Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping

Douaud, Marine; Fève, Katia; Gerus, Marie; Fillon, Valérie; Bardes, Suzanne; Gourichon, David; Dawson, Deborah A.; Hanotte, Olivier; Burke, Terry; Vignoles, Florence; Morisson, Mireille; Tixier-Boichard, Michèle; Vignal, Alain; Pitel, Frédérique
January 2008
BMC Genomics;2008, Vol. 9, Special section p1
Academic Journal
Background: The publication of the first draft chicken sequence assembly became available in 2004 and was updated in 2006. However, this does not constitute a definitive and complete sequence of the chicken genome, since the microchromosomes are notably under-represented. In an effort to develop maps for the microchromosomes absent from the chicken genome assembly, we developed radiation hybrid (RH) and genetic maps with markers isolated from sequence currently assigned to "chromosome Unknown" (chrUn). The chrUn is composed of sequence contigs not assigned to named chromosomes. To identify and map sequence belonging to the microchromosomes we used a comparative mapping strategy, and we focused on the small linkage group E26C13. Results: In total, 139 markers were analysed with the chickRH6 panel, of which 120 were effectively assigned to the E26C13 linkage group, the remainder mapping elsewhere in the genome. The final RH map is composed of 22 framework markers extending over a 245.6 cR distance. A corresponding genetic map was developed, whose length is 103 cM in the East Lansing reference population. The E26C13 group was assigned to GGA25 (Gallus gallus chromosome 25) by FISH (fluorescence in situ hybridisation) mapping. Conclusion: The high-resolution RH framework map obtained here covers the entire chicken chromosome 25 and reveals the existence of a high number of intrachromosomal rearrangements when compared to the human genome. The strategy used here for the characterization of GGA25 could be used to improve knowledge on the other uncharacterized small, yet gene-rich microchromosomes.


Related Articles

  • Comparative mapping of mink ( Mustela vision) chromosome 8p: Localization of three human BAC clones. Zhdanova, N. S. // Russian Journal of Genetics;Aug2007, Vol. 43 Issue 8, p890 

    Using fluorescent in situ hybridization (FISH), three human BAC clones, localized in the terminal region of human chromosome 17p (HSA17p13; 1.44–3.68 Mp), were mapped in chromosome 8p of American mink (MVI8p). It was demonstrated that in MVI8p the region, homeologous to HSA17p13, was...

  • Sex chromosome differentiation in Humulus japonicus Siebold & Zuccarini, 1846 (Cannabaceae) revealed by fluorescence in situ hybridization of subtelomeric repeat. Alexandrov, Oleg S.; Divashuk, Mikhail G.; Yakovin, Nikolay A.; Karlov, Gennady I. // Comparative Cytogenetics;2012, Vol. 6 Issue 3, p239 

    Humulus japonicus Siebold & Zucc (Japanese hop) is a dioecious species of the family Cannabaceae. he chromosome number is 2n = 16 = 14 + XX for females and 2n = 17 = 14 + XY1Y2 for male. To date, no fluorescence in situ hybridization (FISH) markers have been established for the identification of...

  • Integrating physical and genetic maps: from genomes to interaction networks. Beyer, Andreas; Bandyopadhyay, Sourav; Ideker, Trey // Nature Reviews Genetics;Sep2007, Vol. 8 Issue 9, p699 

    Physical and genetic mapping data have become as important to network biology as they once were to the Human Genome Project. Integrating physical and genetic networks currently faces several challenges: increasing the coverage of each type of network; establishing methods to assemble individual...

  • A systematic, high-resolution linkage of the cytogenetic and physical maps of the human genome. Kirsch, Ilan R.; Green, Eric D.; Yonescu, Raluca; Strausberg, Robert; Carter, Nigel; Bentley, David; Leversha, Margaret A.; Dunham, Ian; Braden, Valerie V.; Hilgenfeld, Eva; Schuler, Greg; Lash, Alex E.; Shen, Grace L.; Martelli, Maria; Kuehl, W. Michael; Klausner, Richard D.; Ried, Thomas // Nature Genetics;Apr2000, Vol. 24 Issue 4, p339 

    Discusses the Cancer Chromosome Aberration Project which aims to integrate systematically the cytogenetic and physical maps of the human genome by high-resolution fluorescence in-situ hybridization. Mapping procedure; Analysis of genomic regions associated with chromosome aberrations.

  • Clinical implementation of whole-genome array CGH as a first-tier test in 5080 pre and postnatal cases. Park, Sang-Jin; Eun Hye Jung; Ryu, Ran-Suk; Hyun Woong Kang; Jung-Min Ko; Kim, Hyon J.; Chong Kun Cheon; Sang-Hyun Hwang; Ho-Young Kang // Molecular Cytogenetics (17558166);2011, Vol. 4 Issue 1, p12 

    Background: Array comparative genomic hybridization (CGH) is currently the most powerful method for detecting chromosomal alterations in pre and postnatal clinical cases. In this study, we developed a BAC based array CGH analysis platform for detecting whole genome DNA copy number changes...

  • Comparative genomic analysis links karyotypic evolution with genomic evolution in the Indian Muntjac ( Muntiacus muntjak vaginalis). Zhou, Qi; Huang, Ling; Zhang, Jianguo; Zhao, Xiangyi; Zhang, Qingpeng; Song, Fei; Chi, Jianxiang; Yang, Fengtang; Wang, Wen // Chromosoma;Dec2006, Vol. 115 Issue 6, p427 

    The karyotype of Indian muntjacs ( Muntiacus muntjak vaginalis) has been greatly shaped by chromosomal fusion, which leads to its lowest diploid number among the extant known mammals. We present, here, comparative results based on draft sequences of 37 bacterial artificial clones (BAC) clones...

  • Comparative FISH mapping of Daucus species (Apiaceae family). Iovene, Marina; Cavagnaro, Pablo; Senalik, Douglas; Buell, C.; Jiang, Jiming; Simon, Philipp // Chromosome Research;Jun2011, Vol. 19 Issue 4, p493 

    The cytogenetic characterization of the carrot genome ( Daucus carota L., 2 n = 18) has been limited so far, partly because of its somatic chromosome morphology and scant of chromosome markers. Here, we integrate the carrot linkage groups with pachytene chromosomes by fluorescent in situ...

  • Duplication and transposition of the NF1 pseudogene regions on chromosomes 2, 14, and 22. Luijten, Mirjam; Redeker, Sandra; Minoshima, Shinsei; Shimizu, Nobuyoshi; Westerveld, Andries; Hulsebos, Theo J. M. // Human Genetics;Jul2001, Vol. 109 Issue 1, p109 

    Numerous NF1 pseudogenes have been identified in the human genome. Those in 2q21, 14q11, and 22q11 form a subset with a similar genomic organization and a high sequence homology. We have studied, by polymerase chain reaction and fluorescence in situ hybridization, the extent of homology of the...

  • Chromosomes with high gene density are preferentially repaired in human cells. Surrallés, J.; Sebastian, S.; Natarajan, A. T. // Mutagenesis;Nov1997, Vol. 12 Issue 6, p437 

    It is known that DNA repair is heterogeneous in human cells since open chromatin, active genes and their transcribed strands are preferentially repaired. It is thus expected that DNA repair is clustered in chromosomes with high gene density. We have employed a DNA repair inhibitor, cytosine...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics