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Mascher M, Marone MP, Schreiber M, Stein N. Are cereal grasses a single genetic system? NATURE PLANTS 2024; 10:719-731. [PMID: 38605239 DOI: 10.1038/s41477-024-01674-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 03/17/2024] [Indexed: 04/13/2024]
Abstract
In 1993, a passionate and provocative call to arms urged cereal researchers to consider the taxon they study as a single genetic system and collaborate with each other. Since then, that group of scientists has seen their discipline blossom. In an attempt to understand what unity of genetic systems means and how the notion was borne out by later research, we survey the progress and prospects of cereal genomics: sequence assemblies, population-scale sequencing, resistance gene cloning and domestication genetics. Gene order may not be as extraordinarily well conserved in the grasses as once thought. Still, several recurring themes have emerged. The same ancestral molecular pathways defining plant architecture have been co-opted in the evolution of different cereal crops. Such genetic convergence as much as cross-fertilization of ideas between cereal geneticists has led to a rich harvest of genes that, it is hoped, will lead to improved varieties.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Marina Püpke Marone
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Mona Schreiber
- University of Marburg, Department of Biology, Marburg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany.
- Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
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2
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Adel S, Carels N. Plant Tolerance to Drought Stress with Emphasis on Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112170. [PMID: 37299149 DOI: 10.3390/plants12112170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/16/2023] [Accepted: 03/29/2023] [Indexed: 06/12/2023]
Abstract
Environmental stresses, such as drought, have negative effects on crop yield. Drought is a stress whose impact tends to increase in some critical regions. However, the worldwide population is continuously increasing and climate change may affect its food supply in the upcoming years. Therefore, there is an ongoing effort to understand the molecular processes that may contribute to improving drought tolerance of strategic crops. These investigations should contribute to delivering drought-tolerant cultivars by selective breeding. For this reason, it is worthwhile to review regularly the literature concerning the molecular mechanisms and technologies that could facilitate gene pyramiding for drought tolerance. This review summarizes achievements obtained using QTL mapping, genomics, synteny, epigenetics, and transgenics for the selective breeding of drought-tolerant wheat cultivars. Synthetic apomixis combined with the msh1 mutation opens the way to induce and stabilize epigenomes in crops, which offers the potential of accelerating selective breeding for drought tolerance in arid and semi-arid regions.
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Affiliation(s)
- Sarah Adel
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Nicolas Carels
- Laboratory of Biological System Modeling, Center of Technological Development for Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro 21040-361, Brazil
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3
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Levy AA, Feldman M. Evolution and origin of bread wheat. THE PLANT CELL 2022; 34:2549-2567. [PMID: 35512194 PMCID: PMC9252504 DOI: 10.1093/plcell/koac130] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/18/2022] [Indexed: 05/12/2023]
Abstract
Bread wheat (Triticum aestivum, genome BBAADD) is a young hexaploid species formed only 8,500-9,000 years ago through hybridization between a domesticated free-threshing tetraploid progenitor, genome BBAA, and Aegilops tauschii, the diploid donor of the D subgenome. Very soon after its formation, it spread globally from its cradle in the fertile crescent into new habitats and climates, to become a staple food of humanity. This extraordinary global expansion was probably enabled by allopolyploidy that accelerated genetic novelty through the acquisition of new traits, new intergenomic interactions, and buffering of mutations, and by the attractiveness of bread wheat's large, tasty, and nutritious grain with high baking quality. New genome sequences suggest that the elusive donor of the B subgenome is a distinct (unknown or extinct) species rather than a mosaic genome. We discuss the origin of the diploid and tetraploid progenitors of bread wheat and the conflicting genetic and archaeological evidence on where it was formed and which species was its free-threshing tetraploid progenitor. Wheat experienced many environmental changes throughout its evolution, therefore, while it might adapt to current climatic changes, efforts are needed to better use and conserve the vast gene pool of wheat biodiversity on which our food security depends.
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Affiliation(s)
- Avraham A Levy
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Moshe Feldman
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100 Israel
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Robert NSM, Sarigol F, Zimmermann B, Meyer A, Voolstra CR, Simakov O. Emergence of distinct syntenic density regimes is associated with early metazoan genomic transitions. BMC Genomics 2022; 23:143. [PMID: 35177000 PMCID: PMC8851819 DOI: 10.1186/s12864-022-08304-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/10/2022] [Indexed: 12/03/2022] Open
Abstract
Background Animal genomes are strikingly conserved in terms of local gene order (microsynteny). While some of these microsyntenies have been shown to be coregulated or to form gene regulatory blocks, the diversity of their genomic and regulatory properties across the metazoan tree of life remains largely unknown. Results Our comparative analyses of 49 animal genomes reveal that the largest gains of synteny occurred in the last common ancestor of bilaterians and cnidarians and in that of bilaterians. Depending on their node of emergence, we further show that novel syntenic blocks are characterized by distinct functional compositions (Gene Ontology terms enrichment) and gene density properties, such as high, average and low gene density regimes. This is particularly pronounced among bilaterian novel microsyntenies, most of which fall into high gene density regime associated with higher gene coexpression levels. Conversely, a majority of vertebrate novel microsyntenies display a low gene density regime associated with lower gene coexpression levels. Conclusions Our study provides first evidence for evolutionary transitions between different modes of microsyntenic block regulation that coincide with key events of metazoan evolution. Moreover, the microsyntenic profiling strategy and interactive online application (Syntenic Density Browser, available at: http://synteny.csb.univie.ac.at/) we present here can be used to explore regulatory properties of microsyntenic blocks and predict their coexpression in a wide-range of animal genomes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08304-2.
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Affiliation(s)
- Nicolas S M Robert
- Department of Neurosciences and Developmental Biology, University of Vienna, Althanstrasse 14, 1090, Wien, Austria.
| | - Fatih Sarigol
- Department of Neurosciences and Developmental Biology, University of Vienna, Althanstrasse 14, 1090, Wien, Austria
| | - Bob Zimmermann
- Department of Neurosciences and Developmental Biology, University of Vienna, Althanstrasse 14, 1090, Wien, Austria
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78457, Constance, Germany
| | | | - Oleg Simakov
- Department of Neurosciences and Developmental Biology, University of Vienna, Althanstrasse 14, 1090, Wien, Austria.
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Shariatipour N, Heidari B, Tahmasebi A, Richards C. Comparative Genomic Analysis of Quantitative Trait Loci Associated With Micronutrient Contents, Grain Quality, and Agronomic Traits in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:709817. [PMID: 34712248 PMCID: PMC8546302 DOI: 10.3389/fpls.2021.709817] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/06/2021] [Indexed: 05/02/2023]
Abstract
Comparative genomics and meta-quantitative trait loci (MQTLs) analysis are important tools for the identification of reliable and stable QTLs and functional genes controlling quantitative traits. We conducted a meta-analysis to identify the most stable QTLs for grain yield (GY), grain quality traits, and micronutrient contents in wheat. A total of 735 QTLs retrieved from 27 independent mapping populations reported in the last 13 years were used for the meta-analysis. The results showed that 449 QTLs were successfully projected onto the genetic consensus map which condensed to 100 MQTLs distributed on wheat chromosomes. This consolidation of MQTLs resulted in a three-fold reduction in the confidence interval (CI) compared with the CI for the initial QTLs. Projection of QTLs revealed that the majority of QTLs and MQTLs were in the non-telomeric regions of chromosomes. The majority of micronutrient MQTLs were located on the A and D genomes. The QTLs of thousand kernel weight (TKW) were frequently associated with QTLs for GY and grain protein content (GPC) with co-localization occurring at 55 and 63%, respectively. The co- localization of QTLs for GY and grain Fe was found to be 52% and for QTLs of grain Fe and Zn, it was found to be 66%. The genomic collinearity within Poaceae allowed us to identify 16 orthologous MQTLs (OrMQTLs) in wheat, rice, and maize. Annotation of promising candidate genes (CGs) located in the genomic intervals of the stable MQTLs indicated that several CGs (e.g., TraesCS2A02G141400, TraesCS3B02G040900, TraesCS4D02G323700, TraesCS3B02G077100, and TraesCS4D02G290900) had effects on micronutrients contents, yield, and yield-related traits. The mapping refinements leading to the identification of these CGs provide an opportunity to understand the genetic mechanisms driving quantitative variation for these traits and apply this information for crop improvement programs.
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Affiliation(s)
- Nikwan Shariatipour
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Bahram Heidari
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Ahmad Tahmasebi
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Christopher Richards
- USDA ARS National Laboratory for Genetic Resources Preservation, Fort Collins, CO, United States
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Tufan HA, Taşkin BG, Maccormack R, Boyd LA, Kaya Z, Türet M. The utility of NBS-profiling for characterization of yellow rust resistance in an F 6 durum wheat population. J Genet 2019; 98:98. [PMID: 31767816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Seedling and adult plant (field) resistance to yellow rust in the durum wheat (Triticum turgidum ssp. durum) cross Kunduru-1149 x Cham-1 was characterized using a functionally-targeted DNA marker system, NBS-profiling. Chi-squared analysis indicated a four gene model conferring seedling yellow rust resistance against Puccinia striiformis f. sp. tritici isolate WYR85/22 (virulent on Yr2, Yr6, Yr7 and Yr9). Interval mapping located two QTL for yellow rust resistance on the long arm of chromosome 1B, while Kruskal-Wallis single marker regression identified a number of additional marker loci associated with seedling and/or adult plant, field resistance to yellow rust. These results suggested that much of the yellow rust resistance seen in the field may be due to seedling expressed resistance (R) genes. Characterization of the DNA sequence of three NBS marker loci indicated that all showed significant homology to functionally-characterized R-genes and resistance gene analogues (RGAs), with the greatest homology being NBS-LRR-type R-genes and RGAs from cereal species.
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Affiliation(s)
- Hale A Tufan
- Department of Molecular Biology and Genetics, Bogazici University, 34342 Bebek, Istanbul, Turkey.
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7
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The utility of NBS-profiling for characterization of yellow rust resistance in an F6 durum wheat population. J Genet 2019. [DOI: 10.1007/s12041-019-1143-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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8
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Kumar A, Batra R, Gahlaut V, Gautam T, Kumar S, Sharma M, Tyagi S, Singh KP, Balyan HS, Pandey R, Gupta PK. Genome-wide identification and characterization of gene family for RWP-RK transcription factors in wheat (Triticum aestivum L.). PLoS One 2018; 13:e0208409. [PMID: 30540790 PMCID: PMC6291158 DOI: 10.1371/journal.pone.0208409] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 11/17/2018] [Indexed: 02/07/2023] Open
Abstract
RWP-RKs represent a small family of transcription factors (TFs) that are unique to plants and function particularly under conditions of nitrogen starvation. These RWP-RKs have been classified in two sub-families, NLPs (NIN-like proteins) and RKDs (RWP-RK domain proteins). NLPs regulate tissue-specific expression of genes involved in nitrogen use efficiency (NUE) and RKDs regulate expression of genes involved in gametogenesis/embryogenesis. During the present study, using in silico approach, 37 wheat RWP-RK genes were identified, which included 18 TaNLPs (2865 to 7340 bp with 4/5 exons), distributed on 15 chromosomes from 5 homoeologous groups (with two genes each on 4B,4D and 5A) and 19 TaRKDs (1064 to 5768 bp with 1 to 6 exons) distributed on 12 chromosomes from 4 homoeologous groups (except groups 1, 4 and 5); 2–3 splice variants were also available in 9 of the 37 genes. Sixteen (16) of these genes also carried 24 SSRs (simple sequence repeats), while 11 genes had targets for 13 different miRNAs. At the protein level, MD simulation analysis suggested their interaction with nitrate-ions. Significant differences were observed in the expression of only two (TaNLP1 and TaNLP2) of the nine representative genes that were used for in silico expression analysis under varying levels of N at post-anthesis stage (data for other genes was not available for in silico expression analysis). Differences in expression were also observed during qRT-PCR, when expression of four representative genes (TaNLP2, TaNLP7, TaRKD6 and TaRKD9) was examined in roots and shoots of seedlings (under different conditions of N supply) in two contrasting genotypes which differed in NUE (C306 with low NUE and HUW468 with high NUE). These four genes for qRT-PCR were selected on the basis of previous literature, level of homology and the level of expression (in silico study). In particular, the TaNLP7 gene showed significant up-regulation in the roots and shoots of HUW468 (with higher NUE) during N-starvation; this gene has already been characterized in Arabidopsis and tobacco, and is known to be involved in nitrate-signal transduction pathway.
