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A First Survey Of The Wheat Chromosome 5a Composition Through A Next-Generation Sequencing Approach
Special Abstracts / Journal of Biotechnology 150S (2010) S1–S576
[P-P&F.4] Mutational approach for enhancement of artemisinin in Artemisia annua Fahad Al-Qurainy ∗ , Salim Khan King Saud University, Saudi Arabia Keywords: secondry metabolites; artemisinin; mutation; tissue culture Malaria, one of the world’s most serious parasitic diseases, caused by Plasmodium, has at least 500 million cases globally every year, resulting in more than one million deaths. The synthesis of artimisinin in Artemisia annua is very low and depends on the amorpha-4, 11 dien synthatase gene (ADS) and its product. It is a sesquiterpene cyclase that catalyzes the conversion of farnesyl diphosphate into amorpha-4,11-diene in the biosynthesis of the antimalarial artemisinin. Widespread use of this valuable secondary metabolite has been hampered by low production in vivo and high cost of chemical synthesis in vitro. We developed mutant plants from callus treated with sodium azide on MS media. The developed mutants were screened by restriction digestion of amorpha-4, 11 dien synthatase gene and artimisinin was estimated in all mutant plants. At higher dose of sodium azide, mutation was detected; however developed mutants have high content of artemisinin as compared with control plants. Thus, this approach is attractive alternate method for enhancement of artimisinin in vivo as well as in vitro. doi:10.1016/j.jbiotec.2010.09.708
S473
(TREP complete database). Several transposable element families poorly represented in a close related species such as barley appear to be abundant in wheat chromosome 5A. Apart from few cases, transposable element familes distribution is similar in the two arms. Beside their intrinsic interest, these data can be useful for the construction of the genetic and physical maps of chromosome 5A. doi:10.1016/j.jbiotec.2010.09.709 [P-P&F.6] On the road to a high density genetic linkage map of wheat chromosome 5A D. Barabaschi 1,2,3,4,5,6,∗ , L. Orru’ 1,2,3,4,5,6 , K. Lacrima 1,2,3,4,5,6 , P. Faccioli 1,2,3,4,5,6 , M. Colaiacovo 1,2,3,4,5,6 , P. Bagnaresi 1,2,3,4,5,6 1
CRA – Genomic Research Centre Via San Protaso 302 I-29017 Fiorenzuola D’Arda – PC, Italy 2 Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Sokolovská 6, CZ-77200, Olomouc, Czech Republic 3 Diversity Arrays Technology Pty Ltd, Building 1 CSIRO Forestry1 Wilf Crane Crescent, PO Box 7141, ACT 2600, Yarralumla, Australia 4 Department of Agricultural and Food Sciences, University of Modena and Reggio Emilia Via Amendola 2 I-42100 Reggio Emilia, Italy 5 Genomics Platform, Parco Tecnologico Padano Via Einstein I-26900 Località Cascina Codazza (LO, Italy 6 Department of Environmental and Agro-Forestry Biology and Chemistry, University of Bari Via Amendola 165-A I-70126 Bari, Italy Keywords: wheat; map; genome; food
[P-P&F.5] A First Survey Of The Wheat Chromosome 5a Composition Through A Next-Generation Sequencing Approach N Vitulo 1,3,4,6 , A Albiero 1,2,3,4,6 , C Forcato 1,3,4,6 , D Campagna 1,3,4,6 , F Dal Pero 2,3,4,6 , L Cattivelli 3,4,5,6,∗ 1
CRIBI Biotechnology Center, University of Padova via U.Bassi58/b35131 Padova, Italy 2 Bmr-genomics srl via Redipuglia 21/A35131 Padova, Italy 3 ENEA, Research Center CASACCIA, S.M. Galeria 00163, Rome, Italy 4 ENEA, TRISAIA Research Center, S.S. 106 Ionica75026 Rotondella (Matera), Italy 5 Genomics Research Centre, Italian Agricultural Research Council, via S.Protaso 302, I-29017 Fiorenzuola d’Arda (Pc), Italy 6 Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic Keywords: genome; wheat; transposable element; crop Within the International Wheat Genome Sequencing Consortium, Italy is in charge of Chromosome 5A. As a part of this project, here we present a preliminary shotgun sequencing analysis performed by a of 454 technologies. As a starting material we used the short arm and long arm of chromosome 5A, isolated by flow cytometry. The DNA from the sorted chromosome arms was amplified by GenomiPhi DNA Amplification Kit by GE Healthcare, processed for DNA fragment analysis and run on a Roche 454-Titanium sequencer, producing a coverage of more than 2x for both arms. The preliminary results reveal the presence on both chromosome 5A arms of numerous putative genes and of several putative microRNA-related sequences (microRNA coding genes or microRNA target genes). More than two-thirds of the 454 reads exhibit significant homologies to known Triticeae repeat sequences
