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.
GOALS & OBJECTIVES
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.
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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.
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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).
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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.
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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.
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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.
Uenishi, H.T. Morozumi, T. Toki, T. Eguchi-Ogawa, L.A. Rund, and L.B. Schook. (2012). Large-scale sequencing based on full-length-enriched cDNA libraries in pigs: contribution to annotation of the pig genome draft sequence. BMC Genomics, 13, 581.