in the genic regions, sequences in the intergenic regions, composed of blocks of nested retroelements, are also generally conserved, although a few nonshared retroelements that differentiate the homologous Glu-1 regions were detected in each pair of the A and D genomes. Analysis of the indel frequency and the rate of nucleotide substitution, which represent the most frequent types of sequence changes in the Glu-1 regions, demonstrated that the two A genomes are significantly more divergent than the two B genomes, further supporting the hypothesis that hexaploid wheat may have more than one tetraploid ancestor.
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Affiliation(s)
- Yong Qiang Gu
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA 94710, USA.
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Zhong S, Toubia-Rahme H, Steffenson BJ, Smith KP. Molecular mapping and marker-assisted selection of genes for septoria speckled leaf blotch resistance in barley. PHYTOPATHOLOGY 2006; 96:993-999. [PMID: 18944055 DOI: 10.1094/phyto-96-0993] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
ABSTRACT Septoria speckled leaf blotch (SSLB), caused by Septoria passerinii, has emerged as one of the most important foliar diseases of barley in the Upper Midwest region of the United States. To map and tag genes for SSLB resistance, we developed two populations derived from the resistant accessions CIho 4780 and CIho 10644 and the susceptible malting cv. Foster. Segregation analysis of F(2) plants or F(2:3) families from the Foster/CIho 4780 and Foster/CIho 10644 populations revealed that a single dominant gene conferred resistance at the seedling stage. Bulked segregant analysis identified an amplified fragment length polymorphism marker, E-ACT/M-CAA-170, that co-segregated with the SSLB resistance gene Rsp2 in the Foster/CIho 4780 F(2) population. Southern hybridization analysis with DNA from the wheat/barley addition lines localized E-ACT/M-CAA-170 on the short arm of the barley chromosome 5(1H). Restriction fragment length polymorphism analysis with DNA clones previously mapped to the short arm of chromosome 5(1H) placed Rsp2 at a position flanked by the markers Act8 and ksuD14. A sequence-characterized amplified region (SCAR) marker (E-ACT/M-CAA-170a) was developed that co-segregated with not only Rsp2 in the Foster/CIho 4780 population but also resistance gene Rsp3 in the Foster/CIho 10644 population. This result indicates that Rsp3 is closely linked to Rsp2 on the short arm of chromosome 5(1H). The utility of SCAR marker E-ACT/M-CAA-170a for selecting Rsp2 in two different breeding populations was validated.
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Tian F, Zhu Z, Zhang B, Tan L, Fu Y, Wang X, Sun CQ. Fine mapping of a quantitative trait locus for grain number per panicle from wild rice (Oryza rufipogon Griff.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:619-29. [PMID: 16770601 DOI: 10.1007/s00122-006-0326-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2006] [Accepted: 05/09/2006] [Indexed: 05/10/2023]
Abstract
SIL040, an introgression line (IL) developed by introgressing chromosomal segments from an accession of Oryza rufipogon into an indica cultivar Guichao 2, showed significantly less grains per panicle than the recurrent parent Guichao 2. Quantitative trait locus (QTL) analysis in F2 and F3 generations derived from the cross between SIL040 and Guichao 2 revealed that gpa7, a QTL located on the short arm of chromosome 7, was responsible of this variation. Alleles from O. rufipogon decreased grains per panicle. To fine mapping of gpa7, a high-resolution map with 1,966 F2 plants derived from the cross between SIL040 and Guichao 2 using markers flanking gpa7 was constructed, and detailed quantitative evaluation of the structure of main panicle of each of F3 families derived from recombinants screened was performed. By two-step substitution mapping, gpa7 was finally narrowed down to a 35-kb region that contains five predicted genes in cultivated rice. The fact that QTLs for five panicle traits (length of panicle, primary branches per panicle, secondary branches per panicle, grains on primary branches and grains on secondary branches) were all mapped in the same interval as that for gpa7 suggested that this locus was associated with panicle structure, showing pleiotropic effects. The characterizing of panicle structure of IL SIL040 further revealed that, during the domestication from common wild allele to cultivated rice one at gpa7, not only the number of branches and grains per panicle increased significantly, more importantly, but also the ratio of secondary branches per panicle to total branches per panicle and the ratio of grains on secondary branches per panicle to total grains per panicle increased significantly. All these results reinforced the idea that gpa7 might play an important role in the regulation of grain number per panicle and the ratio of secondary branches per panicle during the domestication of rice panicle.
