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Holušová K, Vrána J, Šafář J, Šimková H, Balcárková B, Frenkel Z, Darrier B, Paux E, Cattonaro F, Berges H, Letellier T, Alaux M, Doležel J, Bartoš J. Physical Map of the Short Arm of Bread Wheat Chromosome 3D. THE PLANT GENOME 2017; 10. [PMID: 28724077 DOI: 10.3835/plantgenome2017.03.0021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bread wheat ( L.) is one of the most important crops worldwide. Although a reference genome sequence would represent a valuable resource for wheat improvement through genomics-assisted breeding and gene cloning, its generation has long been hampered by its allohexaploidy, high repeat content, and large size. As a part of a project coordinated by the International Wheat Genome Sequencing Consortium (IWGSC), a physical map of the short arm of wheat chromosome 3D (3DS) was prepared to facilitate reference genome assembly and positional gene cloning. It comprises 869 contigs with a cumulative length of 274.5 Mbp and represents 85.5% of the estimated chromosome arm size. Eighty-six Mbp of survey sequences from chromosome arm 3DS were assigned in silico to physical map contigs via next-generation sequencing of bacterial artificial chromosome pools, thus providing a high-density framework for physical map ordering along the chromosome arm. About 60% of the physical map was anchored in this single experiment. Finally, 1393 high-confidence genes were anchored to the physical map. Comparisons of gene space of the chromosome arm 3DS with genomes of closely related species [ (L.) P.Beauv., rice ( L.), and sorghum [ (L.) Moench] and homeologous wheat chromosomes provided information about gene movement on the chromosome arm.
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Barabaschi D, Magni F, Volante A, Gadaleta A, Šimková H, Scalabrin S, Prazzoli ML, Bagnaresi P, Lacrima K, Michelotti V, Desiderio F, Orrù L, Mazzamurro V, Fricano A, Mastrangelo A, Tononi P, Vitulo N, Jurman I, Frenkel Z, Cattonaro F, Morgante M, Blanco A, Doležel J, Delledonne M, Stanca AM, Cattivelli L, Valè G. Physical Mapping of Bread Wheat Chromosome 5A: An Integrated Approach. THE PLANT GENOME 2015; 8:eplantgenome2015.03.0011. [PMID: 33228274 DOI: 10.3835/plantgenome2015.03.0011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/21/2015] [Indexed: 06/11/2023]
Abstract
The huge size, redundancy, and highly repetitive nature of the bread wheat [Triticum aestivum (L.)] genome, makes it among the most difficult species to be sequenced. To overcome these limitations, a strategy based on the separation of individual chromosomes or chromosome arms and the subsequent production of physical maps was established within the frame of the International Wheat Genome Sequence Consortium (IWGSC). A total of 95,812 bacterial artificial chromosome (BAC) clones of short-arm chromosome 5A (5AS) and long-arm chromosome 5A (5AL) arm-specific BAC libraries were fingerprinted and assembled into contigs by complementary analytical approaches based on the FingerPrinted Contig (FPC) and Linear Topological Contig (LTC) tools. Combined anchoring approaches based on polymerase chain reaction (PCR) marker screening, microarray, and sequence homology searches applied to several genomic tools (i.e., genetic maps, deletion bin map, neighbor maps, BAC end sequences (BESs), genome zipper, and chromosome survey sequences) allowed the development of a high-quality physical map with an anchored physical coverage of 75% for 5AS and 53% for 5AL with high portions (64 and 48%, respectively) of contigs ordered along the chromosome. In the genome of grasses, Brachypodium [Brachypodium distachyon (L.) Beauv.], rice (Oryza sativa L.), and sorghum [Sorghum bicolor (L.) Moench] homologs of genes on wheat chromosome 5A were separated into syntenic blocks on different chromosomes as a result of translocations and inversions during evolution. The physical map presented represents an essential resource for fine genetic mapping and map-based cloning of agronomically relevant traits and a reference for the 5A sequencing projects.
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Affiliation(s)
- Delfina Barabaschi
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | | | - Andrea Volante
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Agata Gadaleta
- Dep. of Soil, Plant and Food Sciences, Section of Genetic and Plant Breeding, Univ. of Bari, Bari, I-70126
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, CZ-77200
| | | | - Maria Lucia Prazzoli
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Paolo Bagnaresi
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Katia Lacrima
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Vania Michelotti
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Francesca Desiderio
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Luigi Orrù
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Valentina Mazzamurro
- Dep. of Life Sciences, Univ. of Modena and Reggio Emilia, Reggio Emilia, I-42100
| | | | - AnnaMaria Mastrangelo
- Council for Agricultural Research and Economics (CREA)-Cereal Research Centre, Foggia, I-71122
| | - Paola Tononi
- Dep. of Biotechnology, Univ. of Verona, Verona, I-37129
| | - Nicola Vitulo
- CRIBI Biotechnology Center, Univ. of Padova, Padova, I-35121
| | | | - Zeev Frenkel
- Institute of Evolution and Dep. of Evolutionary and Environmental Biology, Univ. of Haifa, Haifa, IL-3498838
| | | | | | - Antonio Blanco
- Dep. of Soil, Plant and Food Sciences, Section of Genetic and Plant Breeding, Univ. of Bari, Bari, I-70126
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, CZ-77200
| | | | - Antonio M Stanca
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
- Dep. of Life Sciences, Univ. of Modena and Reggio Emilia, Reggio Emilia, I-42100
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Giampiero Valè
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
- Council for Agricultural Research and Economics (CREA)-Rice Research Unit, Vercelli, I-13100
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