Source: MICHIGAN STATE UNIV submitted to
NATIONAL ANIMAL GENOME RESEARCH PROGRAM
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
NEW
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
1001690
Grant No.
(N/A)
Project No.
MICL04114
Proposal No.
(N/A)
Multistate No.
NRSP-8
Program Code
(N/A)
Project Start Date
Oct 22, 2013
Project End Date
Sep 30, 2018
Grant Year
(N/A)
Project Director
Ernst, CA, W..
Recipient Organization
MICHIGAN STATE UNIV
(N/A)
EAST LANSING,MI 48824
Performing Department
Animal Science
Non Technical Summary
The advent of next-generation sequencing (NGS) technologies, and the associated exponential decreases in sequencing costs and increases in throughput, have produced seismic shifts in approaches towards, and the scope of, animal genomics research. However, problems remain in that all these methods require alignment with a high quality reference genome. The reference genome is only as useful to breeders and geneticists as it is complete and accurate. Many gaps in the reference need to be filled. Errors in the existing sequence alignment need to be corrected. Genes, especially genes that are unique to poultry, need to be identified and their protein-coding portions accurately mapped. Alternate forms by which the genes are expressed need to be identified and, most important, genes need to be linked with relevant functional information; that is, what does each gene do for the bird? We are using new sequencing technolgy to fill gaps and correct errors and careful bioinformatic analysis to align the sequence with genes and their functions.
Animal Health Component
20%
Research Effort Categories
Basic
90%
Applied
10%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
30432991080100%
Knowledge Area
304 - Animal Genome;

Subject Of Investigation
3299 - Poultry, general/other;

Field Of Science
1080 - Genetics;
Goals / Objectives
Advance the status of reference genomes for all species, including basic annotation of worldwide genetic variation, by broad sequencing among different lines and breeds of animals. Facilitate analysis, curation, storage, distribution and application of the enormous datasets now being generated by next-generation sequencing and related "omics" technologies with regard to animal species of agricultural interest.
Project Methods
Next generation sequencing, especially Illumina methods. Bioinformatic analysis. Optical mapping. Moleculo sequencing methods.

Progress 10/01/16 to 09/30/17

Outputs
Target Audience:Animal science graduate and undergraduate students Animal geneticists Swine and poultry industry professionals Consumers of animal products Genome biologists Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Several graduate students are receiving training and conducting research toward their PhD degrees under this project. In addition, several undergraduate students are also participating in the project and receiving research training in preparation for their future careers. How have the results been disseminated to communities of interest?Refereed journal articles; Presentations at scientific and industry meetings. What do you plan to do during the next reporting period to accomplish the goals?Complete interpretation and integration of mRNA and miRNA eQTL results for longissimus muscle samples from the MSU pig resource population in order to idenfity regulatory pathways, and publish findings. Continue evaluation of transcriptional profiles and DNA methylation patterns in pig tissues.

Impacts
What was accomplished under these goals? We have used the Michigan State University three-generation F2 Duroc-Pietrain resource population to identify expression quantitative loci (eQTL). Single nucleotide polymorphism (SNP) marker genotypes were previously obtained for the F0, F1, and a portion of the F2 pigs using the Illumina SNP60 BeadChip. For this project, total RNA from longissiums dorsi (LD) muscle samples from 176 F2 pigs was used to obtain transcriptional profiles for both mRNA and mircoRNA. The SNP and transcript data is being combined for genetical genomics analyses. For microRNA analyses, 26 significant miRNA eQTL peaks were identified, mapping to 11 chromosomes and associated with 18 miRNAs (FDR< 0.05). Seven of the 26 miRNA eQTL map to a region on SSC15 (133.9 Mb - 140.1 Mb). This is the first miRNA eQTL analysis reported in pigs, and continuing work will assess the biological effects of variation in miRNA expression on the regulation of mRNA associated with economically important pig phenotypes. For mRNA eQTL analyses, we have mapped 242 eQTL for 229 genes (FDR<0.01). Of these eQTL, 60% are local acting regulators, and 27% of the eQTL genes exhibit significantly heritable expression (FDR<0.01). A genome-wide associatin analysis of 960 animals from the same F2 population was previously performed for 67 trait phenotypes, and revealed 58 phenotypic QTL (pQTL) (FDR<0.05). Co-localization of the pQTL with mRNA eQTL identified 42 co-localized eQTL with 29 pQTL, and 64% of the colocalized eQTL were local-acting regulators. Pearson correlation between transcript expressions and phenotypic traits identified 13,481 significant gene-trait correlations for 6,848 transcripts (FDR<0.05). Of these, 164 had an associated eQTL for 94 transcripts, with 15 also co-localizing with a pQTL on SSC1, SSC6, SSC7, SSC12 or SSC15. Several pQTL for meat quality traits, including pH 24 hours post mortem, drip loss, cook yield, protein percent, and sensory panel tenderness, overall tenderness and juiciness, were localized to either an 8.8 Mb region on SSC2 or a 121 Mb region on SSC15. The colocalization analysis highlighted 16 eQTL mapping to these two genomic regions, 5 on SSC2 and 11 on SSC15. Further evaluation and validation of eQTL genes is ongoing, including integration of the mRNA eQTL and miRNA eQTL results. Another effort pursued in 2017 involved assessment of the new pig high-density genotyping array developed by Affymetrix, the AxiomTM Porcine Genotyping Array (Axiom_PigHDv1), which includes over 600K SNP markers. We used the Axiom_PigHDv1 to estimte short-range linkage disequilibrium in US pig breeds, and also to compare the new array with existing SNP panels and determine imputation accuracy. Two additional projects initiated in 2017 were to examine DNA methylation patterns and transcript abundance in pig skeletal muscle, and in pigs before and after weaning. Analysis for these projects is ongoing.

