Gene Discovery and Functional Genomics in the Pig

Advances in gene mapping and genomics in farm animals have been considerable over the past decade. Medium resolution linkage and physical maps have been reported, and specific chromosomal regions and genes associated with traits of biological and economic interest have been identified. We have reached an exciting stage in gene identification, mapping and quantitative trait locus discovery in pigs, as new molecular information is accumulating rapidly. Significant progress has been made by identifying candidate gene associations and low-resolution regions containing quantitative trail loci (QTL). However, we are still disadvantaged by the lack of tools available to efficiently use much of this new information. For example, current pig maps are neither of high enough resolution nor sufficiently informative at the comparative level for positional candidate gene cloning within QTL regions. As well, studying biological mechanisms underlying economically important traits such as reproduction is limited by the lack of molecular resources. This is especially important, as reproduction is very difficult to genetically improve by classical breeding methods due to the relatively low heritability and high expense in data collection. Thus, an improved understanding of porcine reproductive biology is of crucial economic importance, yet reproductive processes are poorly characterized at the molecular level. Recently, new methodologies have been brought to bear on a better understanding of pig molecular biology for accelerating genetic improvement in pigs. Several groups are developing molecular information in the pig, and the total Genbank sequence entries for porcine expressed genes have recently topped 100,000. Our Midwest EST Consortium has produced cDNA libraries containing the majority of genes expressed in major female reproductive tissues, and we have deposited nearly 15,000 gene sequences into public databases. These sequences represent over 8,900 different genes, based on sequence comparison among these data. Furthermore, we have developed computer software to automatically extract sequence similarity of these pig genes with their human counterparts, as well as the mapping information of these human homologues. Within our data set, we have identified nearly 1,500 pig genes with strong similarity to mapped human genes, and we are in the process of mapping 700 of these genes to improve the human-pig comparative map. This work and the complementary work of others can now be used to more rapidly understand and identify the genes controlling reproduction, so that genetic improvement of reproduction phenotypes can accelerate. Disciplines Animal Sciences | Genetics | Genomics | Molecular Genetics Comments This proceeding was published as Tuggle , C. K. , R. S. Prather, M. B. Soares, T. Casavant, D. Pomp, M. F. Rothschild, and W. Beavis. 2001. Gene discovery and functional genomics in the pig. Proc. National Swine Improvement Federation, St. Louis, MO, Dec. 6-7, 2001. Posted with permission. Authors C. K. Tuggle, R. S. Prather, M. B. Soares, T. Casavant, D. Romp, M. F. Rothschild, and W. Beavis This conference proceeding is available at Iowa State University Digital Repository: https://lib.dr.iastate.edu/ans_conf/9 3/7/2018 Gene Discovery and Functional Genomics in the Pig http://www.nsif. com/conferences/2001/tuggle.htm 1/9 Gene Discovery and Functional Genomics in the Pig Tuggle, C. K1. , R. S. Prather2, M. B. Soares3, T. Casavant4, D. Pomp5, M. F. Rothschild1, W. Beavis6 1 Department of Animal Science, Iowa State University, 2255 Kildee Hall Ames, IA 50011 2 Department of Animal Science, 162 ASRC University of Missouri-Columbia, Columbia, MO 65211 3 Department of Pediatrics, University of Iowa, 451 Eckstein Med. Research Bldg, Iowa City, IA 52242 4 Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA 52242 5 Department of Animal Science, University of Nebraska, Lincoln, NE 68583 6 National Center for Genomic Resources, Sante Fe, NM Summary Advances in gene mapping and genomics in farm animals have been considerable over the past decade. Medium resolution linkage and physical maps have been reported, and specific chromosomal regions and genes associated with traits of biological and economic interest have been identified. We have reached an exciting stage in gene identification, mapping and quantitative trait locus discovery in pigs, as new molecular information is accumulating rapidly. Significant progress has been made by identifying candidate gene associations and low-resolution regions containing quantitative trail loci (QTL). However, we are still disadvantaged by the lack of tools available to efficiently use much of this new information. For example, current pig maps are neither of high enough resolution nor sufficiently informative at the comparative level for positional candidate gene cloning within QTL regions. As well, studying biological mechanisms underlying economically