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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Livestock Bio-Systems » Research » Publications at this Location » Publication #238485
Title: Functional Genomic Approaches for the Study of Fetal/Placental Development in Swine with Special Emphasis on Imprinted Genes

Author
item BISCHOFF, STEVE - North Carolina State University
item TSAI, SHENGDAR - North Carolina State University
item HARDISON, NICHOLAS - North Carolina State University
item MOTSINGER-REIF, ALISON - North Carolina State University
item Freking, Bradley - Brad
item PIEDRAHITA, JORGE - North Carolina State University

Submitted to: Reproduction and Fertility Supplement
Publication Type: Review Article
Publication Acceptance Date: 5/27/2009
Publication Date: 6/4/2009
Citation: Bischoff, S.R., Tsai, S., Hardison, N., Motsinger-Reif, A.A., Freking, B.A., Piedrahita, J.A. 2009. Functional Genomic Approaches for the Study of Fetal/Placental Development in Swine with Special Emphasis on Imprinted Genes. In: Control of Pig Reproduction VIII (H. Rodriguez-Martinez, J.L. Vallet and A.J. Ziecik, eds.) Journal of Reproduction and Fertility Supplement. 66:245-264.

Interpretive Summary: Biological research typically dissects structures and functions of individual molecular and cellular components comprising a system. However, the inherent complexity of biological systems, due not only to the large number of their constituents, but also to the interactions between these constituents has proven difficult to understand using reductionist approaches. In this review chapter, we describe the application of functional genomics approaches for the study of the imprinted gene family in swine. Genomic imprinting results in the silencing of a subset of mammalian alleles due to parent-of-origin inheritance. In contrast to the majority of genes where expression is from both alleles, genomic imprinting leads to mono-allelic or differential expression from either the paternal or maternal strand. Understanding and accounting for imprinting in marker assisted management schemes is important for swine production since typical pork production mating systems utilize different germplasm sources or breeds in specifically defined paternal and maternal roles; e.g., Landrace x Yorkshire F1 females mated to Duroc boars in terminal sire production systems. While there are varied definitions of “functional genomics” in general they focus on the application of genomic approaches such as DNA microarrays, single nucleotide polymorphism (SNP) arrays, and other high coverage genomic analysis, and its combination with downstream methods of gene modification such as transgenic approaches using silencing RNA (siRNA), and viral and non-viral transfection. Between the initial data acquisition and the actual genetic manipulation of the system lies the bioinformatics component, whereby massive amounts of data are analyzed to extract the most meaningful information. This area of bioinformatics is in constant flux with an increased emphasis on mining for affected pathways and processes rather than gene lists. In this review we describe examples where we have utilized these global technologies for the study of the imprinted gene family in swine in the context of placental and embryonic development.

Technical Abstract: The overall focus of this chapter will be the application of functional genomic approaches for the study of the imprinted gene family in swine. While there are varied definitions of “functional genomics” in general they focus on the application of genomic approaches such as DNA microarrays, single nucleotide polymorphism (SNP) arrays, and other high coverage genomic analysis, and its combination with downstream methods of gene modification such as transgenic approaches using silencing RNA (siRNA), and viral and non-viral transfection. Between the initial data acquisition and the actual genetic manipulation of the system lies the bioinformatics component, whereby massive amounts of data are analyzed to extract the most meaningful information. This area of bioinformatics is in constant flux with an increased emphasis on mining for affected pathways and processes rather than gene lists. Below we will expand on each of these points and describe examples where we have utilized these technologies for the study of the imprinted gene family in swine. First we will introduce the biological question that interests our laboratory to provide context for the following discussion of the functional genomic approaches and the types of information they generate.