Animal Molecular Genetics Lab

Principle Investigator: Catherine Ernst

Rooms 1205 and 3330
Anthony Hall
474 S. Shaw Lane
East Lansing, MI 48824

Welcome

The Animal Molecular Genetics Laboratory focuses on identification and evaluation of genes and genetic markers associated with genetic improvement of production traits in pigs and other meat animal species. Much of our research is at the interface of structural and functional genomics, including a genetical genomics project to integrate genetic marker and gene expression data to identify genes controlling skeletal muscle and fat deposition, and their relationship to growth, carcass composition and meat quality in pigs. This effort applies both RNAseq and miRNAseq approaches in order to reveal gene regulatory networks and pathways. The lab also uses functional genomics approaches including transcriptome sequencing to study pig skeletal muscle development, and stress response in pigs. Recent efforts also include discovery of RNA editing sites in the transcriptomes of various pig tissues.

Research

Expression Quantitative Trait Loci

The application of genomic technologies is enhancing pig genetic improvement. Genome-wide analyses have revealed genomic regions harboring single nucleotide polymorphisms (SNPs) contributing significant portions of phenotypic trait variation. However, the molecular mechanisms underlying these contributions remain unclear. We aim to identify expression quantitative trait loci (eQTL) in the F2 generation of the Michigan State University Pig Resource Population (MSUPRP) to elucidate the genetic architecture of gene expression variation and gain insight on the genetic contribution underlying differences in polygenic traits. Associating gene expression profiles with genome-wide SNP markers reveals both local and distal regulators of gene expression. Local eQTL identify candidate loci directly influencing the expression of the associated gene and thus infers direct cause of variation in gene expression. Distal eQTL identify candidate gene-gene interactions where the expression of one gene may affect the expression of distant genes through transcriptional co-regulation. As sequencing costs go down, eQTL studies have the potential to be incorporated into expression-assisted evaluations in animal breeding by the use of genetical genomic selection of both phenotypic QTL and expression QTL. Our lab is currently conducting eQTL studies utilizing genotype and transcriptomic data (mRNA and miRNA) from adipose and skeletal muscle tissues to identify genomic loci influencing gene expression and economically-important pig-production phenotypes related to growth, meat quality, and carcass composition.

Transcriptional Profiling of Developing Pig Skeletal Muscle Tissue

The Ernst lab has had a long-term research interest in the mechanisms that control skeletal muscle growth and development. Development, growth and function of skeletal muscle are dynamic processes. Skeletal muscle ultimately becomes meat, the product of pig production, and skeletal muscle accounts for 40-65% of carcass weight. The number of muscle fibers in pigs, as well as most mammals, is determined prenatally. Development of skeletal muscle fibers during fetal development occurs in two waves during which myoblasts proliferate and fuse to form new fibers. Primary fibers form de novo and secondary fibers form around primary fibers. In pigs these processes take place at approximately 30-60 and 54-90 days of gestation, respectively. Our lab has collected skeletal muscle samples from an ontogeny of fetal and post-natal ages. RNA from these samples has been evaluated for transcript abundance and differential expression between ages using expression microarrays and real time quantitative PCR (qPCR). Ongoing work on this project involves examining transcript abundance using RNA-seq and microRNA-seq, as well as applying chromatin immunoprecipitation (ChIP) sequencing and other epigenetic approaches to further annotate the skeletal muscle transcriptome.

RNA Editing

Among the complex ways in which animals can regulate the expression of transcripts, endogenous RNA editing has been shown to be widespread, catalyzed primarily by the nuclear expressed family of adenosine deaminase acting on RNA (ADAR) proteins that perform single adenosine to inosine transitions along premature RNA transcripts. It remains unknown to what degree transcriptome-wide RNA editing exists in livestock species and its overall effect on controlling complex traits. We have built bioinformatic software to streamline the RNA editing detection process from whole genome sequencing and RNA-seq data and have begun to apply it to the pig model, observing inherent associations between candidate RNA editing sites and swine-specific SINE retrotransposons. This work is crucial to understanding the extent to which RNA editing contributes to single nucleotide variation among swine transcriptomes, and ongoing work of ours to analyze the “editomes” of various species can reveal new insights into how distinct retrotransposon sequences influence RNA editing patterns.

Candidate Gene Association

Our lab uses several different pig populations to evaluate genetic variation associated with candidate genes. Most of the genes we study are selected based on their map position within regions of quantitative trait loci (QTL) identified for phenotypic traits in our Duroc x Pietrain resource population. Single nucleotide polymorphisms (SNPs) in candidate genes are either identified in our lab or obtained from the literature, and SNP genotypes are associated with phenotypes. Recent genes that we have evaluated include IGFBP2, CRHR2, PRKAG3 and LEPR. For some genes, we also evaluate transcript abundance in longissimus dorsi muscle, subcutaneous fat and/or liver samples from our resource population pigs.

