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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.