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Affiliation(s)
- Feng Tian
- Department of Plant Genetic and Breeding and State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100094, People's Republic of China
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32
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Shen X, Francki MG, Ohm HW. A resistance-like gene identified by EST mapping and its association with a QTL controllingFusariumhead blight infection on wheat chromosome 3BS. Genome 2006; 49:631-5. [PMID: 16936842 DOI: 10.1139/g06-010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fusarium head blight (FHB) is a major disease in the wheat growing regions of the world. A quantitative trait locus (QTL) on the short arm of chromosome 3B controls much of the variation for resistance. The cloning of candidate disease-resistance genes for FHB QTLs on chromosome 3B can provide further elucidation of the mechanisms that control resistance. However, rearrangements and divergence during plant genome evolution often hampers the identification of sequences with similarity to known disease-resistance genes. This study focuses on the use of wheat expressed sequence tags (ESTs) that map to the region on chromosome 3B containing the QTL for FHB resistance and low-stringency BLAST searching to identify sequences with similarity to known disease-resistance genes. One EST rich with leucine repeats and low similarity to a protein kinase domain of the barley Rpg1 gene was identified. Genetic mapping using a Ning894037 × Alondra recombinant inbred (RI) population showed that this EST mapped to the QTL on the short arm of chromosome 3B and may represent a portion of a newly diverged gene contributing to FHB resistance. The EST is a new marker suitable for marker-assisted selection and provides a starting point to begin map-based cloning for chromosome walking and investigate new diverged genes at this locus.Key words: Fusarium head blight resistance, expressed sequence tags, quantitative trait loci, Rpg1, wheat.
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Affiliation(s)
- Xiaorong Shen
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
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Yang TJ, Kim JS, Kwon SJ, Lim KB, Choi BS, Kim JA, Jin M, Park JY, Lim MH, Kim HI, Lim YP, Kang JJ, Hong JH, Kim CB, Bhak J, Bancroft I, Park BS. Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa. THE PLANT CELL 2006; 18:1339-47. [PMID: 16632644 PMCID: PMC1475497 DOI: 10.1105/tpc.105.040535] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Strong evidence exists for polyploidy having occurred during the evolution of the tribe Brassiceae. We show evidence for the dynamic and ongoing diploidization process by comparative analysis of the sequences of four paralogous Brassica rapa BAC clones and the homologous 124-kb segment of Arabidopsis thaliana chromosome 5. We estimated the times since divergence of the paralogous and homologous lineages. The three paralogous subgenomes of B. rapa triplicated 13 to 17 million years ago (MYA), very soon after the Arabidopsis and Brassica divergence occurred at 17 to 18 MYA. In addition, a pair of BACs represents a more recent segmental duplication, which occurred approximately 0.8 MYA, and provides an exception to the general expectation of three paralogous segments within the B. rapa genome. The Brassica genome segments show extensive interspersed gene loss relative to the inferred structure of the ancestral genome, whereas the Arabidopsis genome segment appears little changed. Representatives of all 32 genes in the Arabidopsis genome segment are represented in Brassica, but the hexaploid complement of 96 has been reduced to 54 in the three subgenomes, with compression of the genomic region lengths they occupy to between 52 and 110 kb. The gene content of the recently duplicated B. rapa genome segments is identical, but intergenic sequences differ.
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Affiliation(s)
- Tae-Jin Yang
- Brassica Genomics Team, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon 441-707, Korea
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He G, Luo X, Tian F, Li K, Zhu Z, Su W, Qian X, Fu Y, Wang X, Sun C, Yang J. Haplotype variation in structure and expression of a gene cluster associated with a quantitative trait locus for improved yield in rice. Genome Res 2006; 16:618-26. [PMID: 16606701 PMCID: PMC1457051 DOI: 10.1101/gr.4814006] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
By constructing nearly isogenic lines (NILs) that differ only at a single quantitative trait locus (QTL), we fine-mapped the yield-improving QTL qGY2-1 to a 102.9-kb region on rice chromosome 2. Comparison analysis of the genomic sequences in the mapped QTL region between the donor (Dongxiang wild rice, Oryza rufipogon Griff.) and recurrent (Guichao2, Oryza sativa ssp. indica) parents used for the development of NILs identified the haplotypes of a leucine-rich repeat receptor kinase gene cluster, which showed extensive allelic variation. The sequences between genes in the cluster had a very high rate of divergence. More importantly, the genes themselves also differed between two haplotypes: Only 92% identity was observed for one allele, and another allele was found to have completely lost its allelic counterpart in Guichao2. The other six shared genes all showed >98% identity, and four of these exhibited obvious regulatory variation. The same haplotype segments also differed in length (43.9-kb in Guichao2 vs. 52.6-kb in Dongxiang wild rice). Such extensive sequence variation was also observed between orthologous regions of indica (cv. 93-11) and japonica (cv. Nipponbare) subspecies of Oryza sativa. Different rates of sequence divergence within the cluster have resulted in haplotype variability in 13 rice accessions. We also detected allelic expression variation in this gene cluster, in which some genes gave unequal expression of alleles in hybrids. These allelic variations in structure and expression suggest that the leucine-rich repeat receptor kinase gene cluster identified in our study should be a particularly good candidate for the source of the yield QTL.
