Data from: Genome wide association study of thyroid hormone levels following challenge with porcine reproductive and respiratory syndrome virus

<p>Porcine reproductive and respiratory syndrome virus (PRRSV) causes respiratory disease in piglets and reproductive disease in sows. Piglet and fetal serum thyroid hormone (i.e., T3 and T4) levels decrease rapidly in response to PRRSV infection. However, the genetic control of T3 and T4 during infection is not completely understood. Our objective was to estimate genetic parameters and identify quantitative trait loci (QTL) for absolute T3 and/or T4 levels of piglets and fetuses challenged with PRRSV. Sera from 5-week-old pigs (N=1792) at 11 days post inoculation (DPI) with PRRSV were assayed for T3 levels (piglet_T3). Sera from fetuses (N=1267) at 12 or 21 days post maternal inoculation (DPMI) with PRRSV of sows (N=145) in late gestation were assayed for T3 (fetal_T3) and T4 (fetal_T4) levels. Animals were genotyped using 60K Illumina or 650K Affymetrix SNP panels. Heritabilities, phenotypic correlations, and genetic correlations were estimated using ASREML; genome wide association studies were performed for each trait separately using JWAS. All three traits were low to moderately heritable (10 to 16%). Phenotypic and genetic correlations of piglet_T3 levels with weight gain (0-42 DPI) were 0.26±0.03 and 0.67±0.14, respectively. Nine significant QTL were identified for piglet_T3, on Sus scrofa chromosomes (SSC) 3, 4, 5, 6, 7, 14, 15, and 17, and collectively explaining 30% of the genetic variation (GV), with the largest QTL identified on SSC5, explaining 15% of the GV. Three significant QTL were identified for fetal_T3 on SSC1 and SSC4, which collectively explained 10% of the GV. Five significant QTL were identified for fetal_T4 on SSC1, 6, 10, 13, and 15, which collectively explained 14% of the GV. Several putative immune-related candidate genes were identified, including CD247, IRF8, and MAPK8. Thyroid hormone levels following PRRSV infection were heritable and had positive genetic correlations with growth rate. Multiple QTL with moderate effects were identified for T3 and T4 levels during challenge with PRRSV and candidate genes were identified, including several immune-related genes. These results advance our understanding of growth effects of both piglet and fetal response to PRRSV infection, revealing factors associated with genomic control of host resilience.</p>
<p>Funded/supported by: US National Pork Board (NPB) (#07-233, #09-208, #10-033, #09-244, and #10-033); swine breeding companies Genus PIC plc, Newsham/Choice Genetics, FAST Genetics, Genetiporc, Genesus, Topigs Norsvin and PigGen Canada, Inc.; PRRS Coordinated Agricultural Project (PRRS-CAP); USDA-NIFA Award #2008-55620-19132; Genome Canada project #2209_F; USDA-NIFA Translational Genomics ( # 2013-68004-20362), USDA sponsored National Research Support Project 8 (NRSP-8) Swine Genome and Bioinformatics research programs; Kansas State University and USDA ARS (1245-32000-098 and 8042-32000-117); USDA ARS (# 8042–32000-102); SCINet project of the USDA ARS (0500-00093-001-00-D); USDA ARS Headquarters Postdoctoral Fellowship; Genome Canada (2014LSARP_8202); Genome Prairie (Project 346143); Genome Alberta. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Genome-wide association study results of piglet and fetal thyroid hormone levels after challenge with porcine reproductive and respiratory syndrome virus challenge.</p> <p>File Name: QTL-Data_Van_Goor.xlsx</p><p>Resource Description: Summary of GWAS results for piglet_T3, fetal_T3, and fetal_T4 with SNP information for each 1-Mb window with more than 1% of the GV. aTriiodothyronine (T3) levels were measured in piglet serum at 11 DPI (piglet_T3), in fetal serum at 12 or 21 DPMI (fetal_T3); thyroxine (T4) levels were measured in fetal serum at 12 or 21 DPMI (fetal_T4)
bChromosome (Chr) where a significant window was identified based on Sus scrofa 11.1 (Sscrofa11.1) build
cPosition (Pos) in megabases (Mb) on given chromosome where significant window was identified based on Sscrofa11.1 build
dSNP name based on Illumina Porcine SNP60 Beadchip version 2 nomenclature
eSNP location based on SSC Sscrofa11.1 build
fPosterior Probability of Inclusion (PPI): frequency with which the SNP was included in the MCMC iterations (post-burn-in)
gMinor allele frequency (MAF) of the SNP within the genotyped populations (N = 1792 animals for piglet_T3, N = 1187 animals for both fetal traits)
hNumber of annotated candidate genes within 400 Kb (200 Kb upstream and 200 Kb downstream) of SNP based on Ensembl Biomart release 107 with the Pig – Duroc (Sscrofa11.1) option accessed on August 30, 2022
</p><p>Resource Software Recommended: Excel,url: <a href="https://www.microsoft.com/en-us/microsoft-365/excel">https://www.microsoft.com/en-us/microsoft-365/excel</a> </p></li><br><li><p>Resource Title: Individual SNPs and window information from JWAS analysis QTL Data .</p> <p>File Name: Individual-SNPs_QTL-Data_Van_Goor.xlsx</p><p>Resource Description: aTrait triiodothyronine (T3) levels were measured in piglet serum at 11 DPI (piglet_T3), in fetal serum at 12 or 21 DPMI (fetal_T3); thyroxine (T4) levels were measured in fetal serum at 12 or 21 DPMI (fetal_T4)
bwindow consecutive window number for a given trait. The genome was split into 1 Mb non-overlapping windows
cchr chromosome where a significant window was identified based on Sus scrofa 11.1 (Sscrofa11.1) build
dwStart window start position in base pairs on given chromosome where the window was identified based on Sscrofa11.1 build
ewEnd window end position in base pairs on given chromosome where the window was identified based on Sscrofa11.1 build
fstart_SNP position of the first SNP in base pairs on given chromosome where the window was identified based on Sscrofa11.1 build
gend_SNP position of the last SNP in base pairs on given chromosome where the window was identified based on Sscrofa11.1 build
hnumSNP is the number of SNPs located within the 1 Mb window
iestimateGenVar is the estimated genetic variation of the 1 Mb window for the given trait
jstdGenVar is the estimated standard deviation of genetic variation of the 1 Mb window for the given trait
kprGenVar is the estimated percentage of the genetic variation of the 1 Mb window for the given trait
lPPA_t is the Posterior Probability of Acceptance: frequency with which the window was included in the MCMC iterations (post-burn-in)
</p><p>Resource Software Recommended: Excel,url: <a href="https://www.microsoft.com/en-us/microsoft-365/excel">https://www.microsoft.com/en-us/microsoft-365/excel</a> </p></li></ul><p></p>

Tags: ars, data-gov, genetics-of-immunity, gwas, np103, pigs, porcine-reproductive-and-respiratory-syndrome, snp, thyroid-hormone-levels
Organization: Department of Agriculture