Livestock Genome Sequencing Initiative

PI: L.B. Schook, J.E. Beever, H.A. Lewin
Total Award Amount: $3,644,280
Grant: AG 2003-34480-13172
Award Amount: $417,923
Start Date: June 1, 2003
End Date: May 31, 2004
The ordered physical maps of BAC clones will provide a necessary resource for the targeted sequencing of chromosomal regions containing genes of economic importance and the eventual complete sequencing of the cattle and pig genomes. Understanding the molecular basis for the major phenotypic differences among closely related mammals is a high priority for agricultural research. A major challenge is to identify those genes and the accompanying genetic mechanisms that are responsible for the economically important traits of food animal species. By using the complete DNA sequences of the human and mouse genomes and by applying comparative genomics technologies, U.S. animal geneticists will be able to identify genes that have identical function in different mammals, including those that have diverged significantly from an evolutionary standpoint. In addition, species-specific genes that might contribute to the unique features of the mammalian orders can also be identified, thus providing a unique resource for identifying genes that are responsible for specific adaptations (e.g., the ruminant digestive system). Discovering all the genes and their functions in livestock will thus provide the raw materials needed to perform highly selective breeding, to make genetic modifications through transgenesis, or to develop novel "farmaceuticals" for the animal agriculture sector.
Grant: AG 2004-34480-14417
Award Amount: $626,827
Start Date: June 1, 2004
End Date: May 31, 2005
Grant: AG 2005-34480-15939
Award Amount: $760,236
Start Date: July 1, 2005
End Date: June 30, 2006
Grant: AG 2006-34480-17150
Award Amount: $753,240
Start Date: July 15, 2006
End Date: July 14, 2009
Rapid population growth, urbanization, and growing affluence in the most populous parts of the world are resulting in expanding world markets for livestock products. Enormous future growth is very likely, as developing countries improve both political and economic systems. To compete effectively for those markets, Illinois and the nation must be among the first to implement new livestock technology derived from genomics.
Grant: AG 2008-34480-19328
Award Amount: $560,244
Start Date: August 1, 2008
End Date: July 31, 2010
Grant: AG 2009-34480-19875
Award Amount: $525,810
Start Date: August 1, 2009
End Date: July 31, 2012

In the new millennium, the demands of a rapidly growing world population will continue to put pressure on the U.S. animal agriculture industry. The industry must develop new products that create value within the agricultural system, and as a result, increase the profitability of agriculture and revitalize rural America. These challenges come at a time when many current agricultural technologies are being questioned, when key productivity enhancers (such as medicated feeds) are in jeopardy, and when waste management constrains the formation of economically viable units. At the same time, the safety of the food supply is in question because of the incidence of BSE (Mad Cow Disease) and foot and mouth disease in Europe as well as frequent outbreaks of food-borne pathogens here in the U.S. The Livestock Genome Sequencing Initiative directly addresses these major challenges. Results of this project to date have provided producers and the breeding industry with genetic tests to reduce the incidence of genetic and infectious diseases, to trace the origin of meat and dairy products, and to increase productivity of swine and cattle. These genomically-based tools thus provide for the sustainable and secure production of meat and dairy products for American consumers and world markets. A major challenge is to identify additional genes and the accompanying genetic mechanisms that are responsible for the economically-important traits of food animal species. Only a few of the "low hanging fruit" have been harvested for direct application by the livestock industry. By using the complete DNA sequences of the human, mouse, cattle, and pig genomes, and by applying comparative genomics and other advanced technologies developed at Illinois, we will be able to identify many more genes affecting economically-important traits, probably faster than any other group in the world. To date, scientists at Illinois have been directly involved in the discovery and characterization of a significant share of the genes for production and disease traits. With the new tools and technologies for rapid, high throughput genotyping and sequencing, scientists at Illinois are uniquely positioned to move their discovery pipeline to the next level, and to deliver new technologies to producers and the private sector. Thus, the timing is right to continue down our productive path and to set the stage for the next wave of gene discovery.


