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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #367269
Research Project: Identifying Genomic Solutions to Improve Efficiency of Swine Production

Location: Genetics and Animal Breeding

Title: From phenotype to gene discovery: A case study of host genetics influencing porcine circovirus 2 susceptibility

Author
item WALKER, L - University Of Nebraska
item WIJESENA, H - University Of Nebraska
item SUTTON, K - University Of Nebraska
item VU, H - University Of Nebraska
item Nonneman, Danny - Dan
item Smith, Timothy - Tim
item PLASTOW, G - University Of Alberta
item KACHMAN, S - University Of Nebraska
item CIOBANU, D - University Of Nebraska

Submitted to: International Society for Animal Genetics (ISAG)
Publication Type: Abstract Only
Publication Acceptance Date: 4/1/2019
Publication Date: 7/12/2019
Citation: Walker, L., Wijesena, H., Sutton, K., Vu, H., Nonneman, D., Smith, T., Plastow, G., Kachman, S., Ciobanu, D. 2019. From phenotype to gene discovery: A case study of host genetics influencing porcine circovirus 2 susceptibility [abstract]. In proceedings: 37th International Society for Animal Genetics (ISAG). 7-12 July 2019, Lleida, Spain. p. 7. Abstract OP25.

Interpretive Summary:

Technical Abstract: Porcine Circovirus type 2 (PCV2) is the etiological agent of a group of associated diseases (PCVAD) that impact production efficiency and can lead to mortality. The objective of this research was to characterize the role of host genetics in susceptibility to PCV2. A genome-wide association of experimentally infected pigs (n = 974) genotyped with Porcine SNP60 BeadArray, provided evidence that host genetics has an important role in PCV2 susceptibility. The SNP genotypes combined explained 64% of the phenotypic variation for viral load with 2 major QTLs identified on SSC7 and SSC12. Gene annotation in the QTL regions was integrated with RNA/genome sequencing, high-density genotyping and in vitro siRNA/gene editing models to uncover genes and functional polymorphisms that could explain variation in susceptibility to PCV2. A missense polymorphism (SYNGR2 p.Arg63Cys) located in SYNGR2, was found to be responsible for the effect mapped on SSC12. The direct role of SYNGR2 in PCV2 replication was demonstrated by in vitro siRNA and gene-editing models. The QTL mapped on SSC7 is located near the swine leukocyte antigen complex class II (SLAII) locus, a region involved in antigen recognition and immune response in a variety of infectious diseases and characterized by extended LD and highly polymorphic genes. Since the Porcine SNP60 BeadArray is relatively scarce in SNPs located in SLAII region, a novel Affymetrix Axiom myDesign SNP array was designed (SowPro90, 103,476 SNPs) which saturated the SLA locus with over 3,100 SNPs (70X fold increase). This information provided critical knowledge of the effective genetic diversity in pigs and the role of this locus in viral disease susceptibility. Together this research will aid in the development of genetic tests for early identification of genetic susceptibility to PCV2 and ability to monitor genetic diversity that could lead to improvement in the general health and welfare of pigs.