Plant and Animal Genome XXIII 2015 Meeting

Swine-related selected poster summaries

by Neil Jorgenson Swine Travel Award winner Melanie Trenhaile (UN-Lincoln)

For poster abstracts and more details, refer to on specific author names or the poster numbers.

  1. P0344 Genomics Meets Metabolomics: Developing a Systems Biology Approach to Understand the Genetic Mechanisms Affecting Complex Traits in Pigs.

    By Luca Fontanesi

    Summary: The relationships between genotype and metobotype and metabotype and phenotype were studied. Heritability varied between metabotypes. There were correlations between metabotype and phenotype. Candidate genes were identified that affect individual metabotypes.

  2. P0345 Variable Selection in Whole-Genome Association Studies Using Lasso-Based Techniques.

    By Tianfu Yang

    Summary: Adaptive lasso and lasso-based permutation tests improve success rate but not true discovery rate.

  3. P0347 Improving Porcine Transcriptome Annotation By Integrating EST, mRNAs and Whole Blood RNA-Seq Data.

    By Haibo Liu

    Summary: ESTs and mRNA from RNA-seq data were used to improve the annotation of the pig genome. UTR and isoform annotation was enhanced, and novel genes and polyA sites were discovered.

  4. P0348 Genome-Wide Association Analyses of Biological Responses to Heat Stress in Pigs.

    By Kwan-Suk Kim

    Author Summary: Rectal temperature is correlated with heat stress in pigs, and selection for this trait can be used to develop pigs that are less susceptible to heat stress.

  5. P0349 Production of GGTA1 Targeted Pigs Using TALEN-Mediated Genome Editing Technology

    Jungtaek Kang

    Summary: TALEN-mediated genome editing was used to generate α-Gal knockout and hDAF expressing transgenic pigs. These pigs can produce organs for xenotransplantation that may not undergo hyperacute rejection.

  6. P0350 Genome Wide Analysis of Porcine miRNA Editing

    By Anoop Arya

    Summary: As part of the FAANG project, miRNA editing is being studied, particularly A to I editing events, as these are the most common.

  7. P0351 Multi-Population Genomic Selection in Pigs

    By Renata Veroneze

    Summary: Using multiple populations for GBV estimation may or may not improve accuracy depending on the allelic frequencies in the validation set.

  8. P0352 Annotation-Based Whole Genomic Prediction and Selection: An Application to Feed Efficiency and Growth Traits in Pigs

    By Haja N. Kadarmideen

    Summary: Genomic prediction with several methods have comparable accuracy to each other and phenotyping. There is a linear relationship between accuracy and number of SNPs in each group.

  9. P0353 The SLA Haplotype Analysis in Yucatan Miniature Pigs in Korea

    By Dongwon Seo

    Summary: Three haplotypes were identified in the SLAI and SLAII regions, respectively, of Korean Yucatan miniature pigs. Together, there are six haplotypes: four heterozygous and two homozygous. Homozygous haplotypes can be bred for use in biomedical research.

  10. P0354 Genome Wide Distributions and Functional Characterization of Copy Number Variations Between Chinese and Western Pigs

    By Hongyang Wang

    Summary: Novel CNVs were discovered that were generated during domestication. Many were specific to Chinese or Western breeds due to the emphasis of different traits during selection.

  11. P0355 Twenty Years of Artificial Directional Selection Have Shaped the Genome of the Italian Large White Pig Breed

    By Luca Fontanesi

    Summary: Twenty years of selection substantially modified the genome of the Italian Large White pig population, and allelic frequencies of four out of five SNPs studied showed evidence of selection in the direction favorable for production traits.

  12. P0356 Analyzing the Muscle Transcriptome and the Splicing Variants of Pigs with Divergent Lipid Phenotypes Through RNA-Seq

    By Angela Canovas

    Summary: Ninety-six genes and 30 splice variants were differentially expressed between pigs with extreme high and low fatness phenotypes. Lipid metabolism and fatty acid biosynthesis were enriched functions among these genes. Forty-two cis- and 50 trans- eQTL were identified.

  13. P0357 Whole Genome-Wide Detection of Selection Signatures in Korean Native Black Pig from Jeju Island

    By Jaemin Kim

    Summary: Jeju black pigs (Korean native black pigs from Jeju Island) were analyzed for signatures of selection using XP-EHH, Tajima’s D, and MAF analysis. Many candidate genes under positive selection were identified.

  14. P0358 Intestinal Microbiota Profile of Pigs With and Without In-Feed Antibiotics

    By Mauricio Egidio Cantao

    Summary: Gut microbiota differences were detected between pigs fed a diet with and pigs fed a diet without included antibiotics at 65 days of age, but not at five days of age.

  15. P0359 Origin and Phylogenetic Status of the Local Ashanti Dwarf Pig (ADF) of Ghana Based on Evidence from mtDNA Analysis, MC1R and Y-Chromosome Haplotypes

    By Richard Osei-Amponsah

    Summary: ADFs are most closely related to European pigs, and signatures of selection were identified near genes affecting several various traits.