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Affiliation(s)
- Anuj Kumar
- Advance Center for Computational & Applied Biotechnology, Uttarakhand Council for Biotechnology (UCB), Dehradun, India
| | - Ritu Batra
- Department of Genetics and Plant Breeding, CCS University, Meerut, India
| | - Vijay Gahlaut
- Department of Plant Molecular Biology, South Campus, University of Delhi, Delhi, India
| | - Tinku Gautam
- Department of Genetics and Plant Breeding, CCS University, Meerut, India
| | - Sanjay Kumar
- Bioinformatics Centre, Biotech Park, Lucknow, India
| | - Mansi Sharma
- ICMR- National Institute of Cancer Prevention and Research, Noida, India
| | - Sandhya Tyagi
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Krishna Pal Singh
- Advance Center for Computational & Applied Biotechnology, Uttarakhand Council for Biotechnology (UCB), Dehradun, India
- Ch. Charan Singh Haryana Agricultural University, Hisar, India
| | | | - Renu Pandey
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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9
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Ariyarathna HACK, Oldach KH, Francki MG. A comparative gene analysis with rice identified orthologous group II HKT genes and their association with Na(+) concentration in bread wheat. BMC PLANT BIOLOGY 2016; 16:21. [PMID: 26786911 PMCID: PMC4719669 DOI: 10.1186/s12870-016-0714-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 01/14/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND Although the HKT transporter genes ascertain some of the key determinants of crop salt tolerance mechanisms, the diversity and functional role of group II HKT genes are not clearly understood in bread wheat. The advanced knowledge on rice HKT and whole genome sequence was, therefore, used in comparative gene analysis to identify orthologous wheat group II HKT genes and their role in trait variation under different saline environments. RESULTS The four group II HKTs in rice identified two orthologous gene families from bread wheat, including the known TaHKT2;1 gene family and a new distinctly different gene family designated as TaHKT2;2. A single copy of TaHKT2;2 was found on each homeologous chromosome arm 7AL, 7BL and 7DL and each gene was expressed in leaf blade, sheath and root tissues under non-stressed and at 200 mM salt stressed conditions. The proteins encoded by genes of the TaHKT2;2 family revealed more than 93% amino acid sequence identity but ≤52% amino acid identity compared to the proteins encoded by TaHKT2;1 family. Specifically, variations in known critical domains predicted functional differences between the two protein families. Similar to orthologous rice genes on chromosome 6L, TaHKT2;1 and TaHKT2;2 genes were located approximately 3 kb apart on wheat chromosomes 7AL, 7BL and 7DL, forming a static syntenic block in the two species. The chromosomal region on 7AL containing TaHKT2;1 7AL-1 co-located with QTL for shoot Na(+) concentration and yield in some saline environments. CONCLUSION The differences in copy number, genes sequences and encoded proteins between TaHKT2;2 homeologous genes and other group II HKT gene families within and across species likely reflect functional diversity for ion selectivity and transport in plants. Evidence indicated that neither TaHKT2;2 nor TaHKT2;1 were associated with primary root Na(+) uptake but TaHKT2;1 may be associated with trait variation for Na(+) exclusion and yield in some but not all saline environments.
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Affiliation(s)
- H A Chandima K Ariyarathna
- School of Plant Biology and Institute of Agriculture, The University of Western Australia, Crawley, 6009, Western Australia.
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, 6150, Western Australia.
| | - Klaus H Oldach
- South Australia Research Development Institute, Plant Genomics Centre, Waite Research Precinct, Urrbrae, 5064, South Australia.
| | - Michael G Francki
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, 6150, Western Australia.
- Department of Agriculture and Food Western Australia, South Perth, 6151, Western Australia.
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10
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Muñoz-Amatriaín M, Lonardi S, Luo M, Madishetty K, Svensson JT, Moscou MJ, Wanamaker S, Jiang T, Kleinhofs A, Muehlbauer GJ, Wise RP, Stein N, Ma Y, Rodriguez E, Kudrna D, Bhat PR, Chao S, Condamine P, Heinen S, Resnik J, Wing R, Witt HN, Alpert M, Beccuti M, Bozdag S, Cordero F, Mirebrahim H, Ounit R, Wu Y, You F, Zheng J, Simková H, Dolezel J, Grimwood J, Schmutz J, Duma D, Altschmied L, Blake T, Bregitzer P, Cooper L, Dilbirligi M, Falk A, Feiz L, Graner A, Gustafson P, Hayes PM, Lemaux P, Mammadov J, Close TJ. Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:216-27. [PMID: 26252423 PMCID: PMC5014227 DOI: 10.1111/tpj.12959] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/15/2015] [Accepted: 07/24/2015] [Indexed: 05/18/2023]
Abstract
Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley-Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant.
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Affiliation(s)
- María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Stefano Lonardi
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - MingCheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Kavitha Madishetty
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Jan T Svensson
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Nordic Genetic Resource Center, SE-23053, Alnarp, Sweden
| | - Matthew J Moscou
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Steve Wanamaker
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Tao Jiang
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Andris Kleinhofs
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Gary J Muehlbauer
- Department of Plant Biology, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Roger P Wise
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service & Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011-1020, USA
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Yaqin Ma
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Molefarming Laboratory USA, Davis, CA, 95616, USA
| | - Edmundo Rodriguez
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Departamento de Ciencias Basicas, Universidad Autonoma Agraria Antonio Narro, Narro 1923, Saltillo, Coah, 25315, México
| | - Dave Kudrna
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Prasanna R Bhat
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Monsanto Research Center, Bangalore, 560092, India
| | - Shiaoman Chao
- USDA-ARS Biosciences Research Lab, Fargo, ND, 58105, USA
| | - Pascal Condamine
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Shane Heinen
- Department of Plant Biology, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Josh Resnik
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Ronald Reagan UCLA Medical Center, Los Angeles, CA, 90095, USA
| | - Rod Wing
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Heather N Witt
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Matthew Alpert
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Turtle Rock Studios, Lake Forest, CA, 92630, USA
| | - Marco Beccuti
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Department of Computer Science, University of Turin, Corso Svizzera 185, 10149, Turin, Italy
| | - Serdar Bozdag
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Deptartment of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, 53233, USA
| | - Francesca Cordero
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Department of Computer Science, University of Turin, Corso Svizzera 185, 10149, Turin, Italy
| | - Hamid Mirebrahim
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Rachid Ounit
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Yonghui Wu
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Google Inc., Mountain View, CA, 94043, USA
| | - Frank You
- USDA-ARS, Albany, CA, 94710, USA
- Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Jie Zheng
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- School of Computer Engineering, Nanyang Technological University, Nanyang Avenue, Singapore, 639798, Singapore
| | - Hana Simková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovskį 6, CZ-77200, Olomouc, Czech Republic
| | - Jaroslav Dolezel
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovskį 6, CZ-77200, Olomouc, Czech Republic
| | - Jane Grimwood
- Hudson Alpha Genome Sequencing Center, DOE Joint Genome Institute, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- Hudson Alpha Genome Sequencing Center, DOE Joint Genome Institute, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Denisa Duma
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Houston, TX, 77030, USA
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Tom Blake
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA
| | | | - Laurel Cooper
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Muharrem Dilbirligi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- International Cooperation Department, The Scientific and Technological Research Council of Turkey, Tunus cad. No: 80, 06100, Kavaklidere, Ankara, Turkey
| | - Anders Falk
- Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Leila Feiz
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA
- Boyce Thompson Institute for Plant Research, Cornell University, 533 Tower Road, Ithaca, NY, 14853-1801, USA
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | | | - Patrick M Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Peggy Lemaux
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Jafar Mammadov
- Department of Crop & Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
- Dow AgroSciences LLC, Indianapolis, IN, 46268-1054, USA
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
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11
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Rastogi S, Kalra A, Gupta V, Khan F, Lal RK, Tripathi AK, Parameswaran S, Gopalakrishnan C, Ramaswamy G, Shasany AK. Unravelling the genome of Holy basil: an "incomparable" "elixir of life" of traditional Indian medicine. BMC Genomics 2015; 16:413. [PMID: 26017011 PMCID: PMC4445982 DOI: 10.1186/s12864-015-1640-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 05/18/2015] [Indexed: 01/22/2023] Open
Abstract
Background Ocimum sanctum L. (O. tenuiflorum) family-Lamiaceae is an important component of Indian tradition of medicine as well as culture around the world, and hence is known as “Holy basil” in India. This plant is mentioned in the ancient texts of Ayurveda as an “elixir of life” (life saving) herb and worshipped for over 3000 years due to its healing properties. Although used in various ailments, validation of molecules for differential activities is yet to be fully analyzed, as about 80 % of the patents on this plant are on extracts or the plant parts, and mainly focussed on essential oil components. With a view to understand the full metabolic potential of this plant whole nuclear and chloroplast genomes were sequenced for the first time combining the sequence data from 4 libraries and three NGS platforms. Results The saturated draft assembly of the genome was about 386 Mb, along with the plastid genome of 142,245 bp, turning out to be the smallest in Lamiaceae. In addition to SSR markers, 136 proteins were identified as homologous to five important plant genomes. Pathway analysis indicated an abundance of phenylpropanoids in O. sanctum. Phylogenetic analysis for chloroplast proteome placed Salvia miltiorrhiza as the nearest neighbor. Comparison of the chemical compounds and genes availability in O. sanctum and S. miltiorrhiza indicated the potential for the discovery of new active molecules. Conclusion The genome sequence and annotation of O. sanctum provides new insights into the function of genes and the medicinal nature of the metabolites synthesized in this plant. This information is highly beneficial for mining biosynthetic pathways for important metabolites in related species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1640-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shubhra Rastogi
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015, U.P., India.
| | - Alok Kalra
- Microbial Technology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015, Uttar Pradesh, India.
| | - Vikrant Gupta
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015, U.P., India.
| | - Feroz Khan
- Metabolic and Structural Biology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015, U.P., India.
| | - Raj Kishori Lal
- Genetics and Plant Breeding Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015, U.P., India.
| | - Anil Kumar Tripathi
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015, U.P., India.
| | - Sriram Parameswaran
- Research and Development Unit, Genotypic Technology Private Limited, Bangalore, Karnataka, 560094, India.
| | - Chellappa Gopalakrishnan
- Research and Development Unit, Genotypic Technology Private Limited, Bangalore, Karnataka, 560094, India.
| | - Gopalakrishna Ramaswamy
- Research and Development Unit, Genotypic Technology Private Limited, Bangalore, Karnataka, 560094, India.
| | - Ajit Kumar Shasany
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015, U.P., India.
