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Open Access Research article

Integrative mapping analysis of chicken microchromosome 16 organization

Romain Solinhac1, Sophie Leroux1, Svetlana Galkina2, Olympe Chazara3, Katia Feve1, Florence Vignoles1, Mireille Morisson1, Svetlana Derjusheva2, Bertrand Bed'hom3, Alain Vignal1, Valérie Fillon1 and Frédérique Pitel1*

Author Affiliations

1 UMR INRA/ENVT Laboratoire de Génétique Cellulaire, INRA, Castanet-Tolosan, 31326, France

2 Saint-Petersburg State University, Oranienbaumskoie shosse 2, Stary Peterhof, Saint-Petersburg, 198504, Russia

3 UMR INRA-AgroParisTech Génétique Animale et Biologie Intégrative, INRA, Jouy-en-Josas, 78352, France

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BMC Genomics 2010, 11:616  doi:10.1186/1471-2164-11-616

Published: 4 November 2010

Abstract

Background

The chicken karyotype is composed of 39 chromosome pairs, of which 9 still remain totally absent from the current genome sequence assembly, despite international efforts towards complete coverage. Some others are only very partially sequenced, amongst which microchromosome 16 (GGA16), particularly under-represented, with only 433 kb assembled for a full estimated size of 9 to 11 Mb. Besides the obvious need of full genome coverage with genetic markers for QTL (Quantitative Trait Loci) mapping and major genes identification studies, there is a major interest in the detailed study of this chromosome because it carries the two genetically independent MHC complexes B and Y. In addition, GGA16 carries the ribosomal RNA (rRNA) genes cluster, also known as the NOR (nucleolus organizer region). The purpose of the present study is to construct and present high resolution integrated maps of GGA16 to refine its organization and improve its coverage with genetic markers.

Results

We developed 79 STS (Sequence Tagged Site) markers to build a physical RH (radiation hybrid) map and 34 genetic markers to extend the genetic map of GGA16. We screened a BAC (Bacterial Artificial Chromosome) library with markers for the MHC-B, MHC-Y and rRNA complexes. Selected clones were used to perform high resolution FISH (Fluorescent In Situ Hybridization) mapping on giant meiotic lampbrush chromosomes, allowing meiotic mapping in addition to the confirmation of the order of the three clusters along the chromosome. A region with high recombination rates and containing PO41 repeated elements separates the two MHC complexes.

Conclusions

The three complementary mapping strategies used refine greatly our knowledge of chicken microchromosome 16 organisation. The characterisation of the recombination hotspots separating the two MHC complexes demonstrates the presence of PO41 repetitive sequences both in tandem and inverted orientation. However, this region still needs to be studied in more detail.