LIVESTOCK GENOME SEQUENCING INITIATIVE

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: SPECIAL GRANT
• Reporting Frequency: Annual
• Accession No.: 0218845
• Grant No.: 2009-34480-19875
• Proposal No.: 2009-04235
• Project Start Date: Aug 1, 2009
• Project End Date: Jul 31, 2012
• Grant Year: 2009
• Program Code: [TI]- Livestock Genome Sequencing, IL

Recipient Organization
UNIVERSITY OF ILLINOIS
2001 S. Lincoln Ave.
URBANA,IL 61801

Performing Department
Animal Sciences

Non Technical Summary
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.

Animal Health Component

(N/A)

Research Effort Categories

Basic

100%

Applied

(N/A)

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
304	3399	1080	25%
304	3499	1080	25%
304	3599	1080	50%

Knowledge Area
304 - Animal Genome;

Subject Of Investigation
3499 - Dairy cattle, general/other; 3599 - Swine, general/other; 3399 - Beef cattle, general/other;

Field Of Science
1080 - Genetics;

Keywords

porcine

bovine

health traits

porcine microbiome

gene networks affected by nutrition

neuropathic hydrocephalus

fawn calf syndrome

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.

Project Methods
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.

Progress 08/01/09 to 07/31/12

Outputs
OUTPUTS: Using a combination of whole-genome resequencing and high-density genotyping arrays, genome-wide haplotypes were reconstructed for two of the most important bulls in the history of the dairy cattle industry, Pawnee Farm Arlinda Chief ('Chief') and his son Walkway Chief Mark ('Mark'), each accounting for ∼7% of all current genomes. The genome-wide haplotypes inherited by Mark from Chief were reconstructed using ∼1 million informative SNPs. By using Bovine SNP50 genotypes, the frequencies of Chief alleles for his two haplotypes were determined in 1,149 of his descendants, and the distribution was compared with the frequencies that would be expected assuming no selection. We identified 49 chromosomal segments in which Chief alleles showed strong evidence of selection. Eleven candidate genes were identified with functions related to milk-production, fertility, and disease-resistance traits. Candidate genes and DNA polymorphisms were identified for a quantitative trait loci (QTL) affecting milk yield (MY), fat yield (FY), and protein yield (PY) previously mapped to bovine chromosome 3 (BTA3). Targeted resequencing of ∼1.8 Mbp within the QTL critical region identified 23 single nucleotide polymorphisms (SNPs) within a fine-mapped region that were associated with effects on breeding values for MY, FY, or PY. This multisite haplotype included SNPs located within exons or promoters of four tightly linked genes: RAP1A, ADORA3, OVGP1, and C3H1orf88. An SNP within RAP1A showed strong evidence of a recent selective sweep based on integrated haplotype score and was also associated with breeding value for PY. Because of its known function in alveolar lumen formation in the mammary gland, RAP1A is thus a strong candidate gene for QTL effects on lactation traits. Ten different mutations corresponding to genetic abnormalities in cattle and sheep have been identified. These include two forms of hypotrichosis (HY; Hereford and Galloway), idiopathic epilepsy (IE), arthrogryposis multiplex (AM), neuropathic hydrocephalus (NH), osteopetrosis (OS), 'Tipper syndrome' and contractural arachnodactyly (CA) in cattle. In sheep, the mutations causing GM1 gangliosidosis (GM1) and ectodermal dysplasia (ED) were also identified. The assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia is presented. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ~1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
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.

Publications

• 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.
• 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.
• 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.
• 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 80:528-535.
• 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.A.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.
• 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, M. Perez-Enciso. 2012. Porcine colonization of the Americas: A 60k SNP story. Heredity (In Press).
• 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:e1003100.
• Larkin, D.M., Daetwyler, H.D., Hernandez, A.G., Wright, C.L., Hetrick, L.A., Boucek, L., Bachman, S.L., Band, M.R., Akraiko, T.V., Cohen-Zinder, M., Thimmapuram, J., Macleod, I.M., Harkins, T.T., McCague, J.E., Goddard, M.E., Hayes, B.J. and Lewin, H.A. 2012. Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle. Proc Natl Acad Sci U S A. 109:7693-8.
• Cohen-Zinder, M., Donthu, R., Larkin, D.M., Kumar, C.G., Rodriguez-Zas, S.L., Andropolis, K.E., Oliveira, R. and Lewin, H.A. 2011. Multisite haplotype on cattle chromosome 3 is associated with quantitative trait locus effects on lactation traits. Physiol Genomics 43:1185-97.
• 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.
• 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:e16356.
• 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:e14782.
• 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. 23:43-63.
• K.A. Darfour-Oduro and L.B. Schook. 2012. Livestock marker-assisted selection. Encyclopedia of Biotechnology in Agriculture and Food DOI: 10.1081/E-EBAF-120043003.

