Progress 01/01/08 to 06/30/11

Outputs
OUTPUTS: A robust bacterial artificial chromosome (BAC)-based physical map is essential for many aspects of genomics research, including an understanding of chromosome evolution, high-resolution genome mapping, marker-assisted breeding, positional cloning of genes, and quantitative trait analysis. To facilitate turkey genetics research and better understand avian genome evolution, a BAC-based integrated physical, genetic, and comparative map was developed for this important agricultural species. The turkey genome physical map was constructed based on 74,013 BAC fingerprints (11.9x coverage) from two independent libraries, one of which we constructed, and it was integrated with the turkey genetic map and chicken genome sequence using over 41,400 BAC assignments identified by 3,499 overgo hybridization probes along with over 43,000 BAC end sequence alignments. The physical-comparative map consists of 74 BAC contigs, with an average contig size of 13.6 Mb. All but four of the turkey chromosomes were spanned on this map by three or fewer contigs, with 14 chromosomes spanned by a single contig and nine chromosomes spanned by two contigs. This map predicts 20 to 27 major rearrangements distinguishing turkey and chicken chromosomes, despite up to 40 million years of separate evolution between the two species. Databases of turkey BACs assigned to turkey markers and genes and Genbank assignment numbers for the turkey BES are available online as is our turkey-chicken comparative map that lists the orthologous location in the chicken genome for over 44,400 turkey BACs (currently over 58,000 assignments by either BES or overgo, many of which overlap). PARTICIPANTS: Participants: Jerry Dodgson, project director. Hongbin Zhang, co-P.I. Mary Delany. William Payne, research technician, Y. Zhang, postdoctoral associate, X. Zhang, postdoctoral associate, M.K. Lee, postdoctoral associate, T.H. O'Hare, graduate student, J.J. Dong, technician, C.F. Scheuring, technician, M. Zhang, technician, J.J. Huang, technician, A. Jiang, technician. Partner Organizations: Texas A&M University. U. of California, Davis. TARGET AUDIENCES: Animal scientists. Poultry breeders. Poultry industry representatives. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
The BAC-based turkey-chicken comparative map provides novel insights into the evolution of avian genomes, a framework for assembly of turkey whole genome shotgun sequencing data, and tools for enhanced genetic improvement of these important agricultural and model species. These data elucidate the chromosomal evolutionary pattern within the Phasianidae that led to the modern turkey and chicken karyotypes. Our map predicts 20 to 27 major rearrangements distinguishing turkey and chicken chromosomes, despite up to 40 million years of separate evolution between the two species. The predominant rearrangement mode involves intra-chromosomal inversions, and there is a clear bias for these to result in centromere locations at or near telomeres in turkey chromosomes, in comparison to interstitial centromeres in the orthologous chicken chromosomes. Our BAC-contig comparative map provided the platform with which contigs and scaffolds have been assembled in the recently completed first draft sequence of the turkey genome.

Publications

• Dodgson, J.B., M.E. Delany and H.H. Cheng. 2011. Poultry genome sequences: progress and outstanding challenges. Cytogenetics and Genome Research 134:19-26.
• Romanov, M.N., J.B. Dodgson, R.A. Gonser, and E.M. Tuttle. 2011. Comparative BAC-based mapping in the white-throated sparrow, a novel behavioral genomics model, using interspecies overgo hybridization, BMC Research Notes 4:211.
• Reed K.M., M.M. Bauer, M.S. Monson, B. Benoit, L.D. Chaves, T.H. O'Hare, and M.E. Delany. 2011. Defining the turkey MHC: identification of expressed class I and class IIB-like genes independent of the MHC-B. Immunogenetics, in press.
• 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, submitted for publication.