Selected Publications

  1. Bernal-Rubio, Y.L., J.L. Gualdron-Duarte, R.O. Bates, C.W. Ernst, D. Nonneman, G.A. Rohrer, D.A. King, S.D. Shackelford, T.L. Wheeler, R.J.C. Cantet and J.P. Steibel. 2016. Meta-analysis of genome-wide association from genetic prediction models. Anim. Genet. 47:36-48.

  2. Gualdron Duarte, J.L., R.J. Cantet, Y.L. Bernal-Rubio, R.O. Bates, C.W. Ernst, N.E. Raney, A. Rogberg-Muñoz and J.P. Seibel. 2016. Refining genomewide association for growth and fat deposition traits in an F2 pig population. J. Anim. Sci. 94:1387-1397.

  3. Peñagaricano, F., B.D. Valente, J.P. Steibel, R.O. Bates, C.W. Ernst, H. Khatib and G.J. Rosa. 2015. Exploring causal networks underlying fat deposition and muscularity in pigs through the integration of phenotypic, genotypic and transcriptomic data. BMS Syst. Biol. 9:58.

  4. Prasongsook, S., I. Choi, R.O. Bates, N.E. Raney, C.W. Ernst and S. Tumwasorn. 2015. Association of Insulin-like growth factor binding protein 2 genotypes with growth, carcass and meat quality traits in pigs. J. Anim. Sci. Technol. 57:31.

  5. Schroyen, M., J.P. Steibel, J.E. Koltes, I. Choi, N.E. Raney, C. Eisley, E. Fritz-Waters, J.M. Reecy, J.C. Dekkers, R.R. Rowland, J.K. Lunney, C.W. Ernst and C.K Tuggle. 2015. Whole blood microarray analysis of pigs showing extreme phenotypes after a porcine reproductive and respiratory syndrome virus infection. BMC Genomics. 16:516.

  6. Wang, Y., Y. Zhao, J. Li, H. Liu, C.W. Ernst, X. Liu, G. Liu, Y. Xi and M. Lei. 2015. Evaluation of housekeeping genes for normalizing real-time quantitative PCR assays in pig skeletal muscle at multiple developmental stages. Gene. 565:235-241.

  7. Huang, Y., R.O. Bates, C.W. Ernst, J.S. Fix and J.P. Steibel. 2014. Estimation of US Yorkshire breed composition using genomic data. J. Anim. Sci. 92:1395-1404.

  8. Arceo, M.E., C.W. Ernst, J.K. Lunney, I. Choi, N.E. Raney, T. Huang, C.K. Tuggle, R.R.R. Rowland and J.P. Steibel. 2013. Characterizing differential individual response to Porcine Reproductive and Respiratory Syndrome Virus infection through statistical and functional analysis of gene expression. Frontiers in Genetics (Livestock Genomics). 3:321.

  9. Ernst, C.W. and J.P. Steibel. 2013. Molecular advances in QTL discovery and application in pig breeding. Trends Genet. 29:215-224.

  10. Badke, Y.M., R.O. Bates, C.W. Ernst, C. Schwab, and J.P. Steibel. 2012. Estimation of linkage disequilibrium in four US pig breeds. BMC Genomics. 13:24

  11. Choi, I., R.O. Bates, N.E. Raney, J.P. Steibel and C.W. Ernst. 2012. Evaluation of QTL for carcass merit and meat quality traits in a US commercial Duroc population. Meat Science. 92:132-138.

  12. Kim, K.S., S.W. Kim, N.E. Raney and C.W. Ernst. 2012. Evaluation of BTA1 and BTA5 QTL regions for growth and carcass traits in American and Korean cattle. Asian-Aust. J. Anim. Sci. 25:1521-1528.

  13. Choi, I., J.P. Steibel, R.O. Bates, N.E. Raney, J.M. Rumph and C.W. Ernst. 2011. Identification of carcass and meat quality QTL in an F2 Duroc x Pietrain pig resource population using different least-squares analysis models. Frontiers in Genetics (Livestock Genomics). 2:18.

  14. Sollero, B.P., S.E.F. Guimarães, V.D. Rilington, R.J. Tempelman, N.E. Raney, J.P. Steibel, J.D. Guimarães, P.S. Lopes, M.S. Lopes and C.W. Ernst. 2011. Transcriptional profiling during foetal skeletal muscle development of Piau and Yorkshire-Landrace crossbred pigs. Anim. Genet. 42:600-612. (Epub ahead of print 24 March 2011)

  15. Steibel, J.P., R.O. Bates, G.J.M. Rosa, R.J. Tempelman, V.D. Rilington, A. Ragavendran, N.E. Raney, A.M. Ramos, F.F. Cardoso, D.B. Edwards and C.W. Ernst. 2011. Genome-wide linkage analysis of global gene expression in loin muscle tissue identifies candidate genes in pigs. PLoS ONE. 6:e16766.

  16. Choi, I., J.P. Steibel, R.O. Bates, N.E. Raney, J.M. Rumph and C.W. Ernst. 2010. Application of alternative models to identify QTL for growth traits in an F2 Duroc x Pietrain pig resource population. BMC Genetics. 11:97.