Progress 08/01/10 to 07/31/11

Outputs
OUTPUTS: Contractural arachnodactyly (CA) is a genetic defect that has been reported in Angus cattle (http://www.dpi.nsw.gov.au/agriculture/livestock/health/specific/catt le/ca-angus). Based on pedigree examination of affected calves this genetic defect was determined to have an autosomal recessive mode of inheritance. Due to this recessive inheritance pattern, only calves that are homozygous (i.e., receiving a chromosome with the mutation from both parents) for the mutation causing CA are affected with multiple abnormalities (most often with contractures or joint laxity). The condition is semi-lethal in that most calves survive yet have significantly reduced performance. Some calves born under extensive management will succumb to environmental stressors and fail to survive. Classification of normal appearing individuals is virtually impossible in the absence of planned breeding studies or test matings. The accurate identification and subsequent selection against carriers of the mutation is the only method that can be used to eliminate this genetic defect from the population without concurrent loss of germplasm due to culling based only on pedigree. The development of a method to accurately and efficiently determine the genotype status of an individual is dependent on understanding the molecular basis of the defect. The mutation causing CA has been identified as a deletion of approximately 54,000 base pairs. This deletion encompasses the 3' end of the bovine ADAMTS-like 3 (ADAMTSL3) gene and the intergenic region between ADAMTSL3 and the elongation factor Tu GTP-binding domain containing 1 (EFTUD1) genes. This deletion removes the last four exons of bovine ADAMTSL3 and thus, a complete loss-of-function of ADAMTSL3 would be expected due to the absence of full-length protein when an animal is homozygous for the deletion-containing chromosome. Very little is known about the function of ADAMTSL3 in mammals although it has been implicated in the control of human height. This role would be consistent with CA disease pathology where affected calves are significantly taller than their normal siblings. Hypotrichosis or hairlessness can be found in several breeds of cattle. Previously, we have identified a mutation in the bovine keratin 71 (KRT71) gene that is responsible for recessive hypotrichosis in Hereford cattle. However, the condition has also been reported in Belted Galloway cattle with the same mode of inheritance. Although the pathology in Belted Galloway calves is be remarkably similar to that of Hereford calves, Galloway calves do not share the same KRT71 mutation. A genome-wide association analysis was conducted and the locus causing hypotrichosis in Galloway cattle was mapped to chromosome 29. Resequencing of several candidate genes in the region has resulted in the identification of a mutation in the hephaestin-like protein 1 (HEPHL1) gene. The A-to-T transversion results in the conversion of a lysine codon to a termination codon resulting in premature truncation of the protein. Using the DNA sequence information that has been generated, a DNA-based diagnostic test has been developed that accurately determines an individual's genotype. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Applied diagnostics have been developed and disseminated to the cattle industry enabling breeding management based directly on genotype. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Using the DNA sequence information that has been generated for contractural arachnodactyly (CA) and hypotrichosis (HYG), DNA-based diagnostic tests have been developed that accurately determine an individual's genotype. To date, more than 50,000 Angus and Angus-derivative cattle have been genotyped for the CA mutation. More than 500 Belted Galloway cattle have been genotyped for the HYG mutation.

