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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.