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Affiliation(s)
- Guangming He
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xiaojin Luo
- Department of Plant Genetics and Breeding and State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100094, China
- Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
- Beijing Key Laboratory of Crop Genetic Improvement, Beijing 100094, China
- Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, Beijing 100094, China
| | - Feng Tian
- Department of Plant Genetics and Breeding and State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100094, China
- Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
- Beijing Key Laboratory of Crop Genetic Improvement, Beijing 100094, China
- Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, Beijing 100094, China
| | - Kegui Li
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Zuofeng Zhu
- Department of Plant Genetics and Breeding and State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100094, China
- Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
- Beijing Key Laboratory of Crop Genetic Improvement, Beijing 100094, China
- Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, Beijing 100094, China
| | - Wei Su
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xiaoyin Qian
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yongcai Fu
- Department of Plant Genetics and Breeding and State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100094, China
- Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
- Beijing Key Laboratory of Crop Genetic Improvement, Beijing 100094, China
- Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, Beijing 100094, China
| | - Xiangkun Wang
- Department of Plant Genetics and Breeding and State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100094, China
- Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
- Beijing Key Laboratory of Crop Genetic Improvement, Beijing 100094, China
- Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, Beijing 100094, China
| | - Chuanqing Sun
- Department of Plant Genetics and Breeding and State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100094, China
- Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing 100094, China
- Beijing Key Laboratory of Crop Genetic Improvement, Beijing 100094, China
- Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, Beijing 100094, China
- Corresponding authors.E-mail ; fax 86-10-62731811.E-mail ; fax 86-21-65648376
| | - Jinshui Yang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
- Corresponding authors.E-mail ; fax 86-10-62731811.E-mail ; fax 86-21-65648376
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Morgante M. Plant genome organisation and diversity: the year of the junk! Curr Opin Biotechnol 2006; 17:168-73. [PMID: 16530402 DOI: 10.1016/j.copbio.2006.03.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2006] [Revised: 02/28/2006] [Accepted: 03/02/2006] [Indexed: 01/21/2023]
Abstract
Having gained a thorough understanding of the structure and organization of model plant genomes, such as those of Arabidopsis thaliana and rice, we have now started to investigate the most interesting aspect of genome structure - its variations. Variation in DNA sequence is responsible for the genetic component of phenotypic variation (i.e. the component upon which both natural and artificial selection act). Recent studies have started to shed light on sequence variation outside of the genic regions, owing mainly to large insertion/deletion (indel) polymorphisms caused by the presence or absence of transposable elements of different classes. In addition to long terminal repeat retrotransposons, DNA transposons have been shown to be responsible for these polymorphisms. These comprise Helitrons, CACTA and Mu-like elements that are capable of acquiring and piecing together fragments of plant genes and are often expressed. Future analyses of the functional roles of intergenic sequence variation will tell us if we will need to pay more attention not only to genes, but also to the 'junk' DNA surrounding them.
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Affiliation(s)
- Michele Morgante
- Dipartimento di Scienze Agrarie ed Ambientali, Universita' di Udine, Via delle Scienze 208, I-33100 Udine, Italy.
