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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Livestock Bio-Systems » Research » Publications at this Location » Publication #323691

Title: Development of resources and tools for mapping genetic sources of phenotypic variation

item CIOBANU, DANIEL - University Of Nebraska
item TOSKY, EMILY - University Of Nebraska
item OLSON, SEAN - University Of Nebraska
item TRENHAILE, MELANIE - University Of Nebraska
item Lents, Clay
item Smith, Timothy - Tim
item Nonneman, Danny - Dan
item Rohrer, Gary
item CHIN, JASON - Pacific Biosciences Inc
item MILLER, PHILLIP - University Of Nebraska
item BURKEY, THOMAS - University Of Nebraska
item SPANGLER, MATTHEW - University Of Nebraska
item RIETHOVEN, JEAN-JACK - University Of Nebraska
item PLASTOW, GRAHAM - University Of Alberta
item KACHMAN, STEPHEN - University Of Nebraska

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 1/9/2016
Publication Date: 1/9/2016
Citation: Ciobanu, D.C., Tosky, E., Olson, S., Trenhaile, M., Lents, C.A., Smith, T.P.L., Nonneman, D., Rohrer, G.A., Chin, J., Miller, P.S., Burkey, T., Spangler, M.L., Riethoven, J.-J., Plastow, G.S., Kachman, S.D. 2016. Development of resources and tools for mapping genetic sources of phenotypic variation [abstract]. Plant and Animal Genome XXIV Conference Proceedings. Abstract #W914.

Interpretive Summary:

Technical Abstract: Commercial and experimental genetic resources were established and investigated for a range of reproductive and disease susceptibility phenotypes. The phenotyping efforts were accompanied with RNA and whole genome sequencing and novel assemblies of the swine genome. The efforts were complemented with novel statistical approaches, such as Bayes IM, that integrates Bayesian principles, haplotyping, and interval mapping to explore genetic variation of multiple traits. Specifically, sources of variation in expression of puberty and fertility were investigated by RNAseq of hypothalamic arcuate nucleus, various GWAS approaches, and genome sequencing of sires associated with early and late puberty daughters. Various subsets of SNPs from major 1-Mb windows that explained the largest proportions of variation in the training populations were employed to estimate GPVs in the evaluation data sets in order to assess the potential of genomic information to explain phenotypic variation for age at puberty. In the disease area, a major QTL for PCV2 viremia previously reported was fine mapped on a novel 29 Mb scaffold based on long sequencing reads while gene prediction and annotation provided potential candidates responsible for the phenotypic variation. In addition, new PCV2 challenges targeting pigs of different QTL genotypes in experimentally infected and vaccinated animals confirmed previous results and provided evidence of the host genetic role in viral replication.