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12
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Periyannan S, Bansal U, Bariana H, Deal K, Luo MC, Dvorak J, Lagudah E. Identification of a robust molecular marker for the detection of the stem rust resistance gene Sr45 in common wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:947-55. [PMID: 24469473 DOI: 10.1007/s00122-014-2270-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 01/12/2014] [Indexed: 05/09/2023]
Abstract
Fine mapping of the Ug99 effective stem rust resistance gene Sr45 introgressed into common wheat from the D -genome goatgrass Aegilops tauschii. Stem rust resistance gene Sr45, discovered in Aegilops tauschii, the progenitor of the D -genome of wheat, is effective against commercially important Puccinia graminis f. sp. tritici races prevalent in Australia, South Africa and the Ug99 race group. A synthetic hexaploid wheat (RL5406) generated by crossing Ae. tauschii accession RL5289 (carrying Sr45 and the leaf rust resistance gene Lr21) with a tetraploid experimental line 'TetraCanthatch' was previously used as the source in the transfer of these rust resistance genes to other hexaploid cultivars. Previous genetic studies on hexaploid wheats mapped Sr45 on the short arm of chromosome 1D with the following gene order: centromere-Sr45-Sr33-Lr21-telomere. To identify closely linked markers, we fine mapped the Sr45 region in a large mapping population generated by crossing CS1D5406 (disomic substitution line with chromosome 1D of RL5406 substituted for Chinese Spring 1D) with Chinese Spring. Closely linked markers based on 1DS-specific microsatellites, expressed sequence tags and AFLP were useful in the delineation of the Sr45 region. Sequences from an AFLP marker amplified a fragment that was linked with Sr45 at a distance of 0.39 cM. The fragment was located in a bacterial artificial chromosome clone of contig (ctg)2981 of the Ae. tauschii accession AL8/78 physical map. A PCR marker derived from clone MI221O11 of ctg2981 amplified 1DS-specific sequence that harboured an 18-bp indel polymorphism that specifically tagged the Sr45 carrying haplotype. This new Sr45 marker can be combined with a previously reported marker for Lr21, which will facilitate selecting Sr45 and Lr21 in breeding populations.
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13
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Philippe R, Paux E, Bertin I, Sourdille P, Choulet F, Laugier C, Šimková H, Šafář J, Bellec A, Vautrin S, Frenkel Z, Cattonaro F, Magni F, Scalabrin S, Martis MM, Mayer KFX, Korol A, Bergès H, Doležel J, Feuillet C. A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat. Genome Biol 2013; 14:R64. [PMID: 23800011 PMCID: PMC4054855 DOI: 10.1186/gb-2013-14-6-r64] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 05/24/2013] [Accepted: 06/25/2013] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning. RESULTS Using a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome. CONCLUSIONS Here, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing.
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Affiliation(s)
- Romain Philippe
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Etienne Paux
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Isabelle Bertin
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Pierre Sourdille
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Fréderic Choulet
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Christel Laugier
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic
| | - Jan Šafář
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic
| | - Arnaud Bellec
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326 Castalnet Tolosan, France
| | - Sonia Vautrin
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326 Castalnet Tolosan, France
| | - Zeev Frenkel
- University of Haifa, Institute of Evolution and Department of Evolutionary and Environmental Biology, Haifa 31905, Israel
| | - Federica Cattonaro
- Instituto di Genomica Applicata, Via J. Linussio 51, Udine, 33100, Italy
| | - Federica Magni
- Instituto di Genomica Applicata, Via J. Linussio 51, Udine, 33100, Italy
| | - Simone Scalabrin
- Instituto di Genomica Applicata, Via J. Linussio 51, Udine, 33100, Italy
| | | | - Klaus FX Mayer
- MIPS/IBIS; Helmholtz-Zentrum München, 85764 Neuherberg, Germany
| | - Abraham Korol
- University of Haifa, Institute of Evolution and Department of Evolutionary and Environmental Biology, Haifa 31905, Israel
| | - Hélène Bergès
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326 Castalnet Tolosan, France
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic
| | - Catherine Feuillet
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
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14
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Wang ZN, Banik M, Cloutier S. Divergent evolutionary mechanisms of co-located Tak/Lrk and Glu-D3 loci revealed by comparative analysis of grass genomes. Genome 2013; 56:195-204. [PMID: 23706072 DOI: 10.1139/gen-2012-0172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Seed storage and disease resistance proteins are major traits of wheat. The study of their gene organization and evolution has some implications in breeding. In this study, we characterized the hexaploid wheat D-genome BAC clone TaBAC703A9 that contains a low molecular weight glutenin locus (Glu-D3) and a resistance gene analogue cluster. With a gene density of one gene per 4.8 kb, the cluster contains four resistance gene analogues, namely Tak703-1, Lrr703, Tak703, and Lrk703. This structural cluster unit was conserved across nine grass genomes, but divergent evolutionary mechanisms have been involved in shaping the Tak/Lrk loci in the different species. Gene duplication was the major force for the Tak/Lrk evolution in oats, maize, barley, wheat, sorghum, and Brachypodium, while tandem duplication drove the expansion of this locus in japonica rice. Despite the close proximity of the Glu-D3 and the Tak/Lrk loci in wheat, the evolutionary mechanisms that drove their amplification differ. The Glu-D3 region had a lower gene density, and its amplification was driven by retroelements.
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Affiliation(s)
- Zi-Ning Wang
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg MB R3T 2M9, Canada
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15
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Falistocco E, Marconi G. Cytogenetic characterization by in situ hybridization techniques and molecular analysis of 5S rRNA genes of the European hazelnut (Corylus avellana). Genome 2013; 56:155-9. [PMID: 23659699 DOI: 10.1139/gen-2013-0045] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The European hazelnut (Corylus avellana L.) is widespread in Europe, where it has been cultivated for centuries. Despite progress in genetics, most of the cytogenetic aspects of this species have been overlooked. The aim of this study was to fill in this gap and obtain basic information on the chromosome structure of this species. Karyomorphological analysis confirmed the chromosome number 2n = 22 and showed that, despite their apparent uniformity, the chromosomes could be separated into three groups of different size: large (L), medium (M), and small (S). As a first step towards the physical mapping of the hazelnut chromosomes, we applied FISH to localize the position of rRNA genes (rDNA). The sites of 45S and 5S rDNA enabled us to identify two chromosome pairs belonging, respectively, to the L and S groups. The self-GISH procedure revealed that repetitive DNA is concentrated in the pericentromeric regions of the chromosomes, as with other species with rather small genomes. The analysis of 5S rDNA repeats offered additional information on the hazelnut genome by obtaining the whole sequence of the transcribed region so far unpublished. The overall results constitute a substantial advance in hazelnut cytogenetics. Further investigation of other species of Corylus could be an effective approach to understanding the phylogenesis of the genus and resolving taxonomic problems.
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Affiliation(s)
- E Falistocco
- Department of Applied Biology, University of Perugia, Borgo XX Giugno, 06100 Perugia, Italy.
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16
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Zhang X, Han D, Zeng Q, Duan Y, Yuan F, Shi J, Wang Q, Wu J, Huang L, Kang Z. Fine mapping of wheat stripe rust resistance gene Yr26 based on collinearity of wheat with Brachypodium distachyon and rice. PLoS One 2013; 8:e57885. [PMID: 23526955 PMCID: PMC3589488 DOI: 10.1371/journal.pone.0057885] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 01/27/2013] [Indexed: 11/18/2022] Open
Abstract
The Yr26 gene, conferring resistance to all currently important races of Puccinia striiformis f. sp. tritici (Pst) in China, was previously mapped to wheat chromosome deletion bin C-1BL-6-0.32 with low-density markers. In this study, collinearity of wheat to Brachypodium distachyon and rice was used to develop markers to saturate the chromosomal region containing the Yr26 locus, and a total of 2,341 F2 plants and 551 F2∶3 progenies derived from Avocet S×92R137 were used to develop a fine map of Yr26. Wheat expressed sequence tags (ESTs) located in deletion bin C-1BL-6-0.32 were used to develop sequence tagged site (STS) markers. The EST-STS markers flanking Yr26 were used to identify collinear regions of the rice and B. distachyon genomes. Wheat ESTs with significant similarities in the two collinear regions were selected to develop conserved markers for fine mapping of Yr26. Thirty-one markers were mapped to the Yr26 region, and six of them cosegregated with the resistance gene. Marker orders were highly conserved between rice and B. distachyon, but some rearrangements were observed between rice and wheat. Two flanking markers (CON-4 and CON-12) further narrowed the genomic region containing Yr26 to a 1.92 Mb region in B. distachyon chromosome 3 and a 1.17 Mb region in rice chromosome 10, and two putative resistance gene analogs were identified in the collinear region of B. distachyon. The markers developed in this study provide a potential target site for further map-based cloning of Yr26 and should be useful in marker assisted selection for pyramiding the gene with other resistance genes.
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Affiliation(s)
- Xiaojuan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Yinghui Duan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Fengping Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Jingdong Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, P. R. China
- * E-mail:
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17
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Gottlieb A, Müller HG, Massa AN, Wanjugi H, Deal KR, You FM, Xu X, Gu YQ, Luo MC, Anderson OD, Chan AP, Rabinowicz P, Devos KM, Dvorak J. Insular organization of gene space in grass genomes. PLoS One 2013; 8:e54101. [PMID: 23326580 PMCID: PMC3543359 DOI: 10.1371/journal.pone.0054101] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 12/06/2012] [Indexed: 01/28/2023] Open
Abstract
Wheat and maize genes were hypothesized to be clustered into islands but the hypothesis was not statistically tested. The hypothesis is statistically tested here in four grass species differing in genome size, Brachypodium distachyon, Oryza sativa, Sorghum bicolor, and Aegilops tauschii. Density functions obtained under a model where gene locations follow a homogeneous Poisson process and thus are not clustered are compared with a model-free situation quantified through a non-parametric density estimate. A simple homogeneous Poisson model for gene locations is not rejected for the small O. sativa and B. distachyon genomes, indicating that genes are distributed largely uniformly in those species, but is rejected for the larger S. bicolor and Ae. tauschii genomes, providing evidence for clustering of genes into islands. It is proposed to call the gene islands “gene insulae” to distinguish them from other types of gene clustering that have been proposed. An average S. bicolor and Ae. tauschii insula is estimated to contain 3.7 and 3.9 genes with an average intergenic distance within an insula of 2.1 and 16.5 kb, respectively. Inter-insular distances are greater than 8 and 81 kb and average 15.1 and 205 kb, in S. bicolor and Ae. tauschii, respectively. A greater gene density observed in the distal regions of the Ae. tauschii chromosomes is shown to be primarily caused by shortening of inter-insular distances. The comparison of the four grass genomes suggests that gene locations are largely a function of a homogeneous Poisson process in small genomes. Nonrandom insertions of LTR retroelements during genome expansion creates gene insulae, which become less dense and further apart with the increase in genome size. High concordance in relative lengths of orthologous intergenic distances among the investigated genomes including the maize genome suggests functional constraints on gene distribution in the grass genomes.