Publications

  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Casir� S, Velez-Irizarry D, Ernst CW, Raney NE, Bates RO, Charles MG, Steibel JP. 2017. Genome-wide association study in an F2 Duroc x Pietrain resource population for economically important meat quality and carcass traits. J. Anim.Sci. 95:545-558.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Choi I, Bates RO, Raney NE, Ernst CW. 2017. Association of a corticotropin-releasing hormone receptor 2 (CRHR2)polymorphism with carcass merit, meat quality and stress response traits in pigs. Canadian J. Anim. Sci. 97:536-540.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Daza KR, Steibel JP, Velez-Irizarry D, Raney NE, Bates RO, Ernst CW. 2017. Profiling and characterization of a longissimus dorsi muscle microRNA dataset from an F2 Duroc x Pietrain pig resource population. Genom. Data. 13:50-53.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Funkhouser SA, Bates RO, Ernst CW, Newcom D, Steibel JP. 2017. Estimation of genome-wide and locus-specific breed composition in pigs. Translational Anim. Sci. 1:36-44.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Funkhouser SA, Steibel JP, Bates RO, Raney NE, Schenk D, Ernst CW. 2017. Evidence for transcriptome-wide RNA editing among Sus scrofa PRE-1 SINE elements. BMC Genomics.18:360.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Velez-Irizarry D, Casiro S, Bernal Rubio YL, Bates RO, Raney NE, Steibel JP, Ernst CW. 2017. Expression QTL for longissimus dorsi muscle gene transcripts co-localized with phenotypic QTL for meat quality traits in an F2 Duroc x Pietrain resource population. Proceedings of the 36th International Society for Animal Genetics Conference, Dublin, Ireland.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Funkhouser SA, Steibel JP, Newcom D, Ernst CW. 2017. Evaluation of four US pig breeds using the Affymetrix Axiom Pig HD array. Plant and Animal Genome XV, San Diego, CA.


Progress 10/01/15 to 09/30/16

Outputs
Target Audience:Animal science graduate and undergraduate students Animal geneticists Swine and poultry industry professionals Consumers of animal products Genome biologists Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Several graduate students are receiving training and conducting research toward their PhD degrees under this project. In addition, several undergraduate students are also participating in the project and receiving research training in preparation for their future careers. How have the results been disseminated to communities of interest?Refereed journal articles; Presentations at scientific and industry meetings. What do you plan to do during the next reporting period to accomplish the goals?Complete interpretation of mRNA and miRNA eQTL results for longissimus muscle samples from the MSU pig resource population, and publish findings. Incorporate mRNA and miRNA eQTL results to idenfity regulatory pathways. Continue evaluaiton of RNA editing sites in tissues from pigs and other species.

