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Table 1 PRRS resistance/susceptibility traits for genome wide association studies (GWAS) and gene expression pathway analyses

From: Probing genetic control of swine responses to PRRSV infection: current progress of the PRRS host genetics consortium

Sample Trait Current phenotypic information Potential phenotypic information
Blood serum [collected at -6, 0, 4, 7, 10, 14, 21, 28, 35, 42 dpi] Virus levels PRRS Viral qPCR [4 dpi virus level, 7 dpi virus level, 0-19/21 dpi virus level (= AUC, area under curve); 28 dpi virus level] PRRSV type 1 and 2 Virus sequence, especially during reactivation Presence of other viruses
Blood serum Antibody (Ab) levels IDEXX PRRSV Ab titer PRRSV Serum Neutralizing Abs Decay of maternal anti-PCV2 Ab Ab to other microbes
Blood serum Immune Protein levels Interleukin-8 (IL-8), Interferon-γ (IFN-γ) Selected Luminex bead assays for 8 cytokines More Luminex bead assays for multiple cytokines, chemokines Broad proteomic analyses
Blood RNA (ABI Tempus tubes for RNA collected at 0, 4, 7, 10, 14, 21, 28, 35, 42 dpi) Blood gene expression Microarray (Pigoligoarray) based gene expression QPCR for selected gene expression Identification of “classifier genes” for PRRS resistance next generation sequencing analyses (RNA-seq) Alternate splicing events Bioinformatic analysis of virus/host correlated gene expression Identify eQTL
Growing pig [during infection] Weight gain (kg) Weight gain [Overall 0-42 dpi; Weight gain at peak virus replication] New trials with growth to market weight and extensive growth and pork quality analyses
Ear tissue Genomic DNA SNP genotyping (Illumina PorcineSNP60 Genotyping BeadChip) Targeted SNPs GWAS analyses Broader SNP analyses More Targeted SNPs, e.g., specific regions or candidate genes More extensive GWAS analyses including eQTL and Ref-seq data
Tonsils [at 42 dpi] Mucosal tissue; virus reservoir None PRRSV levels at 42 dpi - PRRSV persistence Gene expression with persistent virus
Oral fluids [pen samples] Virus levels PRRSV levels PRRSV type 1 and 2 Virus sequence, especially during reactivation Presence of other viruses
Oral fluids Antibody (Ab) levels IDEXX PRRSV Ab titer PRRSV Serum Neutralizing Abs Decay of maternal anti-PCV2 Ab Ab to other microbes Comparison of oral fluid versus serum responses
Oral fluids Immune Protein levels Selected Luminex bead assay for cytokines More Luminex bead assays for multiple cytokines, chemokines Broad proteomic analyses
  1. Sample usage plans for current phenotypic information and projected deeper phenotypic data possible with additional tests and funding.