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Affiliation(s)
- Andrea Gottlieb
- Department of Statistics, University of California Davis, Davis, California, United States of America
| | - Hans-Georg Müller
- Department of Statistics, University of California Davis, Davis, California, United States of America
| | - Alicia N. Massa
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Humphrey Wanjugi
- USDA/ARS Western Research Center, Albany, California, United States of America
| | - Karin R. Deal
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Frank M. You
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Xiangyang Xu
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Yong Q. Gu
- USDA/ARS Western Research Center, Albany, California, United States of America
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Olin D. Anderson
- USDA/ARS Western Research Center, Albany, California, United States of America
| | - Agnes P. Chan
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Pablo Rabinowicz
- Institute for Genome Sciences, and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Katrien M. Devos
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Jan Dvorak
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
- * E-mail:
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18
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Chen C, DeClerck G, Tian F, Spooner W, McCouch S, Buckler E. PICARA, an analytical pipeline providing probabilistic inference about a priori candidates genes underlying genome-wide association QTL in plants. PLoS One 2012; 7:e46596. [PMID: 23144785 PMCID: PMC3492367 DOI: 10.1371/journal.pone.0046596] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 09/04/2012] [Indexed: 01/28/2023] Open
Abstract
PICARA is an analytical pipeline designed to systematically summarize observed SNP/trait associations identified by genome wide association studies (GWAS) and to identify candidate genes involved in the regulation of complex trait variation. The pipeline provides probabilistic inference about a priori candidate genes using integrated information derived from genome-wide association signals, gene homology, and curated gene sets embedded in pathway descriptions. In this paper, we demonstrate the performance of PICARA using data for flowering time variation in maize – a key trait for geographical and seasonal adaption of plants. Among 406 curated flowering time-related genes from Arabidopsis, we identify 61 orthologs in maize that are significantly enriched for GWAS SNP signals, including key regulators such as FT (Flowering Locus T) and GI (GIGANTEA), and genes centered in the Arabidopsis circadian pathway, including TOC1 (Timing of CAB Expression 1) and LHY (Late Elongated Hypocotyl). In addition, we discover a regulatory feature that is characteristic of these a priori flowering time candidates in maize. This new probabilistic analytical pipeline helps researchers infer the functional significance of candidate genes associated with complex traits and helps guide future experiments by providing statistical support for gene candidates based on the integration of heterogeneous biological information.
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Affiliation(s)
- Charles Chen
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America.
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19
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Huynh BL, Mather DE, Schreiber AW, Toubia J, Baumann U, Shoaei Z, Stein N, Ariyadasa R, Stangoulis JCR, Edwards J, Shirley N, Langridge P, Fleury D. Clusters of genes encoding fructan biosynthesizing enzymes in wheat and barley. PLANT MOLECULAR BIOLOGY 2012; 80:299-314. [PMID: 22864927 DOI: 10.1007/s11103-012-9949-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 07/23/2012] [Indexed: 05/21/2023]
Abstract
Fructans are soluble carbohydrates with health benefits and possible roles in plant adaptation. Fructan biosynthetic genes were isolated using comparative genomics and physical mapping followed by BAC sequencing in barley. Genes encoding sucrose:sucrose 1-fructosyltransferase (1-SST), fructan:fructan 1-fructosyltransferase (1-FFT) and sucrose:fructan 6-fructosyltransferase (6-SFT) were clustered together with multiple copies of vacuolar invertase genes and a transposable element on two barley BAC. Intron-exon structures of the genes were similar. Phylogenetic analysis of the fructosyltransferases and invertases in the Poaceae showed that the fructan biosynthetic genes may have evolved from vacuolar invertases. Quantitative real-time PCR was performed using leaf RNA extracted from three wheat cultivars grown under different conditions. The 1-SST, 1-FFT and 6-SFT genes had correlated expression patterns in our wheat experiment and in existing barley transcriptome database. Single nucleotide polymorphism (SNP) markers were developed and successfully mapped to a major QTL region affecting wheat grain fructan accumulation in two independent wheat populations. The alleles controlling high- and low- fructan in parental lines were also found to be associated in fructan production in a diverse set of 128 wheat lines. To the authors' knowledge, this is the first report on the mapping and sequencing of a fructan biosynthetic gene cluster and in particular, the isolation of a novel 1-FFT gene from barley.
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Affiliation(s)
- Bao-Lam Huynh
- Australian Centre for Plant Functional Genomics and School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond 5064, South Australia,
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20
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Xuan YH, Piao HL, Je BI, Park SJ, Park SH, Huang J, Zhang JB, Peterson T, Han CD. Transposon Ac/Ds-induced chromosomal rearrangements at the rice OsRLG5 locus. Nucleic Acids Res 2011; 39:e149. [PMID: 21965541 PMCID: PMC3239180 DOI: 10.1093/nar/gkr718] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Previous studies have shown that pairs of closely-linked Ac/Ds transposable elements can induce various chromosomal rearrangements in plant genomes. To study chromosomal rearrangements in rice, we isolated a line (OsRLG5-161) that contains two inversely-oriented Ds insertions in OsRLG5 (Oryza sativa Receptor like kinase Gene 5). Among approximately 300 plants regenerated from OsRLG5-161 heterozygous seeds, 107 contained rearrangements including deletions, duplications and inversions of various sizes. Most rearrangements were induced by previously identified alternative transposition mechanism. Furthermore, we also detected a new class of rearrangements that contain juxtaposed inversions and deletions on the same chromosome. We propose that these novel alleles were generated by a previously unreported type of alternative transposition reactions involving the 5' and 3' termini of two inversely-oriented Ds elements located on the same chromatid. Finally, 11% of rearrangements contained inversions resulting from homologous recombination between the two inverted Ds elements in OsRLG5-161. The high frequency inheritance and great variety of rearrangements obtained suggests that the rice regeneration system results in a burst of transposition activity and a relaxation of the controls which normally limit the transposition competence of individual Ds termini. Together, these results demonstrate a greatly enlarged potential of the Ac/Ds system for plant chromosome engineering.
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Affiliation(s)
- Yuan Hu Xuan
- Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 660-701, Korea
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Hurwitz BL, Kudrna D, Yu Y, Sebastian A, Zuccolo A, Jackson SA, Ware D, Wing RA, Stein L. Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 63:990-1003. [PMID: 20626650 DOI: 10.1111/j.1365-313x.2010.04293.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Rapid progress in comparative genomics among the grasses has revealed similar gene content and order despite exceptional differences in chromosome size and number. Large- and small-scale genomic variations are of particular interest, especially among cultivated and wild species, as they encode rapidly evolving features that may be important in adaptation to particular environments. We present a genome-wide study of intermediate-sized structural variation (SV) among rice (Oryza sativa) and three of its closest relatives in the genus Oryza (Oryza nivara, Oryza rufipogon and Oryza glaberrima). We computationally identified regional expansions, contractions and inversions in the Oryza species genomes relative to O. sativa by combining data from paired-end clone alignments to the O. sativa reference genome and physical maps. A subset of the computational predictions was validated using a new approach for BAC size determination. The result was a confirmed catalog of 674 expansions (25-38 Mb) and 611 (4-19 Mb) contractions, and 140 putative inversions (14-19 Mb) between the three Oryza species and O. sativa. In the expanded regions unique to O. sativa we found enrichment in transposable elements (TEs): long terminal repeats (LTRs) were randomly located across the chromosomes, and their insertion times corresponded to the date of the A genome radiation. Also, rice-expanded regions contained an over-representation of single-copy genes related to defense factors in the environment. This catalog of confirmed SV in reference to O. sativa provides an entry point for future research in genome evolution, speciation, domestication and novel gene discovery.
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Affiliation(s)
- Bonnie L Hurwitz
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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Breen J, Wicker T, Kong X, Zhang J, Ma W, Paux E, Feuillet C, Appels R, Bellgard M. A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block. BMC PLANT BIOLOGY 2010; 10:98. [PMID: 20507561 PMCID: PMC3017796 DOI: 10.1186/1471-2229-10-98] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Accepted: 05/27/2010] [Indexed: 05/29/2023]
Abstract
BACKGROUND The complexity of the wheat genome has resulted from waves of retrotransposable element insertions. Gene deletions and disruptions generated by the fast replacement of repetitive elements in wheat have resulted in disruption of colinearity at a micro (sub-megabase) level among the cereals. In view of genomic changes that are possible within a given time span, conservation of genes between species tends to imply an important functional or regional constraint that does not permit a change in genomic structure. The ctg1034 contig completed in this paper was initially studied because it was assigned to the Sr2 resistance locus region, but detailed mapping studies subsequently assigned it to the long arm of 3B and revealed its unusual features. RESULTS BAC shotgun sequencing of the hexaploid wheat (Triticum aestivum cv. Chinese Spring) genome has been used to assemble a group of 15 wheat BACs from the chromosome 3B physical map FPC contig ctg1034 into a 783,553 bp genomic sequence. This ctg1034 sequence was annotated for biological features such as genes and transposable elements. A three-gene island was identified among >80% repetitive DNA sequence. Using bioinformatics analysis there were no observable similarity in their gene functions. The ctg1034 gene island also displayed complete conservation of gene order and orientation with syntenic gene islands found in publicly available genome sequences of Brachypodium distachyon, Oryza sativa, Sorghum bicolor and Zea mays, even though the intergenic space and introns were divergent. CONCLUSION We propose that ctg1034 is located within the heterochromatic C-band region of deletion bin 3BL7 based on the identification of heterochromatic tandem repeats and presence of significant matches to chromodomain-containing gypsy LTR retrotransposable elements. We also speculate that this location, among other highly repetitive sequences, may account for the relative stability in gene order and orientation within the gene island.Sequence data from this article have been deposited with the GenBank Data Libraries under accession no. GQ422824.
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Affiliation(s)
- James Breen
- Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150, Australia
- Molecular Plant Breeding Co-operative Research Centre (MPBCRC) Murdoch University, South Street, Perth 6150, Australia
| | - Thomas Wicker
- Institute of Plant Biology, University Zurich, Zollikerstrasse 107, Zurich, CH-8008 Switzerland
| | - Xiuying Kong
- Key Laboratory of Crop Germplasm Resources and Utilization, MOA/Institute of Crop Sciences, CAAS/The Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Juncheng Zhang
- Key Laboratory of Crop Germplasm Resources and Utilization, MOA/Institute of Crop Sciences, CAAS/The Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Wujun Ma
- Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150, Australia
- State Agricultural Biotechnology Centre (SABC), Murdoch University, South Street, Perth 6150, Australia
- Department of Agriculture and Food, Western Australia (DAFWA), 3 Baron Hay Court, Perth, 6151 Australia
| | - Etienne Paux
- UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, INRA Site de Crouël, 63100 Clermont-ferrand, France
| | - Catherine Feuillet
- UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, INRA Site de Crouël, 63100 Clermont-ferrand, France
| | - Rudi Appels
- Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150, Australia
| | - Matthew Bellgard
- Centre for Comparative Genomics (CCG), Murdoch University, South Street, Perth 6150, Australia
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Kuraparthy V, Sood S, Gill BS. Molecular genetic description of the cryptic wheat-Aegilops geniculata introgression carrying rust resistance genes Lr57 and Yr40 using wheat ESTs and synteny with rice. Genome 2009; 52:1025-36. [PMID: 19953130 DOI: 10.1139/g09-076] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The cryptic wheat-alien translocation T5DL.5DS-5MgS(0.95), with leaf rust and stripe rust resistance genes Lr57 and Yr40 transferred from Aegilops geniculata (UgMg) into common wheat, was further analyzed. Molecular genetic analysis using physically mapped ESTs showed that the alien segment in T5DL.5DS-5MgS(0.95) represented only a fraction of the wheat deletion bin 5DS2-0.78-1.00 and was less than 3.3 cM in length in the diploid wheat genetic map. Comparative genomic analysis indicated a high level of colinearity between the distal region of the long arm of chromosome 12 of rice and the genomic region spanning the Lr57 and Yr40 genes in wheat. The alien segment with genes Lr57 and Yr40 corresponds to fewer than four overlapping BAC or PAC clones of the syntenic rice chromosome arm 12L. The wheat-alien translocation breakpoint in T5DL.5DS-5MgS(0.95) was further localized to a single BAC clone of the syntenic rice genomic sequence. The small size of the terminal wheat-alien translocation, as established precisely with respect to Chinese Spring deletion bins and the syntenic rice genomic sequence, further confirmed the escaping nature of cryptic wheat-alien translocations in introgressive breeding. The molecular genetic resources and information developed in the present study will facilitate further fine-scale physical mapping and map-based cloning of the Lr57 and Yr40 genes.
