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

被引：9

作者：

Barabaschi, Delfina ^{[1
]}

Magni, Federica ^{[2
]}

Volante, Andrea ^{[1
]}

Gadaleta, Agata ^{[3
]}

Simkova, Hana ^{[4
]}

Scalabrin, Simone ^{[2
]}

Prazzoli, Maria Lucia ^{[1
]}

Bagnaresi, Paolo ^{[1
]}

Lacrima, Katia ^{[1
]}

Michelotti, Vania ^{[1
]}

Desiderio, Francesca ^{[1
]}

Orru, Luigi ^{[1
]}

Mazzamurro, Valentina ^{[5
]}

Fricano, Agostino ^{[6
]}

Mastrangelo, AnnaMaria ^{[7
]}

Tononi, Paola ^{[8
]}

Vitulo, Nicola ^{[9
]}

Jurman, Irena ^{[2
]}

Frenkel, Zeev ^{[10
,11
]}

Cattonaro, Federica ^{[2
]}

Morgante, Michele ^{[2
]}

Blanco, Antonio ^{[3
]}

Dolezel, Jaroslav ^{[4
]}

Delledonne, Massimo ^{[8
]}

Stanca, Antonio M. ^{[1
,5
]}

Cattivelli, Luigi ^{[1
]}

Vale, Giampiero ^{[1
,12
]}

机构：

[1] Council Agr Res & Econ CREA Genom Res Ctr, I-29017 Fiorenzuola Darda, Piacenza, Italy

[2] Inst Appl Genom, I-33100 Udine, Italy

[3] Univ Bari, Dept Soil Plant & Food Sci, Sect Genet & Plant Breeding, I-70126 Bari, Italy

[4] Inst Expt Bot, Ctr Reg Hana Biotechnol & Agr Res, CZ-77200 Olomouc, Czech Republic

[5] Univ Modena & Reggio Emilia, Dept Life Sci, I-42100 Reggio Emilia, Italy

[6] Parco Tecnol Padano, I-26100 Lodi, Italy

[7] Council Agr Res & Econ CREA Cereal Res Ctr, I-71122 Foggia, Italy

[8] Univ Verona, Dept Biotechnol, I-37129 Verona, Italy

[9] Univ Padua, CRIBI Biotechnol Ctr, I-35121 Padua, Italy

[10] Univ Haifa, Inst Evolut, IL-3498838 Haifa, Israel

[11] Univ Haifa, Dept Evolutionary & Environm Biol, IL-3498838 Haifa, Israel

[12] Council Agr Res & Econ CREA Rice Res Unit, I-13100 Vercelli, Italy

来源：

PLANT GENOME | 2015年 / 8卷 / 03期

关键词：

GENE SPACE ORGANIZATION; HEAD BLIGHT RESISTANCE; RADIATION HYBRIDS; WHOLE-GENOME; SPRING WHEAT; MAP; SEQUENCE; MARKER; RESOURCES; IDENTIFICATION;

D O I：

10.3835/plantgenome2015.03.0011

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

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.

引用

页数：24

共 82 条

[21] The deletion stocks of common wheat [J].

Endo, TR ;

Gill, BS .

JOURNAL OF HEREDITY, 1996, 87 (04) :295-307

[22] Contribution of Radiation Hybrids to Genome Mapping in Domestic Animals [J].

Faraut, T. ;

de Givry, S. ;

Hitte, C. ;

Lahbib-Mansais, Y. ;

Morisson, M. ;

Milan, D. ;

Schiex, T. ;

Servin, B. ;

Vignal, A. ;

Galibert, F. ;

Yerle, M. .

CYTOGENETIC AND GENOME RESEARCH, 2009, 126 (1-2) :21-33

[23] Physical mapping of the wheat genome: A coordinated effort to lay the foundation for genome sequencing and develop tools for breeders [J].

Feuillet, Catherine ;

Eversole, Kellye .

ISRAEL JOURNAL OF PLANT SCIENCES, 2007, 55 (3-4) :307-313

[24] Crop genome sequencing: lessons and rationales [J].

Feuillet, Catherine ;

Leach, Jan E. ;

Rogers, Jane ;

Schnable, Patrick S. ;

Eversole, Kellye .

TRENDS IN PLANT SCIENCE, 2011, 16 (02) :77-88

[25] LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes [J].

Frenkel, Zeev ;

Paux, Etienne ;

Mester, David ;

Feuillet, Catherine ;

Korol, Abraham .

BMC BIOINFORMATICS, 2010, 11

[26] A new genetic and deletion map of wheat chromosome 5A to detect candidate genes for quantitative traits [J].

Gadaleta, A. ;

Giancaspro, A. ;

Nigro, D. ;

Giove, S. L. ;

Incerti, Ornella ;

Simeone, R. ;

Piarulli, L. ;

Colasuonno, P. ;

Vale, G. ;

Cattivelli, L. ;

Blanco, A. .

MOLECULAR BREEDING, 2014, 34 (04) :1599-1611

[27]

Gadaleta A, 2012, GENOME, V55, P417, DOI [10.1139/G2012-028, 10.1139/g2012-028]

[28] Insular Organization of Gene Space in Grass Genomes [J].

Gottlieb, Andrea ;

Mueller, Hans-Georg ;

Massa, Alicia N. ;

Wanjugi, Humphrey ;

Deal, Karin R. ;

You, Frank M. ;

Xu, Xiangyang ;

Gu, Yong Q. ;

Luo, Ming-Cheng ;

Anderson, Olin D. ;

Chan, Agnes P. ;

Rabinowicz, Pablo ;

Devos, Katrien M. ;

Dvorak, Jan .

PLOS ONE, 2013, 8 (01)

[29] Grinding up wheat:: A massive loss of nucleotide diversity since domestication [J].

Haudry, A. ;

Cenci, A. ;

Ravel, C. ;

Bataillon, T. ;

Brunel, D. ;

Poncet, C. ;

Hochu, I. ;

Poirier, S. ;

Santoni, S. ;

Glemin, S. ;

David, J. .

MOLECULAR BIOLOGY AND EVOLUTION, 2007, 24 (07) :1506-1517

[30] Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content [J].

Hernandez, Pilar ;

Martis, Mihaela ;

Dorado, Gabriel ;

Pfeifer, Matthias ;

Galvez, Sergio ;

Schaaf, Sebastian ;

Jouve, Nicolas ;

Simkova, Hana ;

Valarik, Miroslav ;

Dolezel, Jaroslav ;

Mayer, Klaus F. X. .

PLANT JOURNAL, 2012, 69 (03) :377-386

← 1 2 3 4 5 6 7 8 9 →