Objective 1: Targeted resequencing of chromosomal regions containing genes of economic importance to the livestock industry. This work will include the resequencing of the genomic regions influencing genetic disease traits in cattle and the resequencing of porcine Toll-like Receptors (TLRs). Two bovine chromosomal regions have been selected for targeted resequencing. The first bovine selected region is a 7.5 Mbp region harboring a locus causing neuropathic hydrocephalus. The second chromosomal region is a 4.3 Mbp segment harboring a locus causing Fawn Calf Syndrome in Angus cattle. In the pig, The aim is to define non-synonymous SNP diversity of porcine TLR genes. There is compelling evidence that the ability of certain individuals to respond properly to TLR ligands may be impaired by SNPs that result in an altered susceptibility to, or the course of, infectious diseases.

Objective 2: Whole genome resequencing of individuals for the direct identification of the genes responsible for livestock production and health traits. A strategy that combines whole-genome sequencing, traditional QTL mapping, and genome-wide association studies (GWAS) has been developed for the identification of DNA polymorphisms underlying quantitative traits in dairy cattle.

Objective 3: Elucidation of host gene networks and physiological systems affected by the dietary energy intake and by different feedstocks. The effect of nutritional management on metabolic and immune function in dairy cattle will be studied. In addition This research will measure microbial diversity, composition and metabolic potential through comparative metagenomic sequencing and culture-independent direct DNA sequencing techniques to define the pig microbiome.


Targeted candidate genes will be sequenced following standard protocols after the elements in each candidate gene, the exon-intron boundaries and their respective exon and intron sizes have been mapped. NimbleGen Sequence Capture technology which allows resequencing up to 5 Mb of selected non-repetitive genomic regions from any individual animal locus will be used in some areas. The resequencing of bovine individuals will use the single-stranded template DNA (sstDNA) library from DBDR bull Walkway Chief Mark ("Mark") that was used previously to generate ~11X coverage will be used to generate an additional ~1X coverage of the genome using Roche/454 Titanium technology. The purpose for the additional 1x coverage is to ensure accurate calling of all alleles on both Mark haplotypes. Reads are mapped to the reference DNA and assembled using gsMAPPER software provided by the vendor. The 12x Mark sequence assembly and combined 7x Chief +12x Mark assembly will be performed on a Dell Large Memory Compute Cluster maintained by the Institute for Genomic Biology at the University of Illinois. All sequences will be made publicly available when the project is completed. The effects of diet on tissue specific gene expression as well as metabolic changes will be done by standard microarray techniques using the annotated bovine oligonucleotide microarray containing >10,000 unique elements. Porcine Microbiome Analysis will use a Roche Titanium Genome Sequencer to produce approximately 1.25 million sequence reads per sample. Specific bar codes and both bacterial and archael primers will help to ensure detection of both dominant (modal microbiome) and poorly represented taxa (rare microbiome). Multiple sequence alignments are used as input to create the maximum likelihood (ML) trees and distance matrices. We will obtain a comprehensive assessment of the breadth and richness of microbial diversity.


The results of resequencing the two dairy bull genomes demonstrate that haplotype reconstruction of an ancestral proband by whole-genome resequencing in combination with high-density SNP genotyping of descendants can be used for rapid, genome-wide identification of the ancestor's alleles that have been subjected to artificial selection. Diagnostics for eight of the mutations causing abnormalities in cattle and sheep have been released for public use. To date, these diagnostics have been used in more than 200,000 individuals world wide. For many of these mutations, the allele frequency within specific populations has decreased significantly. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.


Amaral, A.J., L. Ferretti, H.-J. Megens, R.P.M.A. Crooijmans, H. Nie, S.E. Ramos-Onsins, M. Perez-enciso, L.B. Schook, and M.A.M. Groenen. (2011). Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA. PLoS ONE, 6(4), e14782.

Archibald, A.L., L. Bolund, C. Churcher, M. Fredholm, M.A.M. Gorenen, B. Harlizius, K.T. Lee, D. Milan, J. Rogers, M.F. Rothschild, H. Uenishi, J. Wang, L.B. Schook, and the Swine Genome Sequencing Consortium. (2010). Pig genome sequence: analysis and publication strategy. BMC Genomics, 11, 438.

