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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

BAC clones mapped two by two on chicken metaphases. Three BAC clones were used: WAG137G04 (NOR), WAG523B09 (Y complex), WAG65G09 (B complex). NOR (red) and B complex (green) are located on the same chromosome (a), as for Y complex (green) and NOR (red) (b) and for Y complex (green) and B complex (red) (c). BAC clones WAG523B09 (green, Y complex) and WAG65G09 (red, B complex) are in the same nuclear area (d). WAG523B09 hybridizes several times the chromatin suggesting the presence of repeat sequences.
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Figure 3: BAC clones mapped two by two on chicken metaphases. Three BAC clones were used: WAG137G04 (NOR), WAG523B09 (Y complex), WAG65G09 (B complex). NOR (red) and B complex (green) are located on the same chromosome (a), as for Y complex (green) and NOR (red) (b) and for Y complex (green) and B complex (red) (c). BAC clones WAG523B09 (green, Y complex) and WAG65G09 (red, B complex) are in the same nuclear area (d). WAG523B09 hybridizes several times the chromatin suggesting the presence of repeat sequences.

Mentions: Six BAC clones from GGA16 (Table 1) were mapped two by two on chicken metaphase chromosomes and interphase nuclei (Figure 3). These experiments suggest the B complex is in q-terminal position, whereas the NOR is located at the proximal region of the q arm of GGA16. As already observed, the FISH signals for the B, Y and NOR complexes on condensed mitotic metaphase chromosomes were too close to allow defining their order unequivocally. Intriguingly, WAG523B09, a clone from the Y complex, gave several hybridization signals on interphase nuclei, which might correspond to clusters of repeated sequences dispersed on GGA16 (Figure 3d).


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)

BAC clones mapped two by two on chicken metaphases. Three BAC clones were used: WAG137G04 (NOR), WAG523B09 (Y complex), WAG65G09 (B complex). NOR (red) and B complex (green) are located on the same chromosome (a), as for Y complex (green) and NOR (red) (b) and for Y complex (green) and B complex (red) (c). BAC clones WAG523B09 (green, Y complex) and WAG65G09 (red, B complex) are in the same nuclear area (d). WAG523B09 hybridizes several times the chromatin suggesting the presence of repeat sequences.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: BAC clones mapped two by two on chicken metaphases. Three BAC clones were used: WAG137G04 (NOR), WAG523B09 (Y complex), WAG65G09 (B complex). NOR (red) and B complex (green) are located on the same chromosome (a), as for Y complex (green) and NOR (red) (b) and for Y complex (green) and B complex (red) (c). BAC clones WAG523B09 (green, Y complex) and WAG65G09 (red, B complex) are in the same nuclear area (d). WAG523B09 hybridizes several times the chromatin suggesting the presence of repeat sequences.
Mentions: Six BAC clones from GGA16 (Table 1) were mapped two by two on chicken metaphase chromosomes and interphase nuclei (Figure 3). These experiments suggest the B complex is in q-terminal position, whereas the NOR is located at the proximal region of the q arm of GGA16. As already observed, the FISH signals for the B, Y and NOR complexes on condensed mitotic metaphase chromosomes were too close to allow defining their order unequivocally. Intriguingly, WAG523B09, a clone from the Y complex, gave several hybridization signals on interphase nuclei, which might correspond to clusters of repeated sequences dispersed on GGA16 (Figure 3d).

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