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Affiliation(s)
- Vasu Kuraparthy
- Crop Science Department, North Carolina State University, Raleigh, NC 27695, USA
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Fine mapping and marker development for the crossability gene SKr on chromosome 5BS of hexaploid wheat (Triticum aestivum L.). Genetics 2009; 183:469-81, 1SI-3SI. [PMID: 19652174 DOI: 10.1534/genetics.109.107706] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Most elite wheat varieties cannot be crossed with related species thereby restricting greatly the germplasm that can be used for alien introgression in breeding programs. Inhibition to crossability is controlled genetically and a number of QTL have been identified to date, including the major gene Kr1 on 5BL and SKr, a strong QTL affecting crossability between wheat and rye on chromosome 5BS. In this study, we used a recombinant SSD population originating from a cross between the poorly crossable cultivar Courtot (Ct) and the crossable line MP98 to characterize the major dominant effect of SKr and map the gene at the distal end of the chromosome near the 5B homeologous GSP locus. Colinearity with barley and rice was used to saturate the SKr region with new markers and establish orthologous relationships with a 54-kb region on rice chromosome 12. In total, five markers were mapped within a genetic interval of 0.3 cM and 400 kb of BAC contigs were established on both sides of the gene to lay the foundation for map-based cloning of SKr. Two SSR markers completely linked to SKr were used to evaluate a collection of crossable wheat progenies originating from primary triticale breeding programs. The results confirm the major effect of SKr on crossability and the usefulness of the two markers for the efficient introgression of crossability in elite wheat varieties.
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25
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Randhawa HS, Singh J, Lemaux PG, Gill KS. Mapping barleyDsinsertions using wheat deletion lines reveals high insertion frequencies in gene-rich regions with high to moderate recombination rates. Genome 2009; 52:566-75. [DOI: 10.1139/g09-029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Gene distribution is highly uneven in the large genomes of barley and wheat; however, location, order, and gene density of gene-containing regions are very similar between the two genomes. Flanking sequences from 35 unique, single-copy, barley Ds insertion events were physically mapped using wheat nullisomic-tetrasomic, ditelosomic, and deletion lines. Of the 35 sequences, 23 (66%) detected 34 loci mapping on all 7 homoeologous wheat groups. Seven sequences were not mapped owing to lack of polymorphism and the remaining 5 (14%) were barley-specific. All 34 loci physically mapped to the previously identified gene-rich regions (GRRs) of wheat, making the contained genes candidates for targeted mutagenesis by remobilization. Transpositions occurred preferentially into GRRs with higher recombination rates. The GRRs containing 17 of the 23 Ds insertions accounted for 60%–89% of the respective arm’s recombination. The remaining 6 (17%) insertions mapped to GRRs with <15% of the arm’s recombination. Overall, kb/cM estimates for the Ds-containing GRRs were twofold higher than those for regions without insertions. These results suggest that all genes may be targeted by transposon-based gene cloning, although the transposition frequency for genes present in recombination-poor regions is significantly less than that present in highly recombinogenic regions.
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Affiliation(s)
- Harpinder S. Randhawa
- Department of Crop and Soil Sciences, 277 Johnson Hall, P.O. Box 646420, Washington State University, Pullman, WA 99164-6420, USA
- Department of Plant Science, McGill University, Macdonald Campus, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
| | - Jaswinder Singh
- Department of Crop and Soil Sciences, 277 Johnson Hall, P.O. Box 646420, Washington State University, Pullman, WA 99164-6420, USA
- Department of Plant Science, McGill University, Macdonald Campus, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
| | - Peggy G. Lemaux
- Department of Crop and Soil Sciences, 277 Johnson Hall, P.O. Box 646420, Washington State University, Pullman, WA 99164-6420, USA
- Department of Plant Science, McGill University, Macdonald Campus, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
| | - Kulvinder S. Gill
- Department of Crop and Soil Sciences, 277 Johnson Hall, P.O. Box 646420, Washington State University, Pullman, WA 99164-6420, USA
- Department of Plant Science, McGill University, Macdonald Campus, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
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26
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Dracatos PM, Cogan NOI, Sawbridge TI, Gendall AR, Smith KF, Spangenberg GC, Forster JW. Molecular characterisation and genetic mapping of candidate genes for qualitative disease resistance in perennial ryegrass (Lolium perenne L.). BMC PLANT BIOLOGY 2009; 9:62. [PMID: 19450286 PMCID: PMC2694799 DOI: 10.1186/1471-2229-9-62] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Accepted: 05/19/2009] [Indexed: 05/18/2023]
Abstract
BACKGROUND Qualitative pathogen resistance in both dicotyledenous and monocotyledonous plants has been attributed to the action of resistance (R) genes, including those encoding nucleotide binding site--leucine rich repeat (NBS-LRR) proteins and receptor-like kinase enzymes. This study describes the large-scale isolation and characterisation of candidate R genes from perennial ryegrass. The analysis was based on the availability of an expressed sequence tag (EST) resource and a functionally-integrated bioinformatics database. RESULTS Amplification of R gene sequences was performed using template EST data and information from orthologous candidate using a degenerate consensus PCR approach. A total of 102 unique partial R genes were cloned, sequenced and functionally annotated. Analysis of motif structure and R gene phylogeny demonstrated that Lolium R genes cluster with putative ortholoci, and evolved from common ancestral origins. Single nucleotide polymorphisms (SNPs) predicted through resequencing of amplicons from the parental genotypes of a genetic mapping family were validated, and 26 distinct R gene loci were assigned to multiple genetic maps. Clusters of largely non-related NBS-LRR genes were located at multiple distinct genomic locations and were commonly found in close proximity to previously mapped defence response (DR) genes. A comparative genomics analysis revealed the co-location of several candidate R genes with disease resistance quantitative trait loci (QTLs). CONCLUSION This study is the most comprehensive analysis to date of qualitative disease resistance candidate genes in perennial ryegrass. SNPs identified within candidate genes provide a valuable resource for mapping in various ryegrass pair cross-derived populations and further germplasm analysis using association genetics. In parallel with the use of specific pathogen virulence races, such resources provide the means to identify gene-for-gene mechanisms for multiple host pathogen-interactions and ultimately to obtain durable field-based resistance.
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Affiliation(s)
- Peter M Dracatos
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, 1 Park Drive, La Trobe University Research and Development Park, Bundoora, Victoria 3083, Australia
- Department of Botany, Faculty of Science, Technology and Engineering, La Trobe University, Bundoora, Victoria 3086, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, Victoria, Australia
| | - Noel OI Cogan
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, 1 Park Drive, La Trobe University Research and Development Park, Bundoora, Victoria 3083, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, Victoria, Australia
| | - Timothy I Sawbridge
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, 1 Park Drive, La Trobe University Research and Development Park, Bundoora, Victoria 3083, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, Victoria, Australia
| | - Anthony R Gendall
- Department of Botany, Faculty of Science, Technology and Engineering, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Kevin F Smith
- Department of Primary Industries, Biosciences Research Division, Hamilton Centre, Mount Napier Road, Hamilton, Victoria 3300, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, Victoria, Australia
| | - German C Spangenberg
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, 1 Park Drive, La Trobe University Research and Development Park, Bundoora, Victoria 3083, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, Victoria, Australia
| | - John W Forster
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, 1 Park Drive, La Trobe University Research and Development Park, Bundoora, Victoria 3083, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, Victoria, Australia
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Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci U S A 2009; 106:2071-6. [PMID: 19164767 DOI: 10.1073/pnas.0812798106] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Comparative genomics is a powerful tool to decipher gene and genome evolution. Placing multiple genome comparisons in a phylogenetic context improves the sensitivity of evolutionary inferences. In the genus Oryza, this comparative approach can be used to investigate gene function, genome evolution, domestication, polyploidy, and ecological adaptation. A large genomic region surrounding the MONOCULM1 (MOC1) locus was chosen for study in 14 Oryza species, including 10 diploids and 4 allotetraploids. Sequencing and annotation of 18 bacterial artificial chromosome clones for these species revealed highly conserved gene colinearity and structure in the MOC1 region. Since the Oryza radiation about 14 Mya, differences in transposon amplification appear to be responsible for the different current sizes of the Oryza genomes. In the MOC1 region, transposons were only conserved between genomes of the same type (e.g., AA or BB). In addition to the conserved gene content, several apparent genes have been generated de novo or uniquely retained in the AA lineage. Two different 3-gene segments have been inserted into the MOC1 region of O. coarctata (KK) or O. sativa by unknown mechanism(s). Large and apparently noncoding sequences flanking the MOC1 gene were observed to be under strong purifying selection. The allotetraploids Oryza alta and Oryza minuta were found to be products of recent polyploidization, less than 1.6 and 0.4 Mya, respectively. In allotetraploids, pseudogenization of duplicated genes was common, caused by large deletions, small frame-shifting insertions/deletions, or nonsense mutations.
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28
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Paterson AH, Bowers JE, Feltus FA, Tang H, Lin L, Wang X. Comparative genomics of grasses promises a bountiful harvest. PLANT PHYSIOLOGY 2009; 149:125-31. [PMID: 19126703 PMCID: PMC2613718 DOI: 10.1104/pp.108.129262] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Accepted: 11/05/2008] [Indexed: 05/18/2023]
Affiliation(s)
- Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA.
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29
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Barret P, Brinkmann M, Beckert M. A major locus expressed in the male gametophyte with incomplete penetrance is responsible for in situ gynogenesis in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:581-94. [PMID: 18516584 DOI: 10.1007/s00122-008-0803-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Accepted: 05/09/2008] [Indexed: 05/18/2023]
Abstract
In flowering plants, double fertilization occurs when the egg cell and the central cell are each fertilized by one sperm cell. In maize, some lines produce pollen capable of inducing in situ gynogenesis thereby leading to maternal haploids that originate exclusively from the female plant. In this paper, we present a genetic analysis of in situ gynogenesis in maize. Using a cross between non-inducing and inducing lines, we identified a major locus on maize chromosome 1 controlling in situ gynogenesis (ggi1, for gynogenesis inducer 1). Fine mapping of this locus was performed, and BAC physical contigs spanning the locus were identified using the rice genome as anchor. Genetic component analysis showed that (a) a segregation distortion against the inducer parent was present at this locus, (b) segregation resulted only from male deficiency and (c) there was a correlation between the rate of segregation distortion and the level of gynogenetic induction. In addition, our results showed that the genotype of the pollen determined its capacity to induce the formation of a haploid female embryo, indicating gametophytic expression of the character with incomplete penetrance. We propose the occurrence of a gametophytic-specific process which leads to segregation distortion at the ggi1 locus associated with gynogenetic induction with incomplete penetrance.
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Affiliation(s)
- P Barret
- INRA, UMR1095 Génétique, Diversité et Ecophysiologie des Céréales (GDEC), 234 avenue du Brézet, 63100 Clermont-Ferrand, France.
