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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #364278

Research Project: Identifying Genomic Solutions to Improve Efficiency of Swine Production

Location: Genetics and Animal Breeding

Title: Functional annotation of the porcine genome and ISAFG update

item TUGGLE, CHRISTOPHER - Iowa State University
item ZHOU, HUAIJUN - University Of California
item ERNST, CATHERINE - Michigan State University
item Loving, Crystal
item KOLTES, JAMES - Iowa State University
item REECY, JAMES - Iowa State University
item ROSS, PABLO - University Of California
item Nonneman, Danny - Dan
item Smith, Timothy - Tim
item STEIBEL, JUAN - Michigan State University
item HUANG, WEN - Michigan State University

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 12/4/2018
Publication Date: 1/16/2019
Citation: Tuggle, C.K., Zhou, H., Ernst, C.W., Loving, C.L., Koltes, J.E., Reecy, J.M., Ross, P.J., Nonneman, D.J., Smith, T.P.L., Steibel, J.P., Huang, W. 2019. Functional annotation of the porcine genome and ISAFG update [abstract]. In: Plant and Animal Genome Conference XXVII Proceedings, 12-16 Jan 2019, San Diego, CA. pg. 96. W448. Available:

Interpretive Summary:

Technical Abstract: While the porcine genome assembly has been significantly improved, the lack of functional annotation prevents full exploitation of single nucleotide variant analysis for genetic improvement through traditional breeding, and limits efficiency of gene editing of specific genome components to understand function and accelerate genetic improvement. With new funding from the USDA-NIFA-AFRI Foundational program, we will dramatically increase the depth and breadth of current porcine functional annotation and generate a community resource for scientists in both the public and private sectors. Across all objectives, we will use RNA assays (RNAseq, the 5’ end mapping technique RAMPAGE, and PacBio Iso-seq) and epigenetics assays (histone ChIP-seq, ATAC-seq and DNA methylation) to annotate a tremendous breadth of biological states. In Objective 1, we will triple the number of adult tissues currently being annotated. In Objective 2, we will annotate four tissues at important stages of fetal development, and link allele-specific expression with allele-specific chromatin modifications through analyzing divergent-breed reciprocal crosses. In Objective 3, we will annotate circulating white blood cell populations in healthy pigs, as well as macrophage responses to bacterial and viral mimics. We will also profile gene expression of single cells in complex cell populations to maximize annotation of critical immune tissues. In Objective 4, we will use all these data as well as public FAANG data to generate a first-generation chromatin state segmentation map. At Livestock Genomics 2018, we will describe the current proposed research in detail as well as gather community input on biological priorities. Supported by USDA-NIFA-AFRI- 2018-67015-27501. In November 2018, the Seventh International Symposium on Animal Functional Genomics (ISAFG) was held in Adelaide, Australia. This talk will include a short summary of this meeting, which included an accompanying FAANG session. This session consisted of updates from several groups working in FAANG research areas as well as small group discussions on wet lab methods and quality control and bioinformatics approaches. Summaries of these small group discussions were prepared and will also be recapitulated at the 2019 FAANG Workshop.