Beever, J.E. and B.M. Marron. (2008). A DNA-based diagnostic test for the identification of individuals having the mutation causing the arthrogryposis multiplex (AM) genetic defect in cattle. U.S. Patent Application No. 12/642,028. Washington, DC: U.S. Patent and Trademark Office (Filed 12/18/09).

Beever, J.E. and B.M. Marron. (2006). Screening for the genetic defect causing tibial hemimelia in bovines. U.S. Patent Application No. 11/549,888. Washington, DC: U.S. Patent and Trademark Office (Filed 10/16/06).

Bosse, M., H.J. Megens, O. Madsen, Y. Paudel, L.A.F. Frantz, L.B. Schook, R.P.M.A. Crooijmans, and M.A.M. Groenen. (2012). Regions of homozygosity in the porcine genome: Consequence of demography and the recombination landscape. PLoS Genetics, 8(11), e100310.

The Bovine Genome Sequencing and Analysis Consortium. (2009). The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science, 324, 522-528 (Cover).

Burgos-Paz, W., C.A. Souza, H.J. Megens, Y. Ramayo-Caldas, M. Melo, E. Caa, H.W. Soto, R. Martinez, L.A. Alvarez, L. Aguirre, V. Iniguez, M.A. Revidatti, O.R. Martinez-Lopez, S. Llambi, A. Esteve-Codina, M.C. Rodriguez, R.P.M.A. Crooijmans, S.R. Paiv, L.B. Schook, M.A.M. Groenen, and M. Perez-Enciso. (2012). Porcine colonization of the Americas: A 60k SNP story. Heredity, 110(4), 321-330.

Chen, K., T. Baxter, W.M. Muir, M.A. Groenen, and L.B. Schook. (2007). Genetic resources, genome mapping and evolutionary genomics of the pig (Sus scrofa). Int. J. Biol. Sci. 3, 153-165.

Chen, K., R. Hawken, G.H. Flickinger, S.L. Rodriguez-Zas, L.A. Rund, M.B. Wheeler, M. Abrahamsen, M.S. Rutherford, J.E. Beever, and L.B. Schook. (2012). Association of the porcine transforming growth factor beta type I receptor (TGFBR1) gene with growth and carcass traits. Anim. Biotechnol. 23(1), 43-63.

Chen, K., L.A. Rund, J.E. Beever, and L.B. Schook. (2006). Isolation and molecular characterization of the porcine transforming growth factor beta type I receptor (TGFBR1) gene. Gene, 384, 62-72.

Cohen, M., M. Reichenstein, A. Everts-van der Wind, J.H. Lee, M. Shani, H.A. Lewin, J.I. Weller, M. Ron, and E. Seroussi. (2004). Cloning and characterization of FAM13A1: Evidence for population-wide linkage disequilibrium with a milk protein QTL on BTA6 in Israeli Holsteins. Genomics, 84, 374-383.

Cohen-Zinder, M., R. Donthu, D.M. Larkin, C.G. Kumar, S.L. Rodriguez-Zas, K.E. Andropolis, R. Oliveira, and H.A. Lewin. (2011). Multisite haplotype on cattle chromosome 3 is associated with quantitative trait locus effects on lactation traits. Physiol. Genomics, 43, 1185-1197.

Darfour-Oduro, K.A. and L.B. Schook. (2012). Livestock marker-assisted selection. In Encyclopedia of Biotechnology in Agriculture and Food (pp. 1-3). Boca Raton, FL: CRC Press.

Donthu, R., H.A. Lewin, and D.M. Larkin. (2009). SyntenyTracker: A tool for defining homologous synteny blocks using radiation hybrid maps and whole genome sequence. BMC Research Notes, 2, 148.

Everts-van der Wind, A., S. Kata, M.R. Band, M. Rebeiz, D.M. Larkin, R.E. Everts, C.A. Green, L. Liu, S. Natarajan, T. Goldammer, J.H. Lee, S. McKay, J.E. Womack, and H.A. Lewin. (2004). A 1,463 gene cattle-human comparative map with anchor points defined by human genome sequnce coordinates. Genome Res. 14, 1424-1437.