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30
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Haseneyer G, Ravel C, Dardevet M, Balfourier F, Sourdille P, Charmet G, Brunel D, Sauer S, Geiger HH, Graner A, Stracke S. High level of conservation between genes coding for the GAMYB transcription factor in barley (Hordeum vulgare L.) and bread wheat (Triticum aestivum L.) collections. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:321-31. [PMID: 18488187 PMCID: PMC2755743 DOI: 10.1007/s00122-008-0777-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2007] [Accepted: 04/15/2008] [Indexed: 05/09/2023]
Abstract
The transcription factor GAMYB is involved in gibberellin signalling in cereal aleurone cells and in plant developmental processes. Nucleotide diversity of HvGAMYB and TaGAMYB was investigated in 155 barley (Hordeum vulgare) and 42 wheat (Triticum aestivum) accessions, respectively. Polymorphisms defined 18 haplotypes in the barley collection and 1, 7 and 3 haplotypes for the A, B, and D genomes of wheat, respectively. We found that (1) Hv- and TaGAMYB genes have identical structures. (2) Both genes show a high level of nucleotide identity (>95%) in the coding sequences and the distribution of polymorphisms is similar in both collections. At the protein level the functional domain is identical in both species. (3) GAMYB genes map to a syntenic position on chromosome 3. GAMYB genes are different in both collections with respect to the Tajima D statistic and linkage disequilibrium (LD). A moderate level of LD was observed in the barley collection. In wheat, LD is absolute between polymorphic sites, mostly located in the first intron, while it decays within the gene. Differences in Tajima D values might be due to a lower selection pressure on HvGAMYB, compared to its wheat orthologue. Altogether our results provide evidence that there have been only few evolutionary changes in Hv- and TaGAMYB. This confirms the close relationship between these species and also highlights the functional importance of this transcription factor.
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Affiliation(s)
- Grit Haseneyer
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
- Plant Breeding, Technische Universitaet Muenchen/Centre of Life and Food Sciences Weihenstephan, Am Hochanger 4, 85350 Freising, Germany
| | | | | | | | | | | | | | - Sascha Sauer
- Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany
| | - Hartwig H. Geiger
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599 Stuttgart, Germany
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
| | - Silke Stracke
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
- Department of Crop Sciences, Quality of Plant Products, University of Goettingen, Carl-Sprengel-Weg 1, 37075 Goettingen, Germany
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An SH, Choi HW, Hwang IS, Hong JK, Hwang BK. A novel pepper membrane-located receptor-like protein gene CaMRP1 is required for disease susceptibility, methyl jasmonate insensitivity and salt tolerance. PLANT MOLECULAR BIOLOGY 2008; 67:519-533. [PMID: 18427932 DOI: 10.1007/s11103-008-9337-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Accepted: 04/09/2008] [Indexed: 05/26/2023]
Abstract
Plant receptor proteins are involved in the signaling networks required for defense against pathogens. The novel pepper pathogen-induced gene CaMRP1 was isolated from pepper leaves infected with Xanthomonas campestris pv. vesicatoria (Xcv). This gene is predicted to encode a membrane-located receptor-like protein that has an N-terminal signal peptide and a C-terminal transmembrane helix. A CaMRP1-GFP fusion protein localized primarily to the plasma membrane of plant cells. Strong and early induction of CaMRP1 expression occurred following exposure of pepper plants to Xcv, Colletotricum coccodes, methyl jasmonate (MeJA) and wounding stress. Virus-induced gene silencing (VIGS) of CaMRP1 in pepper conferred enhanced basal resistance to Xcv infection, accompanied by induction of genes encoding basic PR1 (CaBPR1), defensin (CaDEF1) and SAR8.2 (CaSAR82A). In contrast, CaMRP1 overexpression (OX) in transgenic Arabidopsis plants resulted in increased disease susceptibility to Hyaloperonospora parasitica infection. Arabidopsis plants overexpressing CaMRP1 exhibited insensitivity to MeJA by causing reduced expression of MeJA-responsive genes. Overexpression also resulted in tolerance to NaCl and during salt stress, the expression of several abscisic acid-responsive genes was induced. Together, these results suggest that pepper CaMRP1 may belong to a new subfamily of membrane-located receptor-like proteins that regulate disease susceptibility, MeJA-insensitivity and salt tolerance.
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Affiliation(s)
- Soo Hyun An
- Laboratory of Molecular Plant Pathology, School of Life Sciences and Biotechnology, Korea University, Anam-dong, Sungbuk-ku, Seoul 136-713, Republic of Korea
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Van K, Kim DH, Cai CM, Kim MY, Shin JH, Graham MA, Shoemaker RC, Choi BS, Yang TJ, Lee SH. Sequence level analysis of recently duplicated regions in soybean [Glycine max (L.) Merr.] genome. DNA Res 2008; 15:93-102. [PMID: 18334514 PMCID: PMC2650623 DOI: 10.1093/dnares/dsn001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Accepted: 01/16/2008] [Indexed: 11/18/2022] Open
Abstract
A single recessive gene, rxp, on linkage group (LG) D2 controls bacterial leaf-pustule resistance in soybean. We identified two homoeologous contigs (GmA and GmA') composed of five bacterial artificial chromosomes (BACs) during the selection of BAC clones around Rxp region. With the recombinant inbred line population from the cross of Pureunkong and Jinpumkong 2, single-nucleotide polymorphism and simple sequence repeat marker genotyping were able to locate GmA' on LG A1. On the basis of information in the Soybean Breeders Toolbox and our results, parts of LG A1 and LG D2 share duplicated regions. Alignment and annotation revealed that many homoeologous regions contained kinases and proteins related to signal transduction pathway. Interestingly, inserted sequences from GmA and GmA' had homology with transposase and integrase. Estimation of evolutionary events revealed that speciation of soybean from Medicago and the recent divergence of two soybean homoeologous regions occurred at 60 and 12 million years ago, respectively. Distribution of synonymous substitution patterns, K(s), yielded a first secondary peak (mode K(s) = 0.10-0.15) followed by two smaller bulges were displayed between soybean homologous regions. Thus, diploidized paleopolyploidy of soybean genome was again supported by our study.
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Affiliation(s)
- Kyujung Van
- Department of Plant Science, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul 151-921, South Korea
| | - Dong Hyun Kim
- Department of Plant Science, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul 151-921, South Korea
| | - Chun Mei Cai
- National Institute of Crop Science, Suwon 441-857, South Korea
| | - Moon Young Kim
- Department of Plant Science, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul 151-921, South Korea
- Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, South Korea
| | - Jin Hee Shin
- Department of Plant Science, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul 151-921, South Korea
| | - Michelle A. Graham
- Corn Insect and Crop Genetics Research Unit, USDA-ARS, Iowa State University, Ames, IA 50011, USA
| | - Randy C. Shoemaker
- Corn Insect and Crop Genetics Research Unit, USDA-ARS, Iowa State University, Ames, IA 50011, USA
| | - Beom-Soon Choi
- National Instrumentation Center for Environmental Management, Seoul National University, Seoul 151-921, South Korea
| | - Tae-Jin Yang
- Department of Plant Science, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul 151-921, South Korea
| | - Suk-Ha Lee
- Department of Plant Science, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul 151-921, South Korea
- Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, South Korea
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Diversification of Lrk/Tak kinase gene clusters is associated with subfunctionalization and cultivar-specific transcript accumulation in barley. Funct Integr Genomics 2008; 8:199-209. [PMID: 18414912 DOI: 10.1007/s10142-008-0077-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Revised: 01/28/2008] [Accepted: 01/31/2008] [Indexed: 10/22/2022]
Abstract
Lrk (Lr10 receptor-like kinase) and Tak (Triticum aestivum kinase) belong to the receptor-like kinase (RLK) supergene family in higher plants. Three Lrk/Tak gene regions spanning greater than 600 kb were identified via a genome-wide survey of barley gene-rich BAC clones. Two Lrk/Tak gene clusters are positioned on barley chromosome 3 (3H) and another is localized on chromosome 5 (1H), with each Lrk and Tak open reading frame physically positioned in a back-to-back orientation. Thirteen new Lrk/Tak-like fragments were cloned from the two clusters on 3H and the single cluster on 1H, respectively, and compared phylogenetically with other grass Lrk/Tak-like genes, including a 280-kb Lrk/Tak cluster on rice chromosome 1S. Physically clustered Lrk/Tak-like genes always form monophyletic groups; this suggests that the primary mechanism of expansion of the Lrk/Tak RLK super family was by tandem duplication, of which most members were duplicated after speciation of the Poaceae. Cultivar-dependent transcript accumulation of some Lrk/Tak family members on 3H, as revealed via Barley1 GeneChip microarray analysis, is consistent with the hypothesis of subfunctionalization of Lrk/Tak members following tandem duplication.
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Faris JD, Zhang Z, Fellers JP, Gill BS. Micro-colinearity between rice, Brachypodium, and Triticum monococcum at the wheat domestication locus Q. Funct Integr Genomics 2008; 8:149-64. [PMID: 18210171 DOI: 10.1007/s10142-008-0073-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2007] [Revised: 01/02/2008] [Accepted: 01/02/2008] [Indexed: 01/05/2023]
Abstract
Brachypodium, a wild temperate grass with a small genome, was recently proposed as a new model organism for the large-genome grasses. In this study, we evaluated gene content and microcolinearity between diploid wheat (Triticum monococcum), Brachypodium sylvaticum, and rice at a local genomic region harboring the major wheat domestication gene Q. Gene density was much lower in T. monococcum (one per 41 kb) because of gene duplication and an abundance of transposable elements within intergenic regions as compared to B. sylvaticum (one per 14 kb) and rice (one per 10 kb). For the Q gene region, microcolinearity was more conserved between wheat and rice than between wheat and Brachypodium because B. sylvaticum contained two genes apparently not present within the orthologous regions of T. monococcum and rice. However, phylogenetic analysis of Q and leukotriene A-4 hydrolase-like gene orthologs, which were colinear among the three species, showed that Brachypodium is more closely related to wheat than rice, which agrees with previous studies. We conclude that Brachypodium will be a useful tool for gene discovery, comparative genomics, and the study of evolutionary relationships among the grasses but will not preclude the need to conduct large-scale genomics experiments in the Triticeae.
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Affiliation(s)
- Justin D Faris
- USDA-ARS Cereal Crops Unit, Northern Crop Science Laboratory, 1307 18th Street North, Fargo, ND 58105, USA.
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36
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Castiglione MR, Venora G, Ravalli C, Stoilov L, Gecheff K, Cremonini R. DNA methylation and chromosomal rearrangements in reconstructed karyotypes of Hordeum vulgare L. PROTOPLASMA 2008; 232:215-222. [PMID: 18274698 DOI: 10.1007/s00709-007-0275-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Accepted: 05/23/2007] [Indexed: 05/25/2023]
Abstract
One standard and two reconstructed barley karyotypes were used to study the influence of chromosomal rearrangements on the distribution pattern of DNA methylation detectable at the chromosome level. Data obtained were also compared with Giemsa N-bands and high gene density regions that had been previously described. The effect of chromosomal reconstruction in barley seems to be decidedly prominent in the repositioning of genomic DNA methylation along metaphase chromosomes. In comparison to the standard karyotype, the DNA methylation pattern was found to vary not only in the reconstructed chromosomes but also in the other chromosomes of the complements not subjected to structural alterations. Moreover, differences may occur between corresponding regions of homologues. Some specific chromosomal bands, including the nucleolus-organizing regions, showed a relative constancy in the methylation pattern, but this was not the case when the two satellites were combined by translocation in chromosome 6H(5H) of line T-30. Our results suggest that epigenetic changes like DNA methylation may play an important role in the overall genome reorganization following chromosome reconstruction.
