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 |