Everts-van der Wind, A., D.M. Larkin, C.A. Green, J.S. Elliott, C.A. Olmstead, R. Chiu, J.E. Schein, M.A. Marra, J.E Womack, and H.A. Lewin. (2005). A high-resolution whole-genome cattle-human comparative map reveals details of mammalian chromosome evolution. PNAS, 102, 18526-18531.

Ganu, R.S., T.A. Garrow, M. Sodhi, L.A. Rund, and L.B. Schook. (2011). Molecular characterization and analysis of the porcine betaine homocysteine methyltransferase and betaine homocysteine methyltransferase-2 genes. Gene 473:133-138.

Golik, M., M. Cohen-Zinder, J.J. Loor, J.K. Drackley, M.R. Band, H.A. Lewin, J.I. Weller, M. Ron, and E. Seroussi. (2006). Accelerated expansion of group IID like phospholipase A2 gene in Bos taurus. Genomics, 87, 527-533.

Gray, M.A., C.B. Pollock, L.B. Schook, and E.J. Squires. (2010). Characterization of porcine pregnane X receptor, farnesoid X receptor and their splice variants. Exp. Biol. Med. 235, 718-736.

Groenen, M.A.M., A.L. Archibald, H. Uenishi, C.K. Tuggle, Y. Takeuchi, M.F. Rothschild, C. Rogel-Gaillard, C. Park, D. Milan, H. Megens, S. Li, D. Larkin, H. Kim, L.A.F. Frantz, M. Caccamo, H. Ahn, B.L. Aken, A. Anselmo, C. Anthon, L. Auvil, B. Badaoui, C.W. Beattie, C. Bendixen, D. Berman, F. Blecha, J. Blomberg, L. Bolund, M. Bosse, S. Botti, Z. Bujie, M. Bystrom, B. Capitanu, D. Carvalho-Silva, P. Chardon, C. Chen, R. Cheng, S. Choi, W. Chow, R.C. Clark, C. Clee, R.P.M.A. Crooijmans, H.D. Dawson, P. Dehais, F. De Sapio, B. Dibbits, N. Drou, Z. Du, K. Eversole, J. Fadista, S. Fairley, T. Faraut, G.J. Faulkner, K.E. Fowler, M. Fredholm, E. Fritz, J.G.R. Gilbert, E. Giuffra, J. Gorodkin, D.K. Griffin, J.L. Harrow, A. Hayward, K. Howe, Z. Hu, S.J. Humphray, T. Hunt, H.H. Jensen, P. Jern, M. Jones, J. Jurka, H. Kanamori, R. Kapetanovic, J. Kim, J. Kim, K. Kim, T. Kim, G. Larson, K. Lee, K. Lee, R. Leggett, H.A. Lewin, Y. Li, W. Liu, J.E. Loveland, Y. Lu, J.K. Lunney, J. Ma, O. Madsen, K. Mann, L. Matthews, S. McLaren, T. Morozumi, M. Murtaugh, J. Narayan, D. Truong Nguyen, P. Ni, S. Oh, S. Onteru, F. Panitz, E. Park, H. Park, G. Pascal, Y. Paudel, M. Perez-Enciso, R. Ramirez-Gonzalez, J.M. Reecy, S. Rodriguez-Zas, G.A. Rohrer, L. Rund, Y. Sang, K. Schachtschneider, J. Schraiber, J. Schwartz, L. Scobie, C. Scott, S. Searle, B. Servin, B.R. Southey, G. Sperber, P. Stadler, J. Sweedler, H. Tafer, B. Thomsen, R. Wali, J. Wang, J. Wang, S. White, X. Xu, M. Yerle, J. Zhang, G. Zhang, J. Zhang, S. Zhao, J. Rogers, C. Churcher, and L.B. Schook. (2012). Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491, 393-398 (Cover).

Groenen, M.A.M., L.B. Schook, and A.L. Archibald. (2011). Pig genomics. In M.F. Rothschild and A. Ruvinsky (Eds.), Genetics of the Pig, 2nd ed. (pp. 179-199). Wallingford, Oxfordshire, UK: CABI Publishing.

