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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #391124
Research Project: Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: Large-scale cis-eQTL analysis of gene expression in blood of young healthy pigs using PigGTEx

Author
item KRAMER, LUKE - Iowa State University
item TENG, JINYAN - South China Agricultural University
item LIM, KYU-SANG - Iowa State University
item GAO, YAHUI - University Of Maryland
item YIN, HONGWEI - Chinese Academy Of Agricultural Sciences
item BAI, LIJING - Chinese Academy Of Agricultural Sciences
item Liu, Ge - George
item ZHANG, ZHE - South China Agricultural University
item FANG, LINGZHAO - University Of Edinburgh
item PLASTOW, GRAHAM - University Of Alberta
item TUGGLE, CHRISTOPHER - Iowa State University
item DEKKERS, JACK - Iowa State University

Submitted to: World Congress of Genetics Applied in Livestock Production
Publication Type: Proceedings
Publication Acceptance Date: 2/18/2022
Publication Date: 7/7/2022
Citation: Kramer, L.M., Teng, J., Lim, K., Gao, Y., Yin, H., Bai, L., Liu, G., Zhang, Z., Fang, L., Plastow, G.S., Tuggle, C.K., Dekkers, J.C. 2022. Large-scale cis-eQTL analysis of gene expression in blood of young healthy pigs using PigGTEx. World Congress of Genetics Applied in Livestock Production. Front Matter, Commun. 560, pp. 2321-2324. https://doi.org/10.3920/978-90-8686-940-4_560.
DOI: https://doi.org/10.3920/978-90-8686-940-4_560

Interpretive Summary:

Technical Abstract: RNA sequencing and high-density genotyping or whole genome sequencing can be used in tandem to identify genomic regions associated with the control of gene expression, also known as expression quantitative trait loci (eQTL) mapping. Whole blood is a convenient tissue for many purposes due to its ease of collection and relation to health. Whole blood RNA-seq data and high-density SNP array genotypes were generated from ~1,600 healthy nursery pigs as part of a study of resilience to a polymicrobial disease challenge. This data was used for genotype imputation to whole genome sequence with the reference panel and bioinformatics pipeline developed by the PigGTEx consortium to identify cis-eQTL. Cis-eQTL were typically associated with one to two genes. Chromosome 12 was enriched for cis-eQTL for gene expression in whole blood. The results provide insights into the control of gene expression in whole blood, allowing further study of its relationship with disease resilience.