  16. P0360 Association Analyses Between Missense Variation at 70 Candidate Genes and Porcine Lipid Metabolism Traits

    By Marcel Amills

    Summary: In silico amino acid substitution prediction tools do not yield consistent predictions of the effects of missense polymorphisms.

  17. P0361 Genetic Analysis of the Response to ACTH in Pigs, Relationships with Robustness Traits

    By Pierre Mormede

    Summary: Selection for a response in plasma cortisol levels to ACTH injection results in pigs with increased HPA axis activity, a trait that may improve performance in some reproductive, growth, and carcass traits.

  18. P0363 Gut Microbiota in Swine: Composition, Genetic Parameters, and Links with Immunity and Production Traits

    By Claire Rogel-Gaillard

    Summary: Gut microbiota composition was studied along with links to traits such as body weight and ADG. Looking at gut microbiota along with host genetics and zootechnical and health traits will provide insight into forces shaping animal performance.

  19. P0365 Genome-Wide DNA Methylation Profiles of Fast-Growing and Slow-Growing Weaning Pigs

    By Woori Kwak

    Summary: Methylation patterns were compared in small intestine and liver of fast and slow growing nursery pigs. Insulin receptor and axonal guidance signaling pathway were enriched in liver.

  20. P0366 Beyond GWAS: A Gene-Transcription Factor Network for Number of Teats in Pigs

    By Lucas L. Verardo

    Summary: A GWAS was performed for number of teats using Bayesian methods, candidate genes were identified, and a candidate gene - transcription factor network was constructed. This increased understanding of gene interactions involved in number of teat determination.

  21. P0367 Genomic Analysis of the Interaction Between Energy Intake and SNP Genotypes on Age at Puberty

    By Melanie Trenhaile

    Summary: Restricting energy intake during gilt development positively affects sow fertility. SNPs interacting with diet to influence age at puberty were identified, and candidate genes were located in these regions.

  22. P0368 A Candidate Gene-Transcription Factor Network for Number of Stillborn Piglets

    By Simone Guimaraes

    Summary: A GWAS was performed for number of stillborn piglets using Bayesian methods, candidate genes were identified, and a candidate gene – transcription factor network was constructed. This increased understanding of gene interactions involved in number of stillborn piglets determination and was helpful in identifying the most probably candidate genes.

  23. P0369 MiR-195/497 Inhibited Myoblast Proliferation through Targeting Igflr, Insr and Cyclin Related Genes and Were Negatively Transcriptional Regulated By NF-Kb

    By Xinyun Li

    Summary: miR 195 and 497 increase in longissimus muscle cells as pigs go through fetal development. Results indicate their function could be inhibiting myoblast proliferation through various proteins and genes, and their expression is negatively regulated by NF-Kb.

  24. P0370 A Study of Vertebra Number in Pigs Confirms the Effect of Vertnin and Reveals Additional QTL

    By Gary A. Rohrer

    Summary: GWAS were done for number of ribs, lumbar vertebrae, and thoracolumbar vertebrae. Several regions with effects were found. Large effect regions changed number of ribs or lumbar vertebrae, and this caused a change in thoracolumbar vertebrae, with one exception on SSC18, which affected number of ribs and lumbar vertebrae without changing number of thoracolumbar vertebrae.

  25. P0371 Validation of Genetic Markers for Pig Resistance to PRRSV Infection

    By Pengxia Niu

    Summary: This study validated three markers previously identified as candidate genes for defense against PRRS. GBP1 genotype was associated with growth, viremia, and immune response, CD163 genotype was associated with growth and viremia, and MX1 genotype was associated with immune response for at least one time point.

  26. P0372 Identification of QTL Responsible for Immune Response to Porcine Reproductive and Respiratory Syndrome (PRRS) Virus Infection

    By Igseo Choi

    Author Summary: GWAS was done with pigs with cleared or persistent PRRSV infection. A large effect QTL was identified on SSC4 21 days post infection, confirming a previously identified QTL. Different genes play a role in viremia at 21 vs. 42 days post infection. The largest QTL identified was on SSC18 at 42 days post infection.

  27. P0373 The Recent Update of the Swine Leukocyte Antigen (SLA) Nomeclature System

    By Jun Heon Lee

    Summary: The SLA nomenclature committee validates newly identified SLA sequences, assigns nomenclatures, and manages a SLA database. This is critical to swine immunology and health research, vaccine improvement, and the use of pigs as large animal models in transplantation studies.

  28. P0374 Swine Leukocyte Antigen Class-II Region is Associated with Variation in Porcine Circovirus 2b Susceptibility

    By Emily Tosky

    Author Summary: A QTL in the SLA II region was identified that is associated with PCV2b susceptibility. Associations between viremia and genotype and viremia and ADG have been confirmed in natural infections.

  29. P0376 Identification of Functional Polymorphisms in the Coding Sequence of Swine Toll-Like Receptors

    By Armand Sanchez

    Author Summary: Variation was found in coding regions of toll-like receptors, and many made changes that could have functional consequences. This huge amount of variation could explain differences in immune response.


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