Hamernik, D.L., H.A. Lewin and L.B. Schook. (2003). Allerton III: Beyond livestock genomics. Anim. Biotechnol. 14, 77-82.

Ho, C.S., J.K. Lunney, A. Ando, C. Rogel-Gaillard, J.H. Lee, L.B. Schook, and D.M. Smith. (2009). Nomenclature for factors of the SLA system, update 2008. Tissue Antigens, 73(4), 307-315.

Ho, C.S., E.S. Rochelle, G.W. Martens, L.B. Schook, and D.M. Smith. (2006). Characterization of swine leukocyte antigen polymorphism by sequence-based and PCR-SSP methods in Meishan pigs. Immunogenetics, 11, 873-882.

Humphray, S.J., C.E. Scott, R. Clark, B. Marron, C. Bender, N. Camm, J. Davis, A. Jenks, A. Noon, M. Patel, H. Sehra, F. Yang, M.B. Rogatcheva, D. Milan, P. Chardon, G. Rohrer, D. Nooneman, P. de Jong, S.N. Meyers, A. Archibald, J.E. Beever, L.B. Schook, and J. Rogers. (2007). A high utility integrated map of the pig genome. Genome Biol. 8(7), R139.

Jensen, T.W., M.J. Mazur, J.E. Pettigrew, B.G. Perez-Mendoza, J. Zachary, and L.B. Schook. (2010). A cloned pig model for examining atherosclerosis induced by high fat, high cholesterol diets. Anim. Biotechnol. 21, 179-187.

Jeraldo, P., M. Sipos, N. Chia, J.M. Brulc, A.S. Dhillon, M.E. Konkel, C.L. Larson, K.E. Nelson, A. Qu, L.B. Schook, F. Yang, B.A. White, and N. Goldenfeld. (2012). Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes. PNAS, 109(25), 9692-9698.

Kumar, C.G., J.H. Larson, M.R. Band, and H.A. Lewin. (2007). Discovery and characterization of 91 novel transcripts expressed in cattle placenta. BMC Genomics, 8, 113.

Larkin, D.M., N.M. Astakhova, M.A. Prokhorovich, H.A. Lewin, and N.S. Zhdanova. (2006). Comparative mapping of cattle chromosome 19: Cytogenetic localization of 19 BAC clones. Cytogenet. Genome Res. 112, 235-240.

Larkin, D.M., H.D. Daetwyler, A.G. Hernandez, C.L. Wright, L.A. Hetrick, L. Boucek, S.L. Bachman, M.R. Band, T.V. Akraiko, M. Cohen-Zinder, J. Thimmapuram, I.M. Macleod, T.T. Harkins, J.E. McCague, M.E. Goddard, B.J. Hayes, and H.A. Lewin. (2012). Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle. PNAS, 109(20), 7693-7698.

Larkin, D.M., A. Everts-van der Wind, M. Rebeiz, P.A. Schweitzer, S. Bachman, C. Green, C.L. Wright, E.J. Campos, L.D. Benson, J. Edwards, L. Liu, K. Osoegawa, J.E. Womack, P.E. de Jong, and H.A. Lewin. (2003). A cattle-human comparative map built with cattle BAC-ends and human genome sequence. Genome Res. 13, 1966-1972.

Larkin, D.M., G. Pape, R. Donthu, L. Auvil, M. Welge, and H.A. Lewin. (2009). Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories. Genome Res. 19, 770-777.

Larson, J.H., C.G. Kumar, R.E. Everts, C.A. Green, A. Everts-van der Wind, M.R. Band, and H.A. Lewin. (2006). Discovery of eight novel divergent homologs expressed in cattle placenta. Physiol. Genomics, 25, 405-413.

Larson, J.H., B.M. Marron, J.E. Beever, B.A. Roe, and H.A. Lewin. (2006). Genomic organization and evolution of the ULBP genes in cattle. BMC Genomics, 7, 227-241.

