Menu Chicken Genetic Linkage Map Microsatellite Marker Information and Primer Kits Chicken Gene Primer Sets BAC Library Filter Sets BAC Library PCR-screenable DNA Pools Database of SNPs used in Illumina Corp. Chicken Genotype Project Database of BACs Assigned to Chicken Genes and Markers Database of BACs Assigned to Turkey Genes and Markers Turkey BAC locations by homology of BAC end sequences to chicken sequence Genbank accession numbers for TURKEY BAC END SEQUENCES and the corresponding BAC end name Database of BACs Assigned to Zebra Finch Genes and Markers Description of Overgo Hybridization Probes Used for Turkey and Zebra Finch Mapping Downloadable Files

Picture courtesy of Agricultural Research Service, USDA

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Gene Primer Kits  

Contain pairs of PCR primers designed using published chicken gene sequence data (usually cDNA) to amplify segments of the gene's cDNA for use in RT-PCR or other gene expression assays. (Generally these do not amplify well using genomic DNA as template due to introns which separate primer binding sites.) Supplies of each primer pair are limited; up to 20-40 primer pairs of your choice distributed at a time.

Contact Hans Cheng (hcheng@msu.edu) or Jerry Dodgson (dodgson@msu.edu)

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BAC Libraries and Filter Sets: 

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).

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BAC Library PCR-screenable DNA Pools

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).

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Database of SNPs used in Illumina Corp. Chicken Genotype Project

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.

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Database of BACs Assigned to Chicken Genes and Markers

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/.

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

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Database of BACs Assigned to Turkey Genes and Markers

MS Excel file of BAC assignments to markers or genes. Probes have been screened against the CHORI-260 turkey BAC library. CHORI-260 BACs can be purchased from BACPAC at the Children's Hospital of Oakland Research Institute, http://www.chori.org/bacpac/home.htm.  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. 
Email dodgson@msu.edu with any questions or comments. 

Turkey BAC orthologous locations on chicken genome sequence.  Turkey BACs from the CHORI-260 library were positioned via homology of end sequences (BES) to the chicken genome by BLAT analysis (Zhang, Dodgson and colleagues, manuscript in preparation).  Four spreadsheets are included.  The first positions those BACs for which the two BES match single orthologous locations separated by an appropriate distance and with appropriate strand orientation ("consistent" end pairs).  The second describes BACs for which the two BES match single orthologous locations by computer analysis but the two locations are not "consistent".  This list has been manually annotated which, in most cases, resolves the reason (e.g., a repetitive or partially repetitive sequence) for the inconsistency and, where possible, provides the most likely BAC orthologous location, relative to the chicken genome.  The third list includes those BACs for which only one BES is available.  In these cases, the likely location is estimated as the site of the single BES match +/- 200 kbp.  The fourth list includes BACs for which one or more BES matched multiple locations above the chosen BLAT cutoff score.  This list is now in the process of manual annotation and will be updated as additional positions are determined.  Note also, that our website provides a separate list of CHORI-260 BACs placed on the comparative map by overgo hybridization and a list of Genbank accession numbers for all BES.