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![[Two chicks standing on Genomic Map] Picture courtesy of Agricultural Research Service, USDA](../image/chickmap.jpg) Picture courtesy of Agricultural Research Service, USDA |
Chicken Genetic Linkage Map
Download Site for Map Manager: a genetic mapping software program.
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We still have a few of the robot-spotted filter sets of the chicken BAC library constructed at Texas A&M, using the UCD001 Jungle Fowl line as it's DNA source. If interested, email me at dodgson@msu.edu. The filter sets contain arrays of 39,400 BAC clones with BamHI-derived inserts. A requirement for receiving a free filter set is that the user agree to provide the name of the probe used and clone locations at a later date, so all users can benefit from coordination resources. Alternatively, filter sets can be obtained directly from GENEfinder Genomic Resources (http://hbz.tamu.edu) at the cost of preparing them. In either case, once your clone of interest is identified by hybridization, individual clones can be obtained at cost from GENEfinder. BACs have also been constructed with EcoRI and HindIII inserts (~39,400 each into pECBAC1) to insure complete coverage of the genome. For those wishing to use PCR rather than filter hybridization to screen for your gene(s) of interest, see BAC pool information in the section below. Martien Groenen and Richard Crooijmans have also constructed a BAC library in collaboration with Texas A&M (Crooijmans et al., Mammalian Genome 11: 360-363, 2000). For more information, see www.zod.wau.nl/vf. If you wish to purchase or use the Groenen-Crooijmans library, either contact www.zod.wau.nl/abg/hs/research/molecular/intro.html, the UK Human Genome Mapping Project Resource Center at http://www.hgmp.mrc.ac.uk, who sell filter sets of this library, or GENEfinder Genomic Resources (http://hbz.tamu.edu).
Pooled BAC DNAs have been prepared by Research Genetics using ~30,000 BamHI BAC clones (plates 21-100). They are arrayed for multiplex screening using PCR. There are 80 plate pools (384 BACs each), 64 row pools (20 plates each for a total of 480 BACs each) and 96 column pools (20 plates each for a total of 320 BACs each). Pool DNA concentration is ~300pg/ul, and 1 ul per pool is recommended per PCR reaction. If interested, contact H. Cheng (hcheng@msu.edu) or J. Dodgson (dodgson@msu.edu) or Research Genetics (www.resgen.com).
MS Excel file of SNPs used in Illumina Corp. Chicken Genotype Project. (note: the previous phrase would be hyperlinked to downloading the file). These SNP sites were selected from putative SNPs detected by the International Chicken Polymorphism Map Consortium (Nature 432:717-722, 2004) by H. Cheng and used in collaboration with another consortium of academic, commercial and Federal researchers to genotype a wide variety of chicken populations (Cheng et al., submitted for publication). High throughput Illumina Corporation technology was employed. Note that in referencing a particular SNP, either the dbSNP rs or ss numbers should be used. rs stands for reference cluster ID while ss stands for NCBI assay ID. The "SNP name" is that used for this Illumina project, but is not universal to other applications. Note also that SNP locations change in difference builds of the draft chicken genome sequence. Contact hcheng@msu.edu with any questions.
MS Excel file of BAC assignments to markers or genes. Generally, most probes have been screened only on a limited portion of the available libraries (only BamHI filters or only EcoRI filters or only HindIII filters of the Texas A&M library or only the CHORI-261 library, as noted). If you wish to purchase selected Texas A&M BACs from Genefinder (email Felipe Santos at fasantos@neo.tamu.edu or go to "Contact Us" at http://hbz.tamu.edu), it's important that you specify the correct one of their three libraries. CHORI-261 BACs need to be purchased from BACPAC at the Children's Hospital of Oakland Research Institute, http://www.chori.org/bacpac/home.htm.
Hongbin Zhang and colleagues have fingerprinted over 65,000 of their BACs, and a preliminary contig map of the chicken genome has been generated (Ren et al., Genome Research 13:2754-2758); see http://hbz.tamu.edu Physical Mapping - Chicken Map. You can generate contigs on-line at this web site by starting with your BAC of interest. Keep in mind that only about half of the BACs in any one library have been fingerprinted, so just because something doesn't show up in a contig doesn't mean that it doesn't belong there. A much improved contig map (over 180,000 fingerprints) is expected in Jan. 2004 from the Wash U. Genome Center http://genome.wustl.edu/projects/chicken/.
In many cases the quality of the assignment is estimated at three confidence levels, P=probable, T=tentative, and W=weak. These aren't totally objective estimates, but for assignments in the Dodgson lab, P indicates a clear signal on 4 of 4 appropriate overgo pools, T generally indicates either one (of four) fainter or smeared signal or concern about multiple probe hits or inconsistent signal strength, and W usually indicates only 3 of 4 dimensions being positive or some other concern.
Thanks to those who contributed BAC assignments. If there are any errors in your assignments or their attribution, please let me know. If you have new data to contribute, that's always welcome, too. Email dodgson@msu.edu
The turkey BAC contig comparative map is now available in the publication: Zhang, Y., X. Zhang, T.H. O’Hare, W.S. Payne, J.J. Dong, C.F. Scheuring, M. Zhang, J.J. Huang, M.-K. Lee, M.E. Delany, H.-B. Zhang and J.B. Dodgson. 2011. A comparative physical map reveals the pattern of chromosomal evolution between the turkey (Meleagris gallopavo) and chicken (Gallus gallus) genomes, BMC Genomics, 12:447. Updated versions of all the data files previously available at this site are available as supplemental files from BMC Genomics attached to this manuscript.
Genbank accession numbers for CHORI-260 TURKEY BAC END SEQUENCES and the corresponding BAC end name. BAC end sequences were generated by Hongbin Zhang and colleagues by sequencing CHORI-260 BACs. Genbank accession numbers (ER942218-ER962259) are given, along with the corresponding CHORI-260 BAC name and whether the sequence derives from the T7 or SP6 end of the BAC insert. Genbank accession numbers for 78TKNMI TURKEY BAC END SEQUENCES and the corresponding BAC end name. BAC end sequences generated by Hongbin Zhang and colleagues by sequencing 78TKNMI turkey BACs from the library generated by them at Texas A&M are listed. The 78TKNMI BAC name is given followed by S or T, respectively, if the sequence derives from the SP6 or T7 end of the BAC insert, followed by the Genbank identifiers. In this table, clicking on the Genbank accession number (FIxxxxxx) will take you to a FASTA version of the sequence at Genbank ( http://www.ncbi.nlm.nih.gov/nucgss/ ).
MS Excel file of BAC assignments to markers or genes. Probes have been screened against the AGI TG__Ba BAC library. AGI BACs can be purchased from Arizona Genome Institute at http://www.genome.arizona.edu/. In many cases the quality of the assignment is estimated at three confidence levels, P=probable, T=tentative, and W=weak. These aren't totally objective estimates, but generally P indicates a clear signal on 4 of 4 appropriate overgo pools, T generally indicates either one (of four) fainter or smeared signal or concern about multiple probe hits or inconsistent signal strength, and W usually indicates only 3 of 4 dimensions being positive or some other concern.
Email dodgson@msu.edu with any questions or comments.
List of overgo probes used for mapping in turkey and zebra finch including location of homology to the chicken genome, accession number and numbers of BACs isolated in these two species, where applicable.
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