Progress 01/01/10 to 12/31/10

Outputs
OUTPUTS: We have generated a BAC contig-based physical and comparative map of the turkey genome. The following objectives have been met. 1. We generated a second turkey BAC library containing about 40,000 BACs. 2. We fingerprinted 38,400 BACs from this new library for a total of over 85,000 BAC fingerprints. 3. We sequenced an additional 21,500 BES for a total of over 43,000. 4. We used overgo probe hybridization to verify and merge contigs and eliminate gaps. Over 40,000 overgo BAC hybridization assignments have been made and further gap-filling is nearly complete. 5. We performed cytogenetic analyses to integrate the map with turkey chromosomes and localize gaps and inversions/translocations between chicken and turkey genomes. Our map has identified about 40 rearrangements between the chicken and turkey genomes, a remarkably low number given the evolutionary distance between these two species, and many of these have now been confirmed by FISH analysis. Databases of turkey BACs assigned to turkey markers and genes and Genbank assignment numbers for the turkey BES are available online as is our turkey-chicken comparative map that lists the orthologous location in the chicken genome for over 44,400 turkey BACs (currently over 58,000 assignments by either BES or overgo, many of which overlap). Our BAC-contig comparative map provided the platform with which contigs and scaffolds have been assembled in the recently completed first draft sequence of the turkey genome. The turkey autosomal genome is currently covered by 64 contigs. The Z chromosome alone is covered by 24 contigs due to its haploid coverage in BAC libraries. The W chromosome has been ignored due to its very poor assembly in the chicken genome sequence. Most of the gaps between contigs are due to regions of low BAC density (particularly on microchromosomes MGA18 and 24-30). However, some gaps are due to repetitive regions and likely sites of CNV. The average size of the comparative map BAC contigs on the autosomes is over 14.3 Mb with the N50 average autosomal contig size being about 35 Mb. Fourteen chromosomes (MGA2, 3, 9, 11, 12, 13, 16, 17, 18, 19, 20, 21, 23 and 26) are spanned by only a single BAC contig and another nine are spanned by two contigs (MGA5, 6, 8, 10, 14, 15, 22, 28 and 30). Final gap filling on GGAZ and summary publication will be completed shortly. PARTICIPANTS: Jerry Dodgson, project director. Hongbin Zhang, co-P.I. Mary Delany. William Payne, research technician, Turkey Genome Sequencing Consortium. Partner Organizations: Texas A&M University. U. of California, Davis, Virginia Tech, U. of Minnesota, USDA-ARS-BARC. TARGET AUDIENCES: Animal scientists. Poultry breeders. Poultry industry representatives. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
We contributed to the greatly expanded quality of the turkey genome map and have essentially completed the BAC contig-based physical and comparative map. Our BAC-contig comparative map provided the platform with which contigs and scaffolds have been assembled in the recently published first draft sequence of the turkey genome. Interesting evolutionary trends have been detected that distinguish the turkey and chicken genomes.

Publications

• Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Ann Blomberg L, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Frederickson KM, Flicek P, Florea L, Folkerts O, Groenen MA, Harkins TT, Herrero J, Hoffmann S, Megens HJ, Jiang A, de Jong P, Kaiser P, Kim H, Kim KW, Kim S, Langenberger D, Lee MK, Lee T, Mane S, Marcais G, Marz M, McElroy AP, Modise T, Nefedov M, Notredame C, Paton IR, Payne WS, Pertea G, Prickett D, Puiu D, Qioa D, Raineri E, Ruffier M, Salzberg SL, Schatz MC, Scheuring C, Schmidt CJ, Schroeder S, Searle SM, Smith EJ, Smith J, Sonstegard TS, Stadler PF, Tafer H, Tu ZJ, Van Tassell CP, Vilella AJ, Williams KP, Yorke JA, Zhang L, Zhang HB, Zhang X, Zhang Y, Reed KM.. 2010. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biology 8(9):e1000475.
• Dodgson, J.B. 2010. Comparative genome sequencing: low price-high value. Proceedings, Plant and Animal Genome XVIII. (abstract).

Progress 01/01/09 to 12/31/09

Outputs
OUTPUTS: We have generated a BAC contig-based physical and comparative map of the turkey genome. The following objectives have been met. 1. We generated a second turkey BAC library containing about 40,000 BACs. 2. We fingerprinted 38,400 BACs from this new library for a total of over 85,000 BAC fingerprints. 3. We sequenced an additional 21,500 BES for a total of over 43,000. 4. We used overgo probe hybridization to verify and merge contigs and eliminate gaps. Nearly 36,000 overgo BAC hybridization assignments have been made and further gap-filling is underway. 5. We performed cytogenetic analyses to integrate the map with turkey chromosomes and localize gaps and inversions/translocations between chicken and turkey genomes. Turkey and chicken mitotic and pachytene FISH techniques have been optimized. Initial focus is on validating turkey-chicken rearrangements predicted by our comparative map. Our map has identified about 30 rearrangements between the chicken and turkey genomes, a remarkably low number given the evolutionary distance between these two species, and many of these have now been confirmed by FISH analysis. Databases of turkey BACs assigned to turkey markers and genes and Genbank assignment numbers for the turkey BES are available online as is our turkey-chicken comparative map that lists the orthologous location in the chicken genome for over 42,000 turkey BACs (currently approximately 53,000 assignments by either BES or overgo, many of which overlap). Our BAC-contig comparative map provided the platform with which contigs and scaffolds have been assembled in the recently completed first draft sequence of the turkey genome. The turkey autosomal genome is currently covered by 150 contigs. The Z chromosome alone is covered by 131 contigs due to its haploid coverage in BAC libraries and the fact that we have not yet initiated directed gap-filling efforts towards the Z. The W chromosome has been ignored due to its very poor assembly in the chicken genome sequence. Most of the gaps between contigs are due to regions of low BAC density (particularly on microchromosomes MGA18 and 24-30). However, some gaps are due to repetitive regions and likely sites of copy number variations. The average size of the comparative map BAC contigs on the autosomes is over 6.1 Mb with the N50 average autosomal contig size being about 32 Mb. Eight chromosomes (MGA6, 12, 13, 16, 17, 19, 21 and 26) are spanned by only a single BAC contig and another four are spanned by two contigs (MGA9, 11, 15, and 20). Efforts are continuing to close gaps in our map, in particular on the Z chromosome. PARTICIPANTS: Jerry Dodgson, project director. Hongbin Zhang, co-P.I. Mary Delany. William Payne, research technician, Turkey Genome Sequencing Consortium. Partner Organizations: Texas A&M University. U. of California, Davis, Virginia Tech, U. of Minnesota, USDA-ARS-BARC. TARGET AUDIENCES: Animal scientists. Poultry breeders. Poultry industry representatives. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
We contributed to the greatly expanded quality of the turkey genome map and have essentially completed the BAC contig-based physical and comparative map. Our BAC-contig comparative map provided the platform with which contigs and scaffolds have been assembled in the recently completed first draft sequence of the turkey genome.

