Abstract
BackgroundThe 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.ResultsWe 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.ConclusionsThe 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.
Highlights
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
Development of GGA16 markers Seventy five Radiation Hybrid (RH) markers were developed. These were identified as putatively belonging to GGA16 based on several sources of information, including similarity with other B and Y complex gene sequence and synteny conservation with human. Out of all these potential markers, 13 could not be assigned to GGA16 after RH mapping (Additional File 1). - Available GGA16 sequences A total of 432,983 bp are available for GGA16 in the whole genome assembly [6]
In the chicken genome assembly WUGS C2.1/galGal3, the NOR region is located in chicken chromosome 1 [6]; we designed primers in this region to map NOR markers, as they are known to be localized on GGA16. - Comparative mapping Sequence similarities were observed between GGA16 and human chromosome region 6p21, or with other human chromosomes (HSA 1, 2, 5, 16, 19, and 21) [6], and chicken chrUn or EST sequence aligning by sequence similarity to these human regions are a potential source of supplementary markers
Summary
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. Sharing the characteristics of a classical avian karyotype, the chicken genome, as standardized by Ladjali-Mohammedi et al in 1999 [1], is composed of 9 macrochromosomes including the Z and W sex chromosomes and 30 pairs of microchromosomes. These very small chromosomes range in size between 3.5 and 23 Mb [2,3] and are remarkably gene rich [4]. We have shown that many chicken cDNA and EST (Expressed Sequence Tag) sequence contigs are absent from the assembly, including in the chrUn fraction, suggesting the total absence of large amounts of the corresponding genomic DNA [10]
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