Le, M.T.,  H. Choi, M.K. Choi, D.T. Nguyen, J.H. Kim, H.G. Seo, S.Y. Cha, K. Seo, T. Chun, L.B. Schook, and C. Park. (2012). Comprehensive and high-resolution typing of swine leukocyte antigen DQA from genomic DNA and determination of 25 new SLA class II haplotypes. Tissue Antigens, 6, 528-35.

Lee, K.T., M.J. Byun, K.S. Kang, E.W. Park, S.H. Lee, S. Cho, H.Y. Kim, K.W. Kim, T. Lee, J. Park, W. Park, D. Shin, H.S. Park, J.T. Jeon, B.H. Choi, G.W. Jang, S.H. Choi, D.W. Kim, J.H. Kim, D. Lim, H.S. Park, M.R. Park, J. Ott, L.B. Schook, T.H. Kim, and H. Kim. (2011). Neuronal genes for subcutaneous fat thickness in human and pig are identified by local genomic sequencing and combined SNP association study. PLoS ONE, 6(2), e16356.

Lewin, H.A. (2004). The future of cattle genomics: The beef is here. Cytogenet. Genome Res. 102, 10-15.

Lewin, H.A. (2009). It's a bull's market. Science, 324, 478-479.

Lewin, H.A., D.M. Larkin, J. Pontius, and S.J. O'Brien. (2009). Every genome sequence needs a good map. Genome Res. 19(11), 1925-1928.

Luetkemeier, E.S., R.S. Malhi, J.E. Beever, and L.B. Schook. (2009). Diversification of porcine MHC class II genes: evidence for selective advantage. Immunogenetics, 61, 119-129.

Luetkemeier, E.S., M. Sodhi, L.B.Schook, and R.S. Malhi. (2010). Multiple Asian pig origins revealed through genomic analyses. Mol. Phylogenet. Evol. 54(3), 680-686.

Ma, J.G., H. Yasue, K. Eyer, H. Hiraiwa, T. Shimogiri, S.N. Meyers, J.E. Beever, L.B. Schook, C.W. Beattie, and W.S. Liu. (2009). An integrated RH map of porcine chromosome 10 (SSC10). BMC Genomics, 10, 211.

Murphy, W.J., D.M. Larkin, A. Everts-van der Wind, G. Bourque, G. Tesler, L. Auvil, J.E. Beever, B.P. Chowdhary, F. Galibert, L. Gatzke, C. Hitte, D. Milan, S.N. Meyers, E.A. Ostrander, G. Pape, H.G. Parker, T. Raudsepp, M.B. Rogatcheva, L.B. Schook, L.C. Skow, M. Welge, J.E. Womack, S.J. O'Brien, P.A. Pevzner, and H.A. Lewin. (2005). Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science, 309, 613-617.

Piontkivska, H., M.Q. Yang, D.M. Larkin, H.A. Lewin, J. Reecy, and L. Elnitski. (2009). Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts. BMC Genomics 10, 189.

Pollock, C.B., M.B. Rogatcheva, and L.B. Schook. (2007). Comparative genomics of xenobiotics metabolism: a porcine-human PXR gene comparison. Mamm. Genomics, 18, 210-219.

Ramos, A.M., R.P.M.A Crooijmans, N.A. Affara, A.J.Amaral, A.L. Archibald, J.E.Beever, C. Bendixen, C.Churcher, R.Clark, P.Dehais, M.S. Hansen, J. Hedegaard, Z.L.Hu,  H.H. Kerstens, A.S. Law, H.J. Megens, D. Milan, D.J.Nonneman, G.A. Rohrer, M.F. Rothschild, T.P.L. Smith, R.D. Schnabel, C.P. Van Tassell, J.F. Taylor, R.T. Wiedmann, L.B. Schook, and M.A.M. Groenen. (2009). Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS ONE, 4(8), e6524.

Roca, A.L. and L.B. Schook. (2010). Genomics: captive breeding and wildlife conservation.  In Encyclopedia of Biotechnology in Agriculture and Food (pp. 320-325). Boca Raton, FL: CRC Press.