Publications

• Dodgson, J.B. 2010. Comparative genome sequencing: low price-high value Proceedings, Plant and Animal Genome XVIII. (abstract).

Progress 01/01/08 to 12/31/08

Outputs
OUTPUTS: The following objectives have been met. 1. We generated a second turkey BAC library containing about 40,000 BACs. 2. We fingerprinted 38,400 BACs from this new library for a total of over 85,000 BAC fingerprints. 3. We sequenced an additional 21,500 BES for a total of over 43,000. 4. We used overgo probe hybridization to verify and merge contigs and eliminate gaps. Over 23,000 overgo hybridization assignments have been made and further gap-filling is underway. 5. We performed cytogenetic analyses to integrate the map with turkey chromosomes and localize gaps and inversions/translocations between chicken and turkey genomes. Turkey and chicken mitotic and pachytene FISH techniques have been optimized. Initial focus is on validating turkey-chicken rearrangements predicted by BES comparative maps. We recently identified a 0.6 Mb inversion between GGA14/MGA16 suggesting that we can FISH map inversions of 0.5 Mb or less. 6. Turkey SNP-BES marker generation is being tested in chicken with funds from another source. However, this objective may be replaced by high throughput sequencing the turkey genome. 7. We assembled the data into an integrated, on-line turkey map resource. Databases of turkey BACs assigned to turkey markers and genes and Genbank assignment numbers for the CHORI-260 Turkey BES are available at http://poultry.mph.msu.edu/resources/Resources.htm. New BES information and overgo hybridization results will be added to these tables shortly. More important, our initial turkey-chicken comparative map is available at this site in the form of a multi-spreadsheet database that lists the orthologous location in the chicken genome (Build 2) for over 20,000 turkey BACs (currently over 27,800 assignments by either BES or overgo, many of which overlap). Current efforts are focused on integrating the new BAC library fingerprint and BES data into our first generation physical/comparative map, manually annotating our map to resolve uncertain assignments and identify gaps, filling those gaps by directed overgo hybridization approaches and resolving turkey-chicken rearrangements by FISH. PARTICIPANTS: Participants: Jerry Dodgson, project director. Hongbin Zhang, co-P.I. Mary Delany, co-P.I. William Payne, research technician. Laura Daniels, research technician. M.K. Lee, postdoctoral assistant. Xiaojun Zhang, postdoctoral assistant. Yang Zhang, postdoctoral assistant. Hyun Jung Park, postdoctoral assistant. J. Jianmin Dong, postdoctoral assistant. Chantel Scheuring, research technician. Partner Organizations: Texas A&M University. U. of California, Davis. Training: five postdoctoral associates. TARGET AUDIENCES: Animal scientists. Poultry breeders. Poultry industry representatives. Vaccine production industry. Veterinarians and poultry health workers. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
We contributed to the greatly expanded quality of the turkey genome map and expect to have a physical map at a sequence-ready state soon. The rapid development of high throughput sequencing and our BES comparative mapping results demonstrate that it will be possible to sequence the turkey genome cost effectively and assemble that sequence on the platform of our physical/comparative map. We are working with colleagues who have obtained pilot funding to begin this project and are hoping to have 2X coverage within the next year.

Publications

• Lee, M.-K., B. Payne, J. Dong, H.J. Park, X. Zhang, J. Dodgson, and H.-B. Zhang. 2008. First-generation physical and comparative map of the turkey genome constructed by BAC fingerprint analysis with capillary electrophoresis. Proceedings, Plant and Animal Genome XVI. (abstract).
• Sazanova, A.L., M.N. Romanov, I.Y. Blagoveshenski, K.A. Fomichev, V.A. Stekol'nikova, M. Nefedov, W.S. Modi, O.A. Ryder, J.B. Dodgson, and A.A. Sazanov. 2008. Cytogenetic localization of avian Z- and W-linked genes using large-insert BAC clones. Proceedings, Plant and Animal Genome XVI. (abstract).
• Lee, M.-K., X. Zhang, Y. Zhang, B. Payne, H.J. Park, J.J. Dong, C. Scheuring, M.E. Delany, J. Dodgson, and H.-B. Zhang. 2009. Toward a robust BAC-based physical and comparative map of the turkey genome. Proceedings, Plant and Animal Genome XVII. (abstract).
• Dodgson, J.B. 2009. Post-genomic chicken nuggets: an acquired taste. Proceedings, Plant and Animal Genome XVII. (abstract).