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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Reproduction Research » Research » Research Project #434555

Research Project: Functional Annotation of the Porcine Genome

Location: Reproduction Research

Project Number: 3040-31000-099-01-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Apr 1, 2018
End Date: Jan 31, 2020

Goal of the proposal is comprehensive functional genome annotation of porcine biological states, with an emphasis on tissues and biological states that are most directly connected to annotating markers associated with important phenotypes. Specific Aim: 1. Complete functional annotation of healthy adult porcine tissues relevant to phenotypes important for genetic improvement. 2. Determine the extent to which allele-specific expression and imprinting contribute to the functioning of the genome during fetal development. 3. Identify the functional components of the immune response as a resource for improving resilience in pigs

ARS investigator role is to prepare long-read sequencing libraries, sequence and analyze transcripts from isolated immune cell populations for transcriptional and epigenetic evaluation. Cells to be analyzed include 8 immune cell populations from blood (sorted using both magnetic and fluorescence based cell sorting techniques), alveolar and liver macrophages stimulated with lipopolysaccharide or viral ligands for 2 and 6 hours, and preserved single cell suspensions of bone marrow, thymus, spleen and lymph node from 2 pigs. Allele-specific expression and imprinting of transcripts will be determined from sequences we obtained from fetal tissues derived from reciprocal crosses of diverse breeds consisting of Commercial and Meishan pigs.