Table 1

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

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


Sample usage plans for current phenotypic information and projected deeper phenotypic data possible with additional tests and funding.

Lunney et al. BMC Proceedings 2011 5(Suppl 4):S30   doi:10.1186/1753-6561-5-S4-S30

Open Data