  17. Steibel, J.P., M. Wysocki, J.K. Lunney, A.M. Ramos, Z.-L. Hu, M.F. Rothschild and C.W. Ernst. 2009. Assessment of the swine protein-annotated oligonucleotide microarray. Animal Genetics. 40:883-893.

  18. Edwards, D.B., C.W. Ernst, R.J. Tempelman, G.J.M. Rosa, N.E. Raney, M.D. Hoge and R.O. Bates. 2008. Quantitative trait loci mapping in an F2 Duroc x Pietrain resource population: I. Growth traits. J. Anim. Sci. 86:241-253.

  19. Edwards, D.B., C.W. Ernst, N.E. Raney, M.E. Doumit, M.D. Hoge and R.O. Bates. 2008. Quantitative trait locus mapping in an F2 Duroc x Pietrain resource population: II. Meat quality traits. J. Anim. Sci. 86:254-266.

  20. Martinez-Montemayor, M.M., G.M. Hill, N.E. Raney, V.D. Rilington, R.J. Tempelman, J.E. Link, C.P. Wilkinson and C.W. Ernst. 2008. Gene expression profiling in hepatic tissue of newly weaned pigs fed pharmacological zinc and phytase supplemented diets. BMC Genomics. 9:421.

Additional publications may be found at ResearchGate, PubMed, and Google Scholar

Members

Dr. Cathy Ernst
Principle Investigator
Email: ernstc@msu.edu

I started my research program at MSU in 1997 and I am currently a professor of Animal Science. I also hold a partial administrative appointment as Director of the MSU interdepartmental Genetics Graduate Program. Nationally, I serve as Pig Genome Co-Coordinator for the USDA National Animal Genome Research Program (NRSP-8), and I serve as a Section Editor for the Journal of Animal Science. Before starting my faculty position, I received my MS from Iowa State University and my PhD from The Ohio State University, and did postdoctoral research at the USDA Meat Animal Research Center in Clay Center, NE. In addition to research, I teach an undergraduate genetics course, an undergraduate biotechnology seminar, and a graduate scientific writing course. Outside of work, I am chauffeur for my teenage daughter, and spend many hours sitting at band performances.

Deborah Velez-Irizarry
Animal Science PhD Candidate
Email: velezdeb@msu.edu

I am a PhD candidate of Animal Science, Breeding and Genetics Group. I completed my Masters Degree in 2012 at the University of Puerto Rico, Mayaguez Campus and was awarded a USDA NIFA National Needs Fellowship to pursue a PhD at Michigan State University. My research at Puerto Rico focused on identifying genetic markers within the bovine calpastatin and calpain genes in commercial cattle and their association with meat quality phenotypes. At MSU I research quantitative methods for high throughput transcriptional profiling to uncover the genetic control of gene expression variation in our pig resource population. Through the use of expression QTL mapping and allele specific expression we aim to identify local and distant regulators of gene expression that show joint association to complex trait phenotypes.

Kaitlyn Daza
Animal Science PhD Candidate
Email: perrykai@msu.edu

I’m currently a PhD candidate in the Department of Animal Science’s Animal Breeding and Genetics Group, and a recipient of the USDA NIFA National Needs Fellowship (2013 – 2016). I earned a B.S. in Animal Science from MSU in 2013, and my previous research experience studied dairy cattle feeding behavior at the William H. Miner Agricultural Research Institute in Chazy, NY (Summer 2013). My current research focuses on understanding the effects of microRNA regulation on meat quality and carcass phenotypes in pigs utilizing GWAS, regulatory network analysis, and molecular genetics techniques. When I’m not working on research, I enjoy spending time with my husband, friends, and family, and adventuring new parks and trails with my dog, Willow.

Nancy Raney
Lab Manager
Email: raney@msu.edu

I have been the lab manager for the Ernst lab since 1997 and am also lab manager for two other faculty members. I received my BS and MS from the University of Kentucky. In addition to conducting research, I am responsible for overseeing the routine functioning of the laboratory as well as training students. When I’m not at work, I’m busy trying to keep up with my four-year old twin girls.

Ryan Corbett
Genetics PhD student
Email: corbet35@msu.edu

My current research involves integrating genome-wide association studies, transcriptomic profiling, and network analyses to identify genetic-variant dependent gene expression in swine adipose tissue, as well as molecular mechanisms governing fat deposition. My other interests include long distance running, traveling, and solving puzzles of all varieties.

Scott Funkhouser
Genetics PhD student
Email: funkhou9@msu.edu

Much of my thesis research is focused on developing and applying software for characterizing and visualizing patterns of RNA editing among mammalian transcriptomes, revealing a wealth of under-studied single nucleotide variation that may be used to explain phenotypic variation. Additionally my research involves developing new methods for prediction of complex traits from existing sources of common genetic variants. In my free time I enjoy golfing, finding new restaurants, learning more about programming and web design, and rooting for Seattle sports teams.

Alumni

Matt Charles
Undergraduate Research Assistant
Email: charle59@msu.edu

Rachel Griffin
Undergraduate Research Assistant
Email: griff504@msu.edu