important traits such as reproduction is limited by the lack of molecular resources. This is especially important, as reproduction is very difficult to genetically improve by classical breeding methods due to the relatively low heritability and high expense in data collection. Thus, an improved understanding of porcine reproductive biology is of crucial economic importance, yet reproductive processes are poorly characterized at the molecular level. Recently, new methodologies have been brought to bear on a better understanding of pig molecular biology for accelerating genetic improvement in pigs. Several groups are developing molecular information in the pig, and the total Genbank sequence entries for porcine expressed genes have recently topped 100,000. Our Midwest EST Consortium has produced cDNA libraries containing the majority of genes expressed in major female reproductive tissues, and we have deposited nearly 15,000 gene sequences into public databases. These sequences represent over 8,900 different genes, based on sequence comparison among these data. Furthermore, we have developed computer software to automatically extract sequence similarity of these pig genes with their human counterparts, as well as the mapping information of these human homologues. Within our data set, we have identified nearly 1,500 pig genes with strong similarity to mapped human genes, and we are in the process of mapping 700 of these genes to improve the human-pig comparative map. This work and the complementary work of others can now be used to more rapidly understand and identify the genes controlling reproduction, so that genetic improvement of reproduction phenotypes can accelerate. Introduction Comparative Mapping The long-term goal of genetic mapping in the pig is the discovery of quantitative or economic trait loci (QTL, ETL). Clearly the detailed mapping information available from the Human Genome Project will become extremely useful for ETL positional cloning success. Identification of the genomic region in welldefined human chromosomes homologous to a pig ETL containing region will identify numerous positional candidate genes for the trait. Development of comparative links between the pig and human/mouse maps is therefore critical to this work. Unfortunately, comparative maps are limited in the pig. Results of comparative mapping have come from two approaches. Bi-directional ZOO-FISH painting results suggest that large regions are conserved between the pig and human (Goureau et al., 1996). However, mapping of individual genes suggests that the gene order between species may be either conserved (Sun et al., 1999a) or quite divergent (Larsen et al., 1999; Sun et al., 1999b). A highly developed comparative map is therefore a necessity, as human gene order is not a good predictor of pig gene order. Pig Reproductive Biology 3/7/2018 Gene Discovery and Functional Genomics in the Pig http://www.nsif. com/conferences/2001/tuggle.htm 2/9 The reproductive process is central to pig production efficiency. Unfortunately there is loss of potential conceptuses during the first month of gestation (Perry, 1954). Several areas exist where there are opportunities for increasing the number and quality of offspring from a given mating. These areas (tissues involved) include: 1) increasing the ovulation rate (ovary, hypothalamus and pituitary); 2) improving fertilization and improving the quality of the conceptus (ovary, conceptus); 3) improving the responsiveness of the dam to the conceptus (uterus, placenta); and 4) understanding the onset of gene expression specific for organogenesis (embryo/fetus). Furthermore, with the likely development of cell culture technologies to clone manipulated pig embryos, it will be possible to use homologous recombination to make specific alternations. While alteration of known genes such as myostatin or MC4R might have significant effects on agricultural productivity, genes that are currently unknown that play a central role in the reproductive process cannot be altered unless first identified. Thus, basic information must be gathered to identify these genes. The evaluation of gene expression differences offers powerful new opportunities for gene discovery. Reports of gene expression changes associated with reproductive phenotypes are mostly gene specific (e.g. Kaminski et al., 1997; Li et al., 1998; Yelich et al., 1997a, b), primarily due to the paucity of resources available for largescale and whole-genome analysis. While the advent of differential display PCR has enabled preliminary investigations of gene expression changes on a whole-tissue level (e.g. Li et al., 1996; Clouscard-Martinato, 1998), the methods are laborious and not facilitative of large-scale analysis of various time points, tissue sources and treatments. Status of Pig Genome Maps At present, over 2,000 markers and genes have been mapped in pigs (Ellegren et al., 1994; Archibald et al., 1995; Marklund et al., 1996; Rohrer et al., 1996), tho