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The Plant Genome Abstract - Original Research

Physical Mapping of Bread Wheat Chromosome 5A: An Integrated Approach

 

doi:10.3835/plantgenome2015.03.0011
  1. Delfina Barabaschi *a,
  2. Federica Magnic,
  3. Andrea Volantea,
  4. Agata Gadaletad,
  5. Hana Šimkováe,
  6. Simone Scalabrinc,
  7. Maria Lucia Prazzoliab,
  8. Paolo Bagnaresia,
  9. Katia Lacrimaa,
  10. Vania Michelottia,
  11. Francesca Desiderioa,
  12. Luigi Orrùa,
  13. Valentina Mazzamurrof,
  14. Agostino Fricanog,
  15. AnnaMaria Mastrangeloh,
  16. Paola Tononii,
  17. Nicola Vituloj,
  18. Irena Jurmanc,
  19. Zeev Frenkelk,
  20. Federica Cattonaroc,
  21. Michele Morgantec,
  22. Antonio Blancod,
  23. Jaroslav Doležele,
  24. Massimo Delledonnei,
  25. Antonio M. Stancaaf,
  26. Luigi Cattivellia and
  27. Giampiero Valèal
  1. a Council for Agricultural Research and Economics (CREA)–Genomics Research Centre, Fiorenzuola d’Arda, Piacenza, I-29017
    c Institute of Applied Genomics, Udine, I-33100
    d Dep. of Soil, Plant and Food Sciences, Section of Genetic and Plant Breeding, Univ. of Bari, Bari, I-70126
    e Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, CZ-77200
    b present address: Fondazione E. Mach (IASMA), S. Michele,Trento, I-38010
    f Dep. of Life Sciences, Univ. of Modena and Reggio Emilia, Reggio Emilia, I-42100
    g Parco Tecnologico Padano, Lodi, I-26900, present address: Council for Agricultural Research and Economics (CREA)–Unità di ricerca per la maiscoltura, Bergamo, I-24126
    h Council for Agricultural Research and Economics (CREA)–Cereal Research Centre, Foggia, I-71122
    i Dep. of Biotechnology, Univ. of Verona, Verona, I-37129
    j CRIBI Biotechnology Center, Univ. of Padova, Padova, I-35121
    k Institute of Evolution and Dep. of Evolutionary and Environmental Biology, Univ. of Haifa, Haifa, IL-3498838
    l Council for Agricultural Research and Economics (CREA)–Rice Research Unit, Vercelli, I-13100

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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