Impacts
What was accomplished under these goals? The MSU pig resource population was established from 4 F0 Duroc sires and 15 F0 Pietrain dams and produced approximately 950 F2 offspring. This population has been used extensively for identification of quantitative trait loci (QTL) influencing growth, carcass composition and meat quality traits, as well as expression QTL (eQTL) for loin muscle tissue to identify potential candidate genes. Previous studies utilized microsatellite markers, and continuation of this work involves analysis of single nucleotide polymorphism (SNP) marker genotypes for the population using a combination of high density (60K, Illumina SNP60 BeadChip) and low density (8.5K, GeneSeek Genomic Profiler for Porcine LD) panels. The F0, F1 and approximately 1/3 of the F2s were genotyped with the 60K panel, while the remaining F2s were genotyped with the low density panel. Imputation of all F2 SNP genotypes was completed in collaboration with MSU colleagues, and SNP genotypes have been used for genome-wide association studies for growth, carcass composition, and meat quality phenotypes. RNAseq technology has been used to obtain transcriptome sequences for 168 longissimus muscle samples from the resource population in order to refine the eQTL analysis for the population. Analysis of this data has revealed novel coding SNPs, including SNPs exhibiting allele-specific expression bias. Sequencing of small RNAs has also been completed for 174 F2 longissimus muscle samples in order to reveal microRNA regulation of gene expression, resulting in identification of 295 mature miRNA expression profiles. An eQTL analysis was performed with the miRNA profiles revealing 26 significant eQTL associated with 18 miRNAs. In addition to eQTL analyses, evaluations have been extended to development of methods for analysis of RNA editing sites. Whole genome sequence along with transciptome sequence for three tissues was obtained for a single pig, revealing over 8500 putatively edited sites including those exhibiting tissue specificity. Of these 8500 sites, 75% exhibited a canonical A-to-G edit expected for modifications catalyzed by the enzyme adenosine deaminase acting on RNA (ADAR) . In addition, the majority of A-to-G mismatches were located within repetitive sequences, with most of these occuring in the PRE-1 retrotransposon.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Bernal-Rubio YL, Gualdron-Duarte JL, Bates RO, Ernst CW, Nonneman D, Rohrer GA, King DA, Shackelford SD, Wheeler TL, Cantet RJC, Steibel JP. 2016. Meta-analysis of genome-wide association from genetic prediction models. Anim. Genet. 47:36-48.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Bernal-Rubio YL, Gualdron-Duarte JL, Bates RO, Ernst CW, Nonneman D, Rohrer GA, King DA, Shackelford SD, Wheeler TL, Cantet RJC, Steibel JP. 2015. Implementing meta-analysis from genome-wide association studies for pork quality traits. J. Anim. Sci. 93:5607-5617.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Gualdron Duarte JL, Cantet RJ, Bernal-Rubio YL, Bates RO, Ernst CW, Raney NE, Rogberg-Mu�oz A, Seibel JP. 2016. Refining genomewide association for growth and fat deposition traits in an F2 pig population. J. Anim. Sci. 94:1387-1397.


Progress 10/01/14 to 09/30/15

Outputs
Target Audience:Animal science graduate and undergraduate students; Animal geneticists; Swine and poultry industry professionals; Consumers of animal products; Genome biologists Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Several graduate students are receiving training and conducting research toward their PhD degrees under this project. In addition, several undergraduate students are also participating in the project and receiving research training in preparation for their future careers. How have the results been disseminated to communities of interest?Refereed journal articles; Industry reports; Presentations at scientific conferences and industry meetings. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? The MSU pig resource population was established from 4 F0 Duroc sires and 15 F0 Pietrain dams and produced approximately 950 F2 offspring. This population has been used extensively for identification of quantitative trait loci (QTL) influencing growth, carcass composition and meat quality traits, as well as expression QTL (eQTL) for loin muscle tissue to identify potential candidate genes. Previous studies utilized microsatellite markers, and continuation of this work involves analysis of single nucleotide polymorphism (SNP) marker genotypes for the population using a combination of high density (60K, Illumina SNP60 BeadChip) and low density (8.5K, GeneSeek Genomic Profiler for Porcine LD) panels. The F0, F1 and approximately 1/3 of the F2s were genotyped with the 60K panel, while the remaining F2s were genotyped with the low density panel. Imputation of all F2 SNP genotypes was completed, and SNP genotypes are being used for genome-wide association studies. RNAseq technology has been used to obtain transcriptome sequences for 160 longissimus muscle samples from the resource population in order to refine the eQTL analysis for the population. This set of samples is being used to evaluate statistical models for optimizing eQTL discovery. Analysis of this data has revealed novel coding SNPs, including SNPs exhibiting allele-specific expression bias. Sequencing of small RNAs has also been completed on 24 samples in order to reveal microRNA regulation of gene expression. Sequencing is underway for 152 additional miRNA samples. In addition to eQTL analyses, evaluations have been extended to development of methods for analysis of RNA editing sites. A complete genome sequence was obtained for an F2 pig from the MSU resource population, and transcriptome sequences for three tissues from this animal were used to detect RNA editing sites, including sites exhibiting tissue specificity. The Michigan Station also contributed to the national PRRS Host Genetics Consortium through use of a whole genome microarray (Pigoligoarray) to identify genes expressed at 0, 4 and 7 days post-infection (using a blocked reference design with time 0 as reference) in pigs from four phenotypic groups [high virus high growth (HvHg), Hv low growth (HvLg), low virus Hg (LvHg), LvLg] in order to reveal genes and pathways contributing to response to PRRS virus infection.

Publications

  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Prasongsook S, Choi I, Bates RO, Raney NE, Ernst CW, Tumwasorn S. 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.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: 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.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: 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.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Yang, W., C. Chen, J.P. Steibel, C.W. Ernst, R.O. Bates, L. Zhou and R.J. Tempelman. 2015. A comparison of alternative random regression and reaction norm models for whole genome predictions. J. Anim. Sci. 93:2678-2692.