Publications

• No publications reported this period

Progress 08/01/09 to 07/31/10

Outputs
OUTPUTS: Specific gene resequencing has focused on 2 gene sets, the BHMT and the TLRs. We have cloned and sequenced the Porcine bhmt and bhmt-2 cDNA including the UTR were amplified using RLM-RACE. It was determined that both the pig bhmt and bhmt-2 genes span approximately 26kb and 16kb, respectively. Both the bhmt and bhmt-2 genes consist of 8 exons and 7 introns similar to that observed in human, rat and mice genes. The deduced amino acid sequences of BHMT and BHMT-2 contain 407 and 363 amino acids, respectively, and shared 78% amino acid identity which included the homocysteine binding domain and cysteine residues responsible for Zn binding. Relative to BHMT-2, BHMT has two additional amino acid sequences, a 9 amino acid N-terminal sequence (86-94) which confers betaine binding specificity and a 34 amino acid sequence at the carboxy terminus (373-407) which is responsible for tetramerization of the BHMT enzyme. Toll-like receptors (TLRs) detect molecular signatures of invaders known as pathogen-associated molecular patterns. The objective of this work was to characterize the genomic organization of porcine TLRs (pTLRs) 6, 1 and 10 and to detect polymorphisms in a ~40 kb region of porcine chromosome 8, including 5′-untranslated exons not previously described. To achieve this objective, a panel of 31 random unrelated samples representing 13 global pig populations was assembled for sequencing and comparison with Duroc 2-14, which the whole genome has been sequenced. This comparative sequence analysis revealed a total of 139 polymorphisms in the largest exons of TLR6-TLR1-TLR10. Neuropathic hydrocephalus (NH) is a genetic defect that has recently been reported in Angus cattle. Based on pedigree examination of affected calves this genetic defect was determined to have an autosomal recessive mode of inheritance. Due to this recessive inheritance pattern, only calves that are homozygous for the mutation causing NH are affected with multiple abnormalities most often including markedly enlarged craniums with severe skull malformations. The cranial cavity is fluid filled with little or no recognizable brain tissue present. Spinal tissue is also predominantly absent. The condition is invariably lethal. Classification of normal appearing individuals (i.e., differentiation of those that are homozygous for the normal allele from heterozygous or carriers of the mutation) is virtually impossible in the absence of planned breeding studies or test matings. The accurate identification and subsequent selection against carriers of the mutation is the only method that can be used to eliminate this genetic defect from the population; without concurrent loss of genetic resources due to culling based only on pedigree. The development of a method to accurately and efficiently determine the genotype status of an individual is dependent on understanding the molecular basis of the defect (i.e., identification of the causative mutation within the DNA sequence). The mutation causing NH has been identified as a single nucleotide polymorphism in exon 19 of the bovine patatin-like phospholipase domain containing 6 (PNPLA6) gene. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
The expression pattern of bhmt and bhmt-2 genes in pigs is similar to humans and further supports the use of the pig as an appropriate animal model to study diseases and gene regulation associated with bhmt and bhmt-2 genes. Nonsynonymous SNPs recognized in this study are located in regions of the pTLR gene that either are implicated in binding microbial products or intracellular signaling. Thus, they could be significant in host responses to important swine diseases. In addition, the protein domain architecture of these three pTLRs was examined between human, mouse, cow, and pig, which revealed 12 regions of conservation in the TLR variable leucine-rich-repeat patterning. Using the DNA sequence information that has been generated, a DNA-based diagnostic test has been developed for neuropathic hydrocephalus that accurately determines an individual's genotype. Thus, the genotype of an animal can be obtained by analysis of any DNA containing sample such as blood, semen, tissue or hair follicles. Internationally, more than 80,000 animals have been screened using this diagnostic.

Publications

• Ma, J.-G., Yasue, H., Eyer, K., Hiraiwa, H., Shimogiri, T., Meyers, S.N., Beever, J.E., Schook, L.B., Beattie, C.W. and Liu, W.-S. 2009. An integrated RH map of porcine chromosome 10 (SSC10). BMC Genomics 10:211 doi:10.1186/1471-2164-10-211.
• Ramos, A.M., Crooijmans, R.P.M.A., Affara, N.A., Amaral, A.J., Archibald, A.L., Beever, J.E., Bendixen, C., Churcher, C., Clark, R., Dehais, P., Hansen, M.S., Hedegaard, J., Hu, Z.-L., Kerstens, H.H., Law, A.S., Megens, H.J., Milan, D., Nonneman, D.J., Rohrer, G.A., Rothschild, M.F., Smith, T.P.L., Schnabel, R.D., Van Tassell, C.P., Taylor, J.F., Wiedmann, R.T., Schook, L.B. and Groenen, M.A.M. 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), art. no. e6524.
• Luetkemeier, E.S., Sodhi, M., Schook, L.B. and Malhi, R.S. 2010. Multiple Asian pig origins revealed through genomic analyses. Molecular Phylogenetics and Evolution 54(3):680-686.
• Roca, A.L. and Schook, L.B. 2010. Genomics: Captive breeding and wildlife conservation. Encyclopedia of biotechnology in Agriculture and Food DOI: 10.1081/E-EBAF-120045214
• Jensen, T.W., Mazur, M.J., Pettigrew, J.E., Perez-Mendoza, B.G., Zachary, J. and Schook, L.B. 2010. Animal Biotechnology, 21:179-187.
• Sodhi, M. and Schook, L.B. 2010. Genomics research: Livestock production. Encyclopedia of Biotechnology in Agriculture and food. Doi: 10.1081/E-EBAF-120043005.
• Archibald, A.L., Bolund, L., Churcher, C., Fredholm, M., Gorenen, M.A.M., Harlizius, B., Lee, K.-T., Milan, D., Rogers, J., Rothschild, M.F., Uenishi, H., Wang, J., Schook, L.B. and the Swine Genome Sequencing Consortium. 2010. Pig genome sequence-analysis and publication strategy. BMC Genomics 11:438.
• Gray, M.A., Pollock, C.B., Schook, L.B. and Squires, E.J. 2010. Characterization of porcine pregnane x receptor, farnesoid x receptor and their splice variants. Experimental Biology and Medicine 235:718-736.
• Groenen, M.A.M., Schook, L.B. and Archibald, A.L. 2011. Chapter 8: Pig Genomics. In: Genetics of the pig, 2nd edition (eds M.F. Rothschild and A. Ruvinsky) pages 179-199.
• Ganu, R.S., Garrow, T.A., Sodhi, M., Rund, L.A. and Schook, L.B. 2011. Molecular characterization and analysis of the porcine betaine homocysteine methyltransferase and betaine homocysteine methyltransferase -2 genes. Gene (In Press).