Rogatcheva, M.B., K. Chen, D.M. Larkin, S.N. Meyers, B.M. Marron, W. He, W., L.B. Schook, and J.E. Beever. (2008). Piggy-BACing the human genome I: constructing a porcine BAC physical map through comparative genomics. Anim. Biotechnol. 19, 28-42.

Rogatcheva, M.M., L.A. Rund, J.E. Beever and L.B. Schook. (2003). Harvesting the genomic promise: recombineering sequences for phenotypes. Anim. Biotechnol. 14, 103-118.

Schook, L., C. Beattie, J. Beever, S. Donovan, R. Jamison, S. Niemi, M. Rothschild, M. Rutherford, D. Smith, and F. Zuckerman. (2005). Swine in biomedical research: creating the building blocks of animal models. Anim. Biotechnol. 16, 183-190.

Schook, L.B., J.E. Beever, J. Roger, S. Humphray, A. Archibald, P. Chardon, D. Milan, G. Rohrer, and K. Eversole. (2005). Swine Genome Sequencing Consortium (SGSC): a strategic roadmap for sequencing the pig genome. Comp. Funct. Genomics, 6, 251-255.

Seo, S. and H.A. Lewin. (2008). Reconstruction of metabolic pathways for the cattle genome. BMC Syst. Biol. 3, 33.

Seroussi, E., H.A. Lewin, M. Band, M. Cohen-Zinder, J. Drackley, D. Larkin, J. Loor, M. Ron, M. Shani, and J. Weller. (2006). Bovine ABCG2 gene missense mutations and uses therofe. U.S. Patent Application No. 11/427,230. Washington, DC: U.S. Patent and Trademark Office (Filed 6/28/06).

Smith, D.M., J.K. Lunney, G.W. Martens, A. Ando, J.H. Lee, C.S. Ho, L.B. Schook, C. Renard, and P. Chardon. (2005). Nomenclature for factors of the SLA class-I system. Tissue Antigens, 65, 136-149.

Smith, D.M., J.K. Lunney, G.W. Martens, A. Ando, J.H. Lee, C.S. Ho, L.B. Schook, C. Raenard, and P. Chardon. (2005). Nomenclature for factors of the SLA class-II system. Tissue Antigens, 66, 623-639.

Snelling,W.M., R. Chiu, J.E. Schein, M. Hobbs, C.A. Abbey, D.L. Adelson, J. Aerts, G.L. Bennett, I.E. Bosdet, M. Boussaha, R. Brauning, A.R. Caetano,  M.M. Costa, A.M. Crawford, B.P. Dalrymple, A. Eggen, A. Everts-van der Wind, S. Floriot, M. Gautier, C.A. Gill, R.D. Green, R. Holt, O. Jann,  S.J.M. Jones,  S.M. Kappes, J.W. Keele, P.J. de Jong, D.M. Larkin, H.A. Lewin, J.C. McEwan, S. McKay, M.A. Marra,  C.A. Mathewson, L.K. Matukumalli, S.S. Moore, B. Murdoch, F.W. Nicholas, K. Osoegawa, A. Roy, H. Salih, L. Schibler, R.D. Schnabel, L. Silveri, L.C. Skow, T.P.L. Smith, T.S. Sonstegard, J.F. Taylor, R. Tellam, C.P. Van Tassell, J.L. Williams, J.E. Womack, N.H. Wye, G. Yang, S. Zhao, and the International Bovine BAC Mapping Consortium. (2007). A physical map of the bovine genome. Genome Biol. 8, R165.

Sodhi, M. and L.B. Schook. (2010). Genomics research: livestock production. In Encyclopedia of Biotechnology in Agriculture and Food (pp. 310-315). Boca Raton, FL: CRC Press.

Tellam, R.L., D.G. Lemay, C.P. Van Tassell, H.A. Lewin, K.C. Worley, and C.G Elsik. (2009). Unlocking the bovine genome. BMC Genomics 10, 193.

Tortereau, F.B. Servin, L. Frantz, H.J. Megens, D. Milan, G. Rohrer, R. Wiedmann, J. Beever, A.L. Archibald, L.B. Schook, and M. Groenen. (2012). A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content. BMC Genomics, 13, 586.

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