A high density genetic map is needed for anchoring BAC contigs during the construction of a physical map and for DNA sequence assembly. The International Wheat Genome Sequencing Consortium is dedicated to the development of physical maps of individual chromosomes as the first step towards the whole genome sequencing of hexaploid wheat. To undertake this challenge for wheat chromosome 5A, we rely on two mapping populations and different parallel approaches for marker development. A Chinese Spring x Renan (CSxR) F2 population is being used, while another F2 population derived from CS x CS-Triticum dicoccoides disomic substitution line for chromosome 5A is under creation. Another promising population is being considered: Triticum monococcum F2 population deriving from DV92 and G3116. For marker development, a Diversity Array Technology (DArT) platform containing about 4000 new probes specific for the short and long arms of wheat chromosome 5A has been established using DNA from flow sorted chromosomes, also including more than 6000 nonchromosome specific wheat probes. Besides the DArTs, a set of SSR (from databases and literature), specific for 5AS and/or 5AL chromosome arms, have been selected. Sequencing and annotation has been undertaken for sorted DNA of 5AL and 5AS. To date, the 2-fold coverage by 454 sequencing aided in thousand of SSR, ISBP, RJJM, RJM marker development. After the assignment to chromosome 5A, performed using CS deletion and aneuploid lines, the markers are being tested for polymorphism between the parents of the two mapping populations. Polymorphic DNA fragments, specific for 5A, have been mapped in CSxR population. The resulting genetic linkage map of the wheat chromosome 5A will be presented. doi:10.1016/j.jbiotec.2010.09.710
[P-P&F.4] Mutational approach for enhancement of artemisinin in Artemisia annua Fahad Al-Qurainy ∗ , Salim Khan King Saud University, Saudi Arabia Keywords: secondry metabolites; artemisinin; mutation; tissue culture Malaria, one of the world’s most serious parasitic diseases, caused by Plasmodium, has at least 500 million cases globally every year, resulting in more than one million deaths. The synthesis of artimisinin in Artemisia annua is very low and depends on the amorpha-4, 11 dien synthatase gene (ADS) and its product. It is a sesquiterpene cyclase that catalyzes the conversion of farnesyl diphosphate into amorpha-4,11-diene in the biosynthesis of the antimalarial artemisinin. Widespread use of this valuable secondary metabolite has been hampered by low production in vivo and high cost of chemical synthesis in vitro. We developed mutant plants from callus treated with sodium azide on MS media. The developed mutants were screened by restriction digestion of amorpha-4, 11 dien synthatase gene and artimisinin was estimated in all mutant plants. At higher dose of sodium azide, mutation was detected; however developed mutants have high content of artemisinin as compared with control plants. Thus, this approach is attractive alternate method for enhancement of artimisinin in vivo as well as in vitro. doi:10.1016/j.jbiotec.2010.09.708
S473
(TREP complete database). Several transposable element families poorly represented in a close related species such as barley appear to be abundant in wheat chromosome 5A. Apart from few cases, transposable element familes distribution is similar in the two arms. Beside their intrinsic interest, these data can be useful for the construction of the genetic and physical maps of chromosome 5A. doi:10.1016/j.jbiotec.2010.09.709 [P-P&F.6] On the road to a high density genetic linkage map of wheat chromosome 5A D. Barabaschi 1,2,3,4,5,6,∗ , L. Orru’ 1,2,3,4,5,6 , K. Lacrima 1,2,3,4,5,6 , P. Faccioli 1,2,3,4,5,6 , M. Colaiacovo 1,2,3,4,5,6 , P. Bagnaresi 1,2,3,4,5,6 1