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Valárik M, Linkiewicz AM, Dubcovsky J. A microcolinearity study at the earliness per se gene Eps-A(m)1 region reveals an ancient duplication that preceded the wheat-rice divergence. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 112:945-57. [PMID: 16432738 DOI: 10.1007/s00122-005-0198-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Accepted: 12/14/2005] [Indexed: 05/06/2023]
Abstract
Wheat flowering is controlled by numerous genes, which respond to environmental signals such as photoperiod and vernalization. Earliness per se (Eps) genes control flowering time independently of these environmental cues and are responsible for the fine tuning of flowering time. We recently mapped the Eps-A(m)1 gene on the end of Triticum monococcum chromosome arm 1A(m)L. As a part of our efforts to clone Eps-A(m)1 we developed PCR markers flanking this gene within a 2.7 cM interval. We screened more than one thousand gametes with these markers and identified 27 lines with recombination between them. Recombinant lines were used to generate a high-density map and to investigate the microcolinearity between wheat and rice in this region. We mapped ten genes from a 149 kb region located at the distal part of rice chromosome 5 (cdo393 - Ndk3) on a 3.7 cM region on wheat chromosome one. This region is part of an ancient duplication between rice chromosomes 5 and 1. Genes present in both rice chromosomes were less similar to each other than to the closest wheat orthologues, suggesting that this duplication preceded the divergence between wheat and rice. This hypothesis was supported by the presence of 18 loci duplicated both in rice chromosomes 5 and 1 and in the colinear wheat chromosomes from homologous groups 1 and 3. Independent gene deletions in wheat and rice lineages explain the alternations of colinearity between rice chromosome 5 and wheat chromosomes 1 and 3. Colinearity between the end of rice chromosome 5 and wheat chromosome 1 was also interrupted by a small inversion, and several non-colinear genes. These results suggest that the distal region of the long arm of wheat chromosome 1 was involved in numerous changes that differentiated wheat and rice genomes. This comparative study provided sufficient markers to saturate the Eps-A(m)1 gene region and to precisely map this gene within a 0.9 cM interval flanked by the VatpC and Smp loci.
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Affiliation(s)
- M Valárik
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA 95616, USA
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Brooks SA, Huang L, Herbel MN, Gill BS, Brown-Guedira G, Fellers JP. Structural variation and evolution of a defense-gene cluster in natural populations of Aegilops tauschii. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 112:618-26. [PMID: 16402192 DOI: 10.1007/s00122-005-0160-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2005] [Accepted: 11/13/2005] [Indexed: 05/06/2023]
Abstract
Genetic mapping and sequencing of plant genomes have been useful for investigating eukaryotic chromosome structural organization. In many cases, analyses have been limited in the number of representatives sampled from specific groups. The degree of intraspecific genome diversity remains in question. The possibility exists that a single model genome may have limited utility for identifying genes in related members of the species or genus. Crop improvement programs have particular interests in disease resistance genes that are harbored by wild relatives of modern cultivated crops. These genes are evolutionarily dynamic and under selective pressure by a broad range of pathogenic organisms. Using resistance gene analogs as models for gene evolution, intraspecific genome comparisons were made among populations of wild diploid wheat (Aegilops tauschii). We observed that deletion haplotypes are occurring frequently and independently in the genome. Haplotypes are geographically correlated and maintenance of gene complements in localized populations indicates selective advantage. Furthermore, deletion haplotypes are not detrimental to plant health, since genes without adaptive value in alternate environments are eliminated from the genome. Deletion haplotypes appear to be a common form of allelic variation in plants, and we address the consequences on genome restructuring and gene evolution.
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Affiliation(s)
- Steven A Brooks
- Plant Science and Entomology Unit, Department of Plant Pathology, USDA-ARS, Manhattan, KS, 66506, USA
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Liu S, Zhang X, Pumphrey MO, Stack RW, Gill BS, Anderson JA. Complex microcolinearity among wheat, rice, and barley revealed by fine mapping of the genomic region harboring a major QTL for resistance to Fusarium head blight in wheat. Funct Integr Genomics 2005; 6:83-9. [PMID: 16270217 DOI: 10.1007/s10142-005-0007-y] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2005] [Revised: 09/04/2005] [Accepted: 09/04/2005] [Indexed: 10/25/2022]
Abstract
A major quantitative trait locus (QTL), Qfhs.ndsu-3BS, for resistance to Fusarium head blight (FHB) in wheat has been identified and verified by several research groups. The objectives of this study were to construct a fine genetic map of this QTL region and to examine microcolinearity in the QTL region among wheat, rice, and barley. Two simple sequence repeat (SSR) markers (Xgwm533 and Xgwm493) flanking this QTL were used to screen for recombinants in a population of 3,156 plants derived from a single F(7) plant heterozygous for the Qfhs.ndsu-3BS region. A total of 382 recombinants were identified, and they were genotyped with two more SSR markers and eight sequence-tagged site (STS) markers. A fine genetic map of the Qfhs.ndsu-3BS region was constructed and spanned 6.3 cM. Based on replicated evaluations of homozygous recombinant lines for Type II FHB resistance, Qfhs.ndsu-3BS, redesignated as Fhb1, was placed into a 1.2-cM marker interval flanked by STS3B-189 and STS3B-206. Primers of STS markers were designed from wheat expressed sequence tags homologous to each of six barley genes expected to be located near this QTL region. A comparison of the wheat fine genetic map and physical maps of rice and barley revealed inversions and insertions/deletions. This suggests a complex microcolinearity among wheat, rice, and barley in this QTL region.