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37
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Zhou H, Li S, Deng Z, Wang X, Chen T, Zhang J, Chen S, Ling H, Zhang A, Wang D, Zhang X. Molecular analysis of three new receptor-like kinase genes from hexaploid wheat and evidence for their participation in the wheat hypersensitive response to stripe rust fungus infection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 52:420-34. [PMID: 17764502 DOI: 10.1111/j.1365-313x.2007.03246.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Considerable progress has been made in understanding the function of receptor-like kinase (RLK) genes in model plants. However, much less is known about these genes in crop species. Here we report the characterization of three new wheat RLK genes (TaRLK-R1, 2 and 3). The primary structure of the putative proteins TaRLK-R1, 2 and 3 contained a signal peptide, a cysteine-rich extracellular domain, a transmembrane domain, and a predicted intracellular kinase domain. The fusions between TaRLK-R1, 2 or 3 and the green fluorescence protein (GFP) were targeted to the plasma membrane; such targeting required the signal peptide, extracellular domain and transmembrane domain. Transcription of TaRLK-R1, 2 and 3 was found mainly in the green organs, and was regulated by light. Transcript levels of TaRLK-R1, 2 and 3 increased during the hypersensitive reaction (HR) to stripe rust fungus. In addition, the TaRLK-R3 transcript level was also upregulated by abiotic stresses. Further experiments revealed that the recombinant kinase domain of TaRLK-R3 exhibited auto-phosphorylation activity in vitro. Knocking down the transcript levels of TaRLK-R1, 2 or 3 individually or all together by virus-induced gene silencing compromised the wheat HR to stripe rust fungus. The demonstration of TaRLK-R1, 2 and 3 as positive contributors in the wheat HR to stripe rust fungus suggests a new direction for further functional studies of this important family of RLK genes, and may facilitate the breeding of wheat varieties resistant to stripe rust disease.
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Affiliation(s)
- Huanbin Zhou
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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38
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Kuraparthy V, Sood S, Gill BS. Genomic targeting and mapping of tiller inhibition gene (tin3) of wheat using ESTs and synteny with rice. Funct Integr Genomics 2007; 8:33-42. [PMID: 17891549 DOI: 10.1007/s10142-007-0057-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Revised: 07/18/2007] [Accepted: 08/03/2007] [Indexed: 11/28/2022]
Abstract
Changes in plant architecture have been central to the domestication of wild species. Tillering or the degree of branching determines shoot architecture and is a key component of grain yield and/or biomass. Previously, a tiller inhibition mutant with monoculm phenotype was isolated and the mutant gene (tin3) was mapped in the distal region of chromosome arm 3AmL of Triticum monococcum. As a first step towards isolating a candidate gene for tin3, the gene was mapped in relation to physically mapped expressed sequence tags (ESTs) and sequence tag site (STS) markers developed based on synteny with rice. In addition, we investigated the relationship of the wheat region containing tin3 with the corresponding region in rice by comparative genomic analysis. Wheat ESTs that had been previously mapped to deletion bins provided a useful framework to identify closely related rice sequences and to establish the most likely syntenous region in rice for the wheat tin3 region. The tin3 gene was mapped to a 324-kb region spanned by two overlapping bacterial artificial chromosomes (BACs) of rice chromosome arm 1L. Wheat-rice synteny was exceptionally high at the tin3 region despite being located in the high-recombination, gene-rich region of wheat. Identification of tightly linked flanking EST and STS markers to the tin3 gene and its localization to highly syntenic rice BACs will assist in the future development of a high-resolution map and map-based cloning of the tin3 gene.
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Affiliation(s)
- Vasu Kuraparthy
- Wheat Genetic and Genomic Resources Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506-5502, USA
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Pastori GM, Huttly A, West J, Sparks C, Pieters A, Luna CM, Jones HD, Foyer CH. The maize Activator/Dissociation system is functional in hexaploid wheat through successive generations. FUNCTIONAL PLANT BIOLOGY : FPB 2007; 34:835-843. [PMID: 32689411 DOI: 10.1071/fp07112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Accepted: 07/03/2007] [Indexed: 06/11/2023]
Abstract
The aim of the present study was to provide useful background information and evidence of the functionality of the maize Activator/Dissociation (Ac/Ds) system in hexaploid wheat. Two transgenic parental wheat lines, one harbouring the immobilised Ac element (iAc) and the other the Ds element (pUbi[Ds-uidA]bar), were crossed. Transient GUS assays confirmed that the iAc transposase is active in hexaploid wheat. Selected F1 and F2 lines were analysed by PCR using primers specific to Ac, uidA and bar genes. The primer pair Ubi/bar-tag was used to detect excision of the Ds-uidA sequence, which occurred at a frequency of 39% in the F1 generation. Lines free of Ac and showing evidence of Ds excision were subject to Southern analysis, which indicated that at least one transposition event might have occurred in these lines. Although more evidence is required to unequivocally support the reintegration of the Ds element in the wheat genome, the evidence presented here nevertheless demonstrates the effectiveness and potential value of using this system to tag genes in wheat.
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Affiliation(s)
- Gabriela M Pastori
- Crop Performance and Improvement Division, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Alison Huttly
- Crop Performance and Improvement Division, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Jevon West
- Crop Performance and Improvement Division, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Caroline Sparks
- Crop Performance and Improvement Division, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Alejandro Pieters
- IVI, Centro de Ecología, Altos de Pipe, Carretera Panamericana Km 11, Apartado 21827, Caracas 1020-A, Venezuela
| | - Celina M Luna
- Instituto de Fitopatología y FisiologíaVegetal (IFFIVE)-INTA, Camino 60 cuadras Km 5, 5009 Cordoba, Argentina
| | - Huw D Jones
- Crop Performance and Improvement Division, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Christine H Foyer
- School of Agriculture, Food and Rural Development, Agriculture Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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40
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She C, Liu J, Diao Y, Hu Z, Song Y. The Distribution of Repetitive DNAs Along Chromosomes in Plants Revealed by Self-genomic in situ Hybridization. J Genet Genomics 2007; 34:437-48. [PMID: 17560530 DOI: 10.1016/s1673-8527(07)60048-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2006] [Accepted: 07/09/2006] [Indexed: 11/17/2022]
Abstract
The distribution of repetitive DNAs along chromosomes is one of the crucial elements for understanding the organization and the evolution of plant genomes. Using a modified genomic in situ hybridization (GISH) procedure, fluorescence in situ hybridization (FISH) with genomic DNA to their own chromosomes (called self-genomic in situ hybridization, self-GISH) was carried out in six selected plant species with different genome size and amount of repetitive DNA. Nonuniform distribution of the fluorescent labeled probe DNA was observed on the chromosomes of all the species that were tested. The signal patterns varied among species and were related to the genome size. The chromosomes of the small Arabidopsis genome were labeled almost only in the pericentromeric regions and the nucleolus organizer regions (NORs). The signals in the relatively small genomes, rice, sorghum, and Brassica oleracea var. capitata L., were dispersed along the chromosome lengths, with a predominant distribution in the pericentromeric or proximal regions and some heterochromatic arms. All chromosomes of the large genomes, maize and barley, were densely labeled with strongly labeled regions and weakly labeled or unlabeled regions being arranged alternatively throughout the lengths. In addition, enhanced signal bands were shown in all pericentromeres and the NORs in B. oleracea var. capitata and in all pericentromeric regions and certain intercalary sites in barley. The enhanced signal band pattern in barley was found consistent with the N-banding pattern of this species. The GISH with self-genomic DNA was compared with FISH with C(o)t-1 DNA in rice, and their signal patterns are found to be basically consistent. Our results showed that the self-GISH signals actually reflected the hybridization of genomic repetitive DNAs to the chromosomes, thus the self-GISH technique would be useful for revealing the distribution of the regions where repetitive DNAs concentrate along chromosomes and some chromatin differentiation associated with repetitive DNAs in plants.
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Affiliation(s)
- Chaowen She
- Department of Biology, Huaihua University, Huaihua 418008, China.
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41
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Pourkheirandish M, Wicker T, Stein N, Fujimura T, Komatsuda T. Analysis of the barley chromosome 2 region containing the six-rowed spike gene vrs1 reveals a breakdown of rice-barley micro collinearity by a transposition. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:1357-65. [PMID: 17375281 DOI: 10.1007/s00122-007-0522-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Accepted: 02/05/2007] [Indexed: 05/14/2023]
Abstract
In cultivated barley (Hordeum vulgare ssp. vulgare), six-rowed spikes produce three times as many seeds per spike as do two-rowed spikes. The determinant of this trait is the Mendelian gene vrs1, located on chromosome 2H, which is syntenous with rice (Oryza sativa) chromosomes 4 and 7. We exploited barley-rice micro-synteny to increase marker density in the vrs1 region as a prelude to its map-based cloning. The rice genomic sequence, covering a 980 kb contig, identified barley ESTs linked to vrs1. A high level of conservation of gene sequence was obtained between barley chromosome 2H and rice chromosome 4. A total of 22 EST-based STS markers were placed within the target region, and the linear order of these markers in barley and rice was identical. The genetic window containing vrs1 was narrowed from 0.5 to 0.06 cM, which facilitated covering the vrs1 region by a 518 kb barley BAC contig. An analysis of the contig sequence revealed that a rice Vrs1 orthologue is present on chromosome 7, suggesting a transposition of the chromosomal segment containing Vrs1 within barley chromosome 2H. The breakdown of micro-collinearity illustrates the limitations of synteny cloning, and stresses the importance of implementing genomic studies directly in the target species.
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Affiliation(s)
- M Pourkheirandish
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
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42
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Pourkheirandish M, Wicker T, Stein N, Fujimura T, Komatsuda T. Analysis of the barley chromosome 2 region containing the six-rowed spike gene vrs1 reveals a breakdown of rice-barley micro collinearity by a transposition. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007. [PMID: 17375281 DOI: 10.1007/s00122‐007‐0522‐4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
Abstract
In cultivated barley (Hordeum vulgare ssp. vulgare), six-rowed spikes produce three times as many seeds per spike as do two-rowed spikes. The determinant of this trait is the Mendelian gene vrs1, located on chromosome 2H, which is syntenous with rice (Oryza sativa) chromosomes 4 and 7. We exploited barley-rice micro-synteny to increase marker density in the vrs1 region as a prelude to its map-based cloning. The rice genomic sequence, covering a 980 kb contig, identified barley ESTs linked to vrs1. A high level of conservation of gene sequence was obtained between barley chromosome 2H and rice chromosome 4. A total of 22 EST-based STS markers were placed within the target region, and the linear order of these markers in barley and rice was identical. The genetic window containing vrs1 was narrowed from 0.5 to 0.06 cM, which facilitated covering the vrs1 region by a 518 kb barley BAC contig. An analysis of the contig sequence revealed that a rice Vrs1 orthologue is present on chromosome 7, suggesting a transposition of the chromosomal segment containing Vrs1 within barley chromosome 2H. The breakdown of micro-collinearity illustrates the limitations of synteny cloning, and stresses the importance of implementing genomic studies directly in the target species.
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Affiliation(s)
- M Pourkheirandish
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
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43
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Lee SH, Neate SM. Sequence tagged site markers to rsp1, rsp2, and rsp3 genes for resistance to septoria speckled leaf blotch in barley. PHYTOPATHOLOGY 2007; 97:162-169. [PMID: 18944371 DOI: 10.1094/phyto-97-2-0162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
ABSTRACT Five random amplified polymorphic DNA markers, two in coupling (OPAH5(545C), and OPBA12(314C)) and three in repulsion phase (UBC285(158R), OPC2(441R), and OPB17(451R)), closely linked to Rsp genes conferring resistance to Septoria speckled leaf blotch (SSLB), were identified using bulked segregant analysis in three F(2) populations, each containing a Rsp gene. These markers were converted into the sequence tagged site (STS) markers SUBC285, SOPC2, SOPAH5, and SOPBA12. Another STS marker (MWG938) linked to Rsp2 in coupling phase was also identified in an F(2) population from the cross Robust/CIho 4780. The STS markers were tested on a set of 42 resistant and susceptible barley germplasm lines and 98 landraces. The expected sizes of marker fragments associated with each allele at Rsp loci were present in resistant or susceptible accessions. Efficiency of marker-assisted selection (MAS) for Rsp1, Rsp2, and Rsp3 using STS markers were evaluated in three F(23) populations in the greenhouse and the field. Results of testing F(23) progeny demonstrated that the accuracy of MAS was, with one exception, greater than 97% in the greenhouse and in two field locations (90% in the Osnabrock, ND trial for Rsp2). The STS markers closely linked to Rsp genes also identified the SSLB resistance corresponding to Rsp1, Rsp2, or Rsp3 in gene pyramiding F(2) populations. The STS markers tightly linked to Rsp genes may be useful for M and for pyramiding with other genes in barley breeding for SSLB resistance.
