National Human Genome Research Institute-funded sequencing of the chicken genome has begun in force at the Washington U. Genome Sequencing Center (http://genome.wustl.edu/projects/chicken/). A "combined" approach is being taken that aims at 8X coverage of the chicken haplid genome, mostly with whole genome shotgun (WGS) reads, supplemented with directed sequencing of selected chicken bacterial artificial chromosome (BAC) inserts. The sequencing libraries and most of the source BAC libraries derive from DNA from a single female of the UCD001 inbred Red Jungle Fowl line described previously in this newsletter. WUGSC reports that as of 3/17/03, 1,375,015 chicken reads had been done, and finishing of 126 chicken BAC clones was underway. WGS reads should be completed by sometime early this fall.

In recognition of the upcoming genome sequence, an International Chicken Genome Workshop was held at the Hinxton Genome Campus in Cambridge, UK on March 10-11, 2003. Hans Cheng attended on behalf of the poultry coordinators. John McPherson (WUGSC) began the workshop with a summary of the sequencing strategy described above. He and several other speakers described the present status of the chicken genome physical map. Bin Liu of the Beijing Genome Institute spoke about plans to sequence additional chicken ESTs and generate SNP markers by comparison to the UCD001 sequence. Ewan Birney and others from the European Bioinformatics Institute, along with Andy Law from the Roslin Institute, described plans for providing bioinformatics support that will be needed for annotation and application of the sequence data. Several speakers discussed the excellent state of EST resources now available for the chicken (reviewed in earlier issues of this newsletter). This was followed by several talks focused on functional genomics of the chicken and its physiology and development and others that summarized numerous on-going QTL searches. Finally, Elliott Margulies of NHGRI described the value of the chicken genome for comparative sequence analysis. An Action Plan was developed by workshop participants, chaired by Dave Burt (Roslin Institute, Dave.Burt@bbsrc.ac.uk) and Olivier Pourquié (Stowers Institute, OLP@Stowers-Institute.org) that includes, among other things, a plan to organize a second chicken genome workshop in summer of 2004, likely to be held at the Stowers Institute in Kansas City. Thanks to Dave Burt for assembling the report on which the above summary is based. Dave and Olivier have also prepared a summary of the workshop that has been submitted to Science. Contact one of them, if interested in further details.

Growing interest in the chicken sequence: Reporting from the Human Genome Org. (HUGO) Meeting in Cancun, Mexico, Helen Pearson of Nature's Science Update News describes interest in future applications of the chicken sequence (http://www.nature.com/nsu/030428/030428-5.html).

PAG-XII will be held January 10-14, 2004 at the usual location, the Town and Country Hotel, San Diego, CA. See www.intl-pag.org/. If you have speaker suggestions or other comments, please contact one of the organizing committee representatives (Abel Ponce de Leon, apl@umn.edu; Cathy Ernst, ernstc@msu.edu; Bhanu Chowdhary, bchowdhary@cvm.tamu.edu; Noelle Cockett, fanoelle@cc.usu.edu; or Martien Groenen, martien.groenen@alg.vf.wau.nl). The new NC-1008 Multistate Research project committee that replaces the former NC-168 (see below) will meet concurrently, with tentative plans to begin at noon on Saturday, January 10. Assuming it's approved, the National Animal Genome Research Program, NRSP-8, will also meet concurrently with PAG-XII.

The Multistate Research Project, Advanced Technologies for the Genetic Improvement of Poultry, formerly NC-168, has been renewed, but with the new number, NC-1008. Thanks to chief renewal author, Marlene Emara; current chairperson, Bill Muir; and Administrative Advisor, Gretel Dentine for their work on the renewal, along with all the objective authors and other members who participated. The NRSP-8, National Animal Genome Research Program project renewal is also moving through the prescribed channels. Response from the NC region has been supportive, and it's hoped that final approval will come in September at the Station Directors' meeting. Speaking of NRSP-8, the 2002 Poultry Coordinator's annual summary is now available on our website at http://poultry.mph.msu.edu/about/Coorpt02.htm.

In other chicken EST news, The Institute for Genome Research (TIGR) has added chicken to those species for which it maintains a Gene Index. The TIGR Gallus gallus Gene Index (GgGI) is at http://www.tigr.org/tdb/tgi/gggi/ . The latest release (5.0; Jan. 5, 2003) generates 35,790 "tentative consensus" genes (EST clusters), 684 "mature transcripts (ETs)", and 71,395 singleton ESTs. The database can be searched for genes or sequences of interest.

Poultry Science Association Annual Meeting, July 6-9, 2003, Madison, Wisconsin. See www.poultryscience.org/psa03 for information.

13^th North American Colloquium on Animal Cytogenetics and Gene Mapping, July 13-17, 2003, Louisville Zoo, Louisville, KY. See http://www.uky.edu/Ag/VetScience/NACACGM/index1.html.

Transgenic Animal Research Conference IV, August 10-14, 2003, Granlibakken Resort, Lake Tahoe, California. Register at http://conferences.ucdavis.edu/transgenic

3^rd European Poultry Genetics Symposium, September 17-19, 2003, Wageningen, The Netherlands. See www.id.wageningen-ur.nl/epgs for more information.

15^th Int'l. Genome Sequencing and Analysis Conference, Sept. 21-24, 2003, Savannah, GA. See www.tigr.org/gsac for further information.