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Affiliation(s)
- Sixin Liu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
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Abstract
Comparative mapping studies have revealed a great deal about the patterns of gene order and gene content evolution in plants. These findings have practical importance for leveraging genomic information from model to nonmodel plant species. However, there is much to be learned about the processes by which gene order and content evolve. The role of gene duplication and loss in the evolution of plant gene order, in particular, appears to be more important than commonly appreciated. An exciting area of current research is the study of gene order and content polymorphism within species. Some recent findings suggest that there may be a functional, and adaptive, relationship between gene order and phenotype that is mediated by the effects of gene order on transcriptional regulation.
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Affiliation(s)
- Todd J Vision
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA.
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Brunner S, Pea G, Rafalski A. Origins, genetic organization and transcription of a family of non-autonomous helitron elements in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 43:799-810. [PMID: 16146520 DOI: 10.1111/j.1365-313x.2005.02497.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Helitron transposable elements carrying gene fragments were recently discovered in maize. These elements are frequently specific to certain maize lineages. Here we report evidence supporting the involvement of helitrons in the rapid evolution of the maize genome, in particular in the multiplication of related genic fragments across the genome. We describe a family of four closely related, non-autonomous maize helitrons and their insertion sites at four non-allelic genetic loci across the maize genome: two specific to the B73 inbred, and two to the Mo17 inbred. We propose the phylogeny of this helitron family and provide an approximate timeline of their genomic insertions. One of these elements, the Mo17-specific helitron on chromosome 1 (bin 1.07), is transcriptionally active, probably as a result of insertion in the vicinity of a promoter. Significantly, it produces an alternatively spliced and chimeric transcript joining together genic segments of different chromosomal origin contained within the helitron. This transcript potentially encodes up to four open reading frames. During the course of evolution, transcribed helitrons containing multiple gene fragments may occasionally give rise to new genes with novel biochemical functions by a combinatorial assembly of exons. Thus helitrons not only constantly reshape the genomic organization of maize and profoundly affect its genetic diversity, but also may be involved in the evolution of gene function.
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Affiliation(s)
- Stephan Brunner
- DuPont Crop Genetics Research, Experimental Station, Building E353, Wilmington, DE 19880-353, USA.
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Lai J, Li Y, Messing J, Dooner HK. Gene movement by Helitron transposons contributes to the haplotype variability of maize. Proc Natl Acad Sci U S A 2005; 102:9068-73. [PMID: 15951422 PMCID: PMC1157042 DOI: 10.1073/pnas.0502923102] [Citation(s) in RCA: 214] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Different maize inbred lines are polymorphic for the presence or absence of genic sequences at various allelic chromosomal locations. In the bz genomic region, located in 9S, sequences homologous to four different genes from rice and Arabidopsis are present in line McC but absent from line B73. It is shown here that this apparent intraspecific violation of genetic colinearity arises from the movement of genes or gene fragments by Helitrons, a recently discovered class of eukaryotic transposons. Two Helitrons, HelA and HelB, account for all of the genic differences distinguishing the two bz locus haplotypes. HelA is 5.9 kb long and contains sequences for three of the four genes found only in the McC bz genomic region. A nearly identical copy of HelA was isolated from a 5S chromosomal location in B73. Both the 9S and 5S sites appear to be polymorphic in maize, suggesting that these Helitrons have been active recently. Helitrons lack the strong predictive terminal features of other transposons, so the definition of their ends is greatly facilitated by the identification of their vacant sites in Helitron-minus lines. The ends of the 2.7-kb HelB Helitron were discerned from a comparison of the McC haplotype sequence with that of yet a third line, Mo17, because the HelB vacant site is deleted in B73. Maize Helitrons resemble rice Pack-MULEs in their ability to capture genes or gene fragments from several loci and move them around the genome, features that confer on them a potential role in gene evolution.
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Affiliation(s)
- Jinsheng Lai
- The Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ 08855, USA
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