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Kuraparthy V, Sood S, Dhaliwal HS, Chhuneja P, Gill BS. Identification and mapping of a tiller inhibition gene (tin3) in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:285-94. [PMID: 17115129 DOI: 10.1007/s00122-006-0431-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Accepted: 10/06/2006] [Indexed: 05/02/2023]
Abstract
Tillering is one of the most important agronomic traits in cereal crops because tiller number per plant determines the number of spikes or panicles per plant, a key component of grain yield and/or biomass. In order to characterize the underlying genetic variation for tillering, we have isolated mutants that are compromised in tillering ability using ethyl methanesulphonate (EMS)-based mutagenesis in diploid wheat (Triticum monococcum subsp. monococcum). The tillering mutant, tiller inhibition (tin3) produces only one main culm compared to the wild type with many tillers. The monoculm phenotype of tin3 is due to a single recessive mutation. Genetic and molecular mapping in an F(2) population of diploid wheat located the tin3 gene on the long arm of chromosome 3A(m). One codominant RFLP marker Xpsr1205 cosegregated with tin3 in the F(2) population. Physical mapping of PSR1205 in a set of Chinese Spring deletion lines of group-3 chromosomes placed the tin3 gene in the distal 10% of the long arm of chromosome 3A, which is a recombination-rich region in wheat. The implications of the mapping of tin3 on chromosome arm 3A(m)L are discussed with respect to putative orthologs of tin3 in the 3L colinear regions across various cereal genomes and other tillering traits in grasses.
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Affiliation(s)
- Vasu Kuraparthy
- Wheat Genetic and Genomic Resources Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506-5502, USA
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45
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Zhao HX, Liu XM, Chen MS. H22, a major resistance gene to the Hessian fly (Mayetiola destructor), is mapped to the distal region of wheat chromosome 1DS. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:1491-6. [PMID: 16972061 DOI: 10.1007/s00122-006-0396-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Accepted: 08/14/2006] [Indexed: 05/11/2023]
Abstract
H22 is a major resistance gene conferring high-level of antibiosis to Hessian fly [Mayetiola destructor (Say)] larvae. It was previously assigned to wheat chromosome 1D through monosomic analysis (Raupp et al. in J Hered 84:142-145, 1993). The objective of this study was to identify molecular markers that can be used for marker-assisted selection for wheat breeding, and to further map this gene toward map-based cloning. Forty-five simple sequence repeat (SSR) and sequence-tagged site (STS) markers specific to chromosome 1D were evaluated for linkage to H22 using a segregating population consisting of 192 F(2:3) families, which were derived from the cross Tugela-Dn1 x KS85WGRC01(H22). The STS Xhor2kv and SSR Xgdm33 are two flanking markers that are tightly linked to H22 at genetic distances of 0.3 and 1.0 cM, respectively. Five other SSR markers including Xgpw7082, Xwmc147, Xcfd15, Xwmc432 and Xwmc336 were also linked to H22 at the distance from 0.8 to 20.8 cM. Analysis of Chinese Spring (CS) deletion lines revealed that all the H22-linked markers are located distal to the breakpoint of del 1DS-5, indicating that the H22 gene is located at the distal 30% region on the short arm of wheat chromosome 1D. Genomic comparison suggested that the H22 gene is located in the same or similar chromosomal region as the leaf rust resistance genes Lr21 and Lr40 on 1DS, and orthologous to the H9 gene cluster of 1AS.
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Affiliation(s)
- H X Zhao
- Department of Entomology, Kansas State University, Manhattan, KS 66506, USA
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46
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Wu C, Wang S, Zhang HB. Interactions among genomic structure, function, and evolution revealed by comprehensive analysis of the Arabidopsis thaliana genome. Genomics 2006; 88:394-406. [PMID: 16806804 DOI: 10.1016/j.ygeno.2006.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Revised: 05/04/2006] [Accepted: 05/10/2006] [Indexed: 11/17/2022]
Abstract
The genome in a higher organism consists of a number of types of nucleotide sequence-specialized components, with each having tens of thousands of members or elements. It is crucial for our understanding of how a genome as an entity is organized, functions, and evolves to determine how these components are organized in the genome and how they relate with each other; however, no such knowledge is available. Here, we report a comprehensive analysis of the organization and interaction of all 40 components constituting the genome of the plant model species, Arabidopsis thaliana, at the whole-genome and chromosome levels. The 40 components include (i) 6 genome structural components consisting of GC%, genes, retrotransposons, DNA transposons, simple repeats, and low complex repeats; (ii) 3 evolutionarily critical features consisting of recombination rate, nucleotide substitutions, and nucleotide insertions/deletions; and (iii) 31 categories of genes with different functions and numbers of functions. We show that the distributions of 39 of the 40 components of the genome (excepting GC%) deviate significantly from the random distribution model and different types of the genome components are significantly correlated. These results remained to be true even when the genomic regions, such as centromeric regions, where transposable and repeat elements are abundant were excluded from the analyses. These findings suggest that DNA molecules contained in the Arabidopsis genome are each organized and structured from their constituting components in an unambiguous manner and that different types of the components that constitute or characterize the genome interact. The analysis also showed that each chromosome consists of a similar set of the components at similar densities, suggesting that the unique organization and interaction pattern of the components in each chromosome may represent, at least in part, the identity of a chromosome or a genome at the genome level, thus partly accounting for the phenotypic variation among different species. The data also provide comprehensive and new insights into many phenomena significant in genome biology, with which we particularly discuss the variation of genetic recombination. The variation of genetic recombination rate along a chromosomal arm is shaped, not only by the distribution of simple repeats, retrotransposons, DNA transposons, and nucleotide substitutions, but also by the functions of genes contained, especially those with multiple functions, suggesting that variation of genetic recombination along a chromosomal arm is the result of interactions among the components constituting local genome structure, function, and evolution.
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Affiliation(s)
- Chengcang Wu
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
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Comparative analysis of A, B, C and D genomes in the genus Oryza with C 0 t-1 DNA of C genome. CHINESE SCIENCE BULLETIN-CHINESE 2006. [DOI: 10.1007/s11434-006-2049-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Royo J, Gómez E, Balandín M, Muñiz LM, Hueros G. ZmLrk-1, a receptor-like kinase induced by fungal infection in germinating seeds. PLANTA 2006; 223:1303-14. [PMID: 16362327 DOI: 10.1007/s00425-005-0179-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2005] [Accepted: 11/08/2005] [Indexed: 05/05/2023]
Abstract
We report here on the identification and characterization of ZmLrk-1, a member of the Lrk class of receptor-like kinases in Zea mays. This gene was found to be located at the bin21.40 region on the short arm of maize chromosome 8, closely linked to the previously reported pseudogene of the same class psiZmLrk (originally called Zm2Lrk). Transient expression experiments in onion epithelium cells, using a ZmLrk-1:GFP fusion protein, indicate that ZmLrk-1 is a membrane protein. ZmLrk-1 is ubiquitously expressed in the maize plant, including roots and aerial parts. In seeds, ZmLrk-1 transcripts can be detected by in situ hybridization exclusively at the basal endosperm transfer cell layer during the first stages of development. However, from 14 days after pollination its transcripts are preferentially detected at the upper half of the kernel, including both the aleurone and the starchy endosperm. ZmLrk-1 expression is not induced after treatment with salicylic acid, jasmonic acid or wounding, but it clearly increases after infection of germinating seeds with Fusarium oxysporum. This suggests that ZmLrk-1 could be involved in a sensing system to activate plant defence mechanisms against fungal attacks during endosperm development and seed germination.
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Affiliation(s)
- Joaquín Royo
- Departamento de Biología Celular y Genética, Universidad de Alcalá, Alcala de Henares, 28871 Madrid, Spain
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Calderini O, Chang SB, de Jong H, Busti A, Paolocci F, Arcioni S, de Vries SC, Abma-Henkens MHC, Lankhorst RMK, Donnison IS, Pupilli F. Molecular cytogenetics and DNA sequence analysis of an apomixis-linked BAC in Paspalum simplex reveal a non pericentromere location and partial microcolinearity with rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 112:1179-91. [PMID: 16463157 DOI: 10.1007/s00122-006-0220-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Accepted: 01/07/2006] [Indexed: 05/06/2023]
Abstract
Apomixis in plants is a form of clonal reproduction through seeds. A BAC clone linked to apomictic reproduction in Paspalum simplex was used to locate the apomixis locus on meiotic chromosome preparations. Fluorescent in situ hybridisation revealed the existence of a single locus embedded in a heterochromatin-poor region not adjacent to the centromere. We report here for the first time information regarding the sequencing of a large DNA clone from the apomixis locus. The presence of two genes whose rice homologs were mapped on the telomeric part of the long arm of rice chromosome 12 confirmed the strong synteny between the apomixis locus of P. simplex with the related area of the rice genome at the map level. Comparative analysis of this region with rice as representative of a sexual species revealed large-scale rearrangements due to transposable elements and small-scale rearrangements due to deletions and single point mutations. Both types of rearrangements induced the loss of coding capacity of large portions of the "apomictic" genes compared to their rice homologs. Our results are discussed in relation to the use of rice genome data for positional cloning of apomixis genes and to the possible role of rearranged supernumerary genes in the apomictic process of P. simplex.
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Affiliation(s)
- Ornella Calderini
- Institute of Plant Genetics CNR, Perugia via della madonna alta 130, 06128 Perugia, Italy
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Rabinowicz PD, Bennetzen JL. The maize genome as a model for efficient sequence analysis of large plant genomes. CURRENT OPINION IN PLANT BIOLOGY 2006; 9:149-56. [PMID: 16459129 DOI: 10.1016/j.pbi.2006.01.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Accepted: 01/20/2006] [Indexed: 05/06/2023]
Abstract
The genomes of flowering plants vary in size from about 0.1 to over 100 gigabase pairs (Gbp), mostly because of polyploidy and variation in the abundance of repetitive elements in intergenic regions. High-quality sequences of the relatively small genomes of Arabidopsis (0.14 Gbp) and rice (0.4 Gbp) have now been largely completed. The sequencing of plant genomes that have a more representative size (the mean for flowering plant genomes is 5.6 Gbp) has been seen as a daunting task, partly because of their size and partly because of the numerous highly conserved repeats. Nevertheless, creative strategies and powerful new tools have been generated recently in the plant genetics community, so that sequencing large plant genomes is now a realistic possibility. Maize (2.4-2.7 Gbp) will be the first gigabase-size plant genome to be sequenced using these novel approaches. Pilot studies on maize indicate that the new gene-enrichment, gene-finishing and gene-orientation technologies are efficient, robust and comprehensive. These strategies will succeed in sequencing the gene-space of large genome plants, and in locating all of these genes and adjacent sequences on the genetic and physical maps.
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Affiliation(s)
- Pablo D Rabinowicz
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
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