CRA – Genomic Research Centre Via San Protaso 302 I-29017 Fiorenzuola D’Arda – PC, Italy 2 Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Sokolovská 6, CZ-77200, Olomouc, Czech Republic 3 Diversity Arrays Technology Pty Ltd, Building 1 CSIRO Forestry1 Wilf Crane Crescent, PO Box 7141, ACT 2600, Yarralumla, Australia 4 Department of Agricultural and Food Sciences, University of Modena and Reggio Emilia Via Amendola 2 I-42100 Reggio Emilia, Italy 5 Genomics Platform, Parco Tecnologico Padano Via Einstein I-26900 Località Cascina Codazza (LO, Italy 6 Department of Environmental and Agro-Forestry Biology and Chemistry, University of Bari Via Amendola 165-A I-70126 Bari, Italy Keywords: wheat; map; genome; food
[P-P&F.5] A First Survey Of The Wheat Chromosome 5a Composition Through A Next-Generation Sequencing Approach N Vitulo 1,3,4,6 , A Albiero 1,2,3,4,6 , C Forcato 1,3,4,6 , D Campagna 1,3,4,6 , F Dal Pero 2,3,4,6 , L Cattivelli 3,4,5,6,∗ 1
CRIBI Biotechnology Center, University of Padova via U.Bassi58/b35131 Padova, Italy 2 Bmr-genomics srl via Redipuglia 21/A35131 Padova, Italy 3 ENEA, Research Center CASACCIA, S.M. Galeria 00163, Rome, Italy 4 ENEA, TRISAIA Research Center, S.S. 106 Ionica75026 Rotondella (Matera), Italy 5 Genomics Research Centre, Italian Agricultural Research Council, via S.Protaso 302, I-29017 Fiorenzuola d’Arda (Pc), Italy 6 Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic Keywords: genome; wheat; transposable element; crop Within the International Wheat Genome Sequencing Consortium, Italy is in charge of Chromosome 5A. As a part of this project, here we present a preliminary shotgun sequencing analysis performed by a of 454 technologies. As a starting material we used the short arm and long arm of chromosome 5A, isolated by flow cytometry. The DNA from the sorted chromosome arms was amplified by GenomiPhi DNA Amplification Kit by GE Healthcare, processed for DNA fragment analysis and run on a Roche 454-Titanium sequencer, producing a coverage of more than 2x for both arms. The preliminary results reveal the presence on both chromosome 5A arms of numerous putative genes and of several putative microRNA-related sequences (microRNA coding genes or microRNA target genes). More than two-thirds of the 454 reads exhibit significant homologies to known Triticeae repeat sequences
A high density genetic map is needed for anchoring BAC contigs during the construction of a physical map and for DNA sequence assembly. The International Wheat Genome Sequencing Consortium is dedicated to the development of physical maps of individual chromosomes as the first step towards the whole genome sequencing of hexaploid wheat. To undertake this challenge for wheat chromosome 5A, we rely on two mapping populations and different parallel approaches for marker development. A Chinese Spring x Renan (CSxR) F2 population is being used, while another F2 population derived from CS x CS-Triticum dicoccoides disomic substitution line for chromosome 5A is under creation. Another promising population is being considered: Triticum monococcum F2 population deriving from DV92 and G3116. For marker development, a Diversity Array Technology (DArT) platform containing about 4000 new probes specific for the short and long arms of wheat chromosome 5A has been established using DNA from flow sorted chromosomes, also including more than 6000 nonchromosome specific wheat probes. Besides the DArTs, a set of SSR (from databases and literature), specific for 5AS and/or 5AL chromosome arms, have been selected. Sequencing and annotation has been undertaken for sorted DNA of 5AL and 5AS. To date, the 2-fold coverage by 454 sequencing aided in thousand of SSR, ISBP, RJJM, RJM marker development. After the assignment to chromosome 5A, performed using CS deletion and aneuploid lines, the markers are being tested for polymorphism between the parents of the two mapping populations. Polymorphic DNA fragments, specific for 5A, have been mapped in CSxR population. The resulting genetic linkage map of the wheat chromosome 5A will be presented. doi:10.1016/j.jbiotec.2010.09.710