Plant, Animal and Microbial Genome XII, joint with NC-168 and NAGRP annual meetings, Jan. 10-14, 2004, Town & Country Convention Center, San Diego, CA. See www.intl-pag.org/.

XXII World Poultry Conference, June 8-12, 2004, Istanbul Turkey. Email WPSA2004@WPSA2004.org. For scientific matters contact Dr. Servet Yalcin, Yalcin@ziraat.ege.edu.tr

ISAG 2004, 29^th International Conference on Animal Genetics, Sept. 11-16, 2004, Surugadai Campus, Meiji University, Tokyo, JAPAN. See http://www2.kobe-u.ac.jp/~isag2004/

Microsatellite primer kits:

Microsatellite primer kits: Information on chicken microsatellite primer pairs can be found at http://poultry.mph.msu.edu/resources/microkits.htm. A version of a framework primer kit (with 147 well-spaced microsatellite marker primer pairs) called the "Comprehensive Mapping Kit #7" is available (thanks in part to a generous donation from Hy-Line International). Our Population Tester Kit (9 highly polymorphic microsatellite markers for strain identification, gene flow studies or testing in other birds) is nearly gone, but we'll soon be replacing this kit. Only this kit plus the new Comprehensive Mapping Kit #7 described above are still available. If interested, contact: (dodgson@.msu.edu) or (hcheng@.msu.edu), describing your desired use of primers.

The chicken BAC library constructed at Texas A&M by Hongbin Zhang and colleagues, using (a female of) the UCD001 Jungle Fowl line as its DNA source, consists of over 115,000 BACs (~39,400 each in three sublibraries with BamHI, EcoRI and HindIII partial digest inserts). Filter sets with 36,864 BACs from the BamHI and HindIII sub-libraries are available at present, email dodgson@msu.edu. A requirement for receiving a free filter set is that the user agree to provide the name of the probe used and clone locations (for the list described below), 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, individual clones can be obtained for a fee from GENEfinder. Contact Felipe Santos at contact@bac-center.tamu.edu to purchase BACs.

Through efforts in my lab and those of others who've received filter sets, over 2000 BAC clones corresponding to nearly 570 different genes and markers have been identified. These are listed at http://poultry.mph.msu.edu/resources/resources.htm#bacdata. We'll be adding CHORI-261 BAC assignments (see below) to this list shortly.

For those wishing to use PCR rather than filter hybridization to screen for your gene(s) of interest, Research Genetics has prepared PCR-ready, superplate, column, and row DNA pools of 30,000 BamHI BACs. This portion of the BAC library can be screened by a 3-dimensional strategy that requires 240 PCR reactions. We will supply limited numbers of screening arrays of aliquots of these pools on request to NRSP-8 member scientists. Alternatively, it may be possible to include your gene/probe of interest if you send us your PCR primers. If interested, please contact Hans Cheng (hcheng@.msu.edu). (Note, some problems with reliability of these pools have been observed.) A more detailed description of the pools is on our website at (http://poultry.mph.msu.edu/resources/resources.htm).

As reported previously, Pieter de Jong (Children's Hospital of Oakland Research Institute) has completed a chicken BAC library with ~195 kb inserts (CHORI-261), using the same UCD001 source DNA. CHORI-261 has ~73,700 BACs for ~12x haploid genome coverage. Pieter has also generated a turkey BAC library (CHORI-260) using DNA from an inbred Nicholas Turkey Breeding Farms bird. If interested in either library and/or filter arrays, see www.chori.org/bacpac/ and access the "Detailed List of Libraries" and/or "Screening Resources". Coordination funds have been used to purchase a limited number of CHORI-261 chicken BAC filter arrays and a set can be provided on request while supplies last (see contact info and requirements at the top of this page). WUGSC is fingerprinting and end-sequencing this library, as well, so we should have contig information for this library by this fall. Pieter's group has also constructed a fosmid library using the same source DNA. If interested, contact BACPAC at www.chori.org/bacpac/. If you want to isolate single genes or small linked gene families, it may be easier to use a fosmid library (inserts ~45 kb) than to have to dissect your gene from a large BAC.

The chicken BAC contig map web interface developed by Zhang and his group at Texas A&M is on-line. Fingerprint data from nearly 60,000 BACS (~20,000 from each of the three sublibraries) are included. The web site can be found at http://hbz.tamu.edu - click on "Chicken" under "Integrated Physical Maps" and scroll down to "Chicken Clone -> FPC Hitting Tool" and click. Enter the ID number of any BAC and search for overlapping BACs, based on the fingerprints. Texas A&M chicken contig building can also be monitored at this web site. As of 5/05/03, the analysis of 58,079 BAC fingerprints plus BAC assignments for 367 gene/markers generates 2331 contigs, most of which include 3 to 50 BACs each (206 contigs contain 51-100 BACs and 30 contigs contain over 100 BACs). The total size of this physical map is 1,510 Mb (1.3x), indicating that there are many additional overlaps to be discovered and contigs to be merged. Further marker-BAC assignments and BAC end sequence screens will reduce the total contig number and enlarge contig sizes.

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, or the UK Human Genome Mapping Project Resource Center at http://www.hgmp.mrc.ac.uk, who sell filter sets of this library.

East Lansing, MI 48824 email: hcheng@msu.edu

email: dodgson@msu.edu