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Integrative mapping analysis of chicken microchromosome 16 organization.

Solinhac R, Leroux S, Galkina S, Chazara O, Feve K, Vignoles F, Morisson M, Derjusheva S, Bed'hom B, Vignal A, Fillon V, Pitel F - BMC Genomics (2010)

Bottom Line: A region with high recombination rates and containing PO41 repeated elements separates the two MHC complexes.The three complementary mapping strategies used refine greatly our knowledge of chicken microchromosome 16 organisation.However, this region still needs to be studied in more detail.

View Article: PubMed Central - HTML - PubMed

Affiliation: UMR INRA/ENVT Laboratoire de Génétique Cellulaire, INRA, Castanet-Tolosan, 31326, France.

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.

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Related in: MedlinePlus

GGA16 genetic map. Marker assignation to one of the three complexes is shown (not at scale) (a). The framework map is 130.7 cM long (b). The other markers are indicated with their best location on the right of the framework map.
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Figure 2: GGA16 genetic map. Marker assignation to one of the three complexes is shown (not at scale) (a). The framework map is 130.7 cM long (b). The other markers are indicated with their best location on the right of the framework map.

Mentions: In order to integrate markers mapped elsewhere, 3 populations were used: our experimental one, the East Lansing backcross one and the Compton backcross one (see Methods section). A total of 16 new informative markers could be added to the GGA16 consensus linkage map [38], eight of which genotyped on our experimental population. Together with the previously available data, the GGA16 genetic map is now composed of 33 markers and is 130.7 cM long (Figure 2).


Integrative mapping analysis of chicken microchromosome 16 organization.

Solinhac R, Leroux S, Galkina S, Chazara O, Feve K, Vignoles F, Morisson M, Derjusheva S, Bed'hom B, Vignal A, Fillon V, Pitel F - BMC Genomics (2010)

GGA16 genetic map. Marker assignation to one of the three complexes is shown (not at scale) (a). The framework map is 130.7 cM long (b). The other markers are indicated with their best location on the right of the framework map.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3091757&req=5

Figure 2: GGA16 genetic map. Marker assignation to one of the three complexes is shown (not at scale) (a). The framework map is 130.7 cM long (b). The other markers are indicated with their best location on the right of the framework map.
Mentions: In order to integrate markers mapped elsewhere, 3 populations were used: our experimental one, the East Lansing backcross one and the Compton backcross one (see Methods section). A total of 16 new informative markers could be added to the GGA16 consensus linkage map [38], eight of which genotyped on our experimental population. Together with the previously available data, the GGA16 genetic map is now composed of 33 markers and is 130.7 cM long (Figure 2).

Bottom Line: A region with high recombination rates and containing PO41 repeated elements separates the two MHC complexes.The three complementary mapping strategies used refine greatly our knowledge of chicken microchromosome 16 organisation.However, this region still needs to be studied in more detail.

View Article: PubMed Central - HTML - PubMed

Affiliation: UMR INRA/ENVT Laboratoire de Génétique Cellulaire, INRA, Castanet-Tolosan, 31326, France.

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.

Show MeSH
Related in: MedlinePlus