Progress 10/22/13 to 09/30/14

Outputs
Target Audience: Animal science graduate and undergraduate students; Animal geneticists; Swine and poultry industry professionals; Consumers of animal products; Genome biologists Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Several graduate students are receiving training and conducting research toward their PhD degrees under this project. In addition, several undergraduate students are also participating in the project and receiving research training in preparation for their future careers. How have the results been disseminated to communities of interest? Refereed journal articles; Industry reports; Presentations at scientific conferences and industry meetings. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? The MSU pig resource population was established from 4 F0 Duroc sires and 15 F0 Pietrain dams and produced approximately 950 F2 offspring. This population has been used extensively for identification of quantitative trait loci (QTL) influencing growth, carcass composition and meat quality traits, as well as expression QTL (eQTL) for loin muscle tissue to identify potential candidate genes. Previous studies utilized microsatellite markers, and continuation of this work involves obtaining single nucleotide polymorphism (SNP) marker genotypes for the population using a combination of high density (60K, Illumina SNP60 BeadChip) and low density (8.5K, GeneSeek Genomic Profiler for Porcine LD) panels. The F0, F1 and approximately 1/3 of the F2s were genotyped with the 60K panel, while the remaining F2s were genotyped with the low density panel. Imputation of all F2 SNP genotypes was completed, and SNP genotypes are being used for genome-wide association studies. RNAseq technology has been used to obtain transcriptome sequences for 24 longissimus muscle samples from the resource population in order to refine the eQTL analysis for the population. This set of samples is being used to evaluate statistical models for optimizing eQTL discovery. Analysis of this data has revealed novel coding SNPs, including SNPs exhibiting allele-specific expression bias. Sequencing of small RNAs has also been completed on these 24 samples in order to reveal microRNA regulation of gene expression. Sequencing is underway for 152 additional longissimus muscle RNA and miRNA samples. In addition to eQTL analyses, evaluations have been extended to development of methods for analysis of RNA editing sites. A complete genome sequence was obtained for an F2 pig from the MSU resource population, and the longissimus muscle transcriptome sequence for this animal was used to detect RNA editing sites, revealing a total of 686 candidate RNA editing sites. In 2014 the Michigan Station also contributed to the national PRRS Host Genetics Consortium through use of a whole genome microarray (Pigoligoarray) to identify genes expressed at 0, 4 and 7 days post-infection (using a blocked reference design with time 0 as reference) in pigs from four phenotypic groups [high virus high growth (HvHg), Hv low growth (HvLg), low virus Hg (LvHg), LvLg] in order to reveal genes and pathways contributing to response to PRRS virus infection.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Chang, C.-F., E.N. Schock, E.A. OHare, J. Dodgson, H.H. Cheng, W.M. Muir, R.E. Edelmann, M.E. Delany and S.A. Brugmann. 2014. The cellular and molecular etiology of the craniofacial defects in the avian ciliopathic mutant, talpid2. Development, 141:3003-3012.
  • Type: Book Chapters Status: Published Year Published: 2014 Citation: Dodgson, J.B. 2014. Genomics of food animals. In N. Van Alfen (ed.), Encyclopedia of Agriculture and Food Systems, Elsevier, Oxford, UK, pp. 433-453.
  • Type: Book Chapters Status: Published Year Published: 2014 Citation: Dodgson, J.B. 2014. Chapter 1: Avian Genomics. In C. Scanes, (ed.), Sturckies Avian Physiology, 6th ed., Elsevier, London, UK, pp. 3-13.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Badke, Y.M., Bates, R.O., Ernst, C.W., Fix J., and Steibel, J.P. 2014. Accuracy of estimation of genomic breeding values in pigs using low density genotypes and imputation. G3. 4:623-631.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Gualdron Duarte, J.L., Cantet, R.J., Bates, R.O., Ernst, C.W., Raney, N.E., and Seibel, J.P. 2014. Rapid screening for phenotype-genotype associations by linear transformations of genomic evaluations. BMC Bioinformatics. 15:246.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Bernal Rubio, Y.L., Gualdr�n Duarte, J.L., Bates, R. O., Ernst, C. W., Nonneman, D., Rohrer, G. A., King, A., Shackelford, S.D. , Wheeler, T.L., Cantet, R.J.C., and Steibel, J.P. 2014. Meta-analysis genomewide association of pork quality traits: Ultimate pH and shear force. J. Anim. Sci. 92(E-Suppl. 2):11.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Velez-Irizarry, D., Ernst, C.W., Lunney, J.K., Raney, N.E., and Steibel, J.P. 2014. Prediction of porcine reproductive and respiratory syndrome virus serum viral level phenotype from gene expression profiles. J. Anim. Sci. 92(E-Suppl. 2):121.