Other workshops and posters. Several other workshops were of special interest. At the Domestic Animal Genome Sequencing Workshop, Mandeep Sekhon (WUGSC) indicated that they've completed fingerprinting and data entry for nearly 72,000 BAC clones. At the moment, these still comprise over 6,700 contigs (see also The BAC Page, below). Nearly 100,000 BAC end sequences have been obtained and complete BAC end sequencing is expected to be finished this spring. She also described their sequencing plans for April-August 2003 (paired ends from plasmids and fosmids) that should provide 6-8X whole genome shotgun coverage of the chicken genome. Support is still being sought for the "finishing" phase of the chicken genome sequence. Martien Groenen (Wageningen) described their use of BAC clones for physical mapping, sequence analysis, and FISH and RH mapping (the latter in collaboration with INRA). They have substantial BAC contig and sequence data for chicken chromosomes 2, 4, 5, 8, 10, 13, 15, 24 and 28. Tuesday evening, the Animal Comparative Mapping Workshop focused on bioinformatics needs. Dave Adelson summarized the results of the recent USDA Stakeholder Electronic Workshop on Animal Bioinformatics, organized by Deb Hamernik of USDA-CSREES. A Summary and Recommendations report based on that workshop and the discussion at PAG-XI will be published shortly. Far too many posters were presented to be summarized here. Abstracts can be searched at http://www.intl-pag.org/11/abstracts/.

Business meetings. The NC-168 business meeting included the report of our administrator, Gretel Dentine, on the prospects for our renewal (for a copy of the renewal proposal and membership info go to www.lgu.umd.edu/login.cfm, enter as a guest, and search for project NC_temp681). Thanks go to Marlene Emara for coordinating the writing and submission of the renewal. Due to the adoption of two year terms, Bill Muir will chair NC-168 for one more year with Doug Foster as secretary. Ron Okimoto will chair NRSP-8 Poultry with Chris Ashwell as secretary again. Cathy Ernst chaired the NRSP-8 business meeting, where Gretel Dentine also described the process and prospects for renewing NRSP-8 and the procedure by which new coordinators would be chosen (all NRSP-8 members were emailed this info). To see the proposal or investigate joining the group, use the same procedure described above for NC-168, except search for project NRSP_temp022. NRSP-8 members enthusiastically expressed their thanks to Cathy Ernst for coordinating this effort. Max Rothschild presented a plaque on behalf of all NRSP-8 members to our recently retired leader, Dick Frahm, thanking him for his 10 years of leadership of the National Animal Genome Research Program and wishing him the best for his future in Blacksburg, VA. We were all pleased that Dick could attend PAG and receive the plaque and our congratulations in person. Deb Hamernik, NPL at USDA-CSREES for Animal Physiology, reported that potential replacements for Dick Frahm had been interviewed and a new Animal Genetics leader would soon be chosen. Abel Ponce de Leon will succeed Cathy as NRSP-8 chairperson, and Bhanu Chowdhary is the secretary/chair-elect.

Next Year! PAG-XII will be held January 10-14, 2004 at the same location. Plenary speakers will begin to be invited soon. 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). See you next year!

As mentioned in our last issue, the proposal to close the East Lansing USDA-ARS Avian Disease and Oncology Lab (ADOL) this year failed in Congress. As was also described, Janet Fulton of Hy-Line International wrote USDA Secretary Ann Veneman requesting an ADOL stakeholders' meeting be held. Even though the USDA declined to sponsor this meeting, the United Egg Producers did so on Dec. 16-17, 2002. Barbara Glenn of FASS acted as conference convener, and she and Janet have written an executive summary (contact Janet at jfulton@hyline.com if you'd like a copy). Janet also chaired a recent meeting of the ADOL User's Liason Group at which it was determined that additional input on the executive summary will be sought from the National Chicken Council and National Turkey Federation prior to submitting the final version to the USDA. Rumors are circulating that the ADOL closure proposal will resurface in the President's 2004 USDA bill.

Gordon Conference on Quantitative Genetics and Genomics, February 9-14, 2003, Ventura, CA. See http://nitro.biosci.arizona.edu/Gordon2003.html

International Symposium on Animal Functional Genomics, May 9-11, 2003, Kellogg Center, Michigan State University, East Lansing, MI. Register at http://www.isafg.msu.edu

Poultry Science Association Annual Meeting, July 6-9, 2003, Madison, Wisconsin. See www.poultryscience.org/psa03 for information. Abstract deadline, February 12, 2003.

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.

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/.

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/

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 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, 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, one or more BAC clones corresponding to nearly 400 different genes and markers have been identified (these are listed at http://poultry.mph.msu.edu/resources/resources.htm#bacdata). We're expanding this list as fast as possible. If you have a marker you wish us to include, please email me asap.

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, we hope to set up routine screening of the pools here at ADOL, and 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). A more detailed description of the pools is on our website at (http://poultry.mph.msu.edu/resources/resources.htm).

As reported last issue, Pieter de Jong (Children's Hospital of Oakland Research Institute) has completed a new chicken BAC library with ~195 kb inserts (CHORI-261), using the same UCD001 source DNA described above. CHORI-261 has ~73,700 BACs for ~12x haploid genome coverage. Pieter has also generating 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). As noted in the PAG-XI report, the WUGSC is fingerprinting and end-sequencing this library, as well, so we should have contig information for this library in the not too distant future. Pieter reported at PAG that his 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 (inserts ~45 kb) than 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. (This is the only active search tool, so far; others will be activated later.) 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 12/02/02, the analysis of 57,269 BAC fingerprints plus BAC assignments for 310 gene/markers generates 2496 contigs, most of which include 3 to 25 BACs each (150 contigs contain 51-100 BACs and 24 contigs contain over 100 BACs). We hope that 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.

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). Due to our limited budget (and the cost of the Marshfield microsatellite patent), we now can supply only our Population Tester Kit (9 highly polymorphic microsatellite markers for strain identification, gene flow studies or testing in other birds [not usually recommended]) or the new Comprehensive Mapping Kit #7. If interested, contact: (dodgson@.msu.edu) or (hcheng@.msu.edu), describing your desired use of primers.

Reminder: The INRA Chicken Radiation Hybrid Panel for RH mapping the chicken genome is now available. The Chick RH6 panel was made by Mireille Morisson, Alain Vignal, and their colleagues (see Genet. Sel. Evol. 34:521-533, 2002). The INRA team is beginning to generate a framework RH map for chicken. The INRA panel is composed of 90 hybrids, distributed in a microtiter plate (5 micrograms of DNA each) with appropriate controls. For those planning to map 20 or more markers, a microplate can be shipped to you. For fewer markers, it may be possible to send primers to INRA, so that they can add them to their pipeline. INRA will coordinate data analysis for all markers. Contact Mireille Morisson (mmorisso@toulouse.inra.fr) or Alain Vignal (vignal@toulouse.inra.fr) if interested.

email: dodgson@msu.edu

email: hcheng@msu.edu