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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 #288370

Title: Use of single nucleotide polymorphisms (SNP) to fine-map quantitative trait loci (QTL) in swine

item Rohrer, Gary
item Lindholm-Perry, Amanda
item Shackelford, Steven
item King, David - Andy
item Wheeler, Tommy
item Nonneman, Danny - Dan

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 11/2/2012
Publication Date: 1/12/2013
Citation: Rohrer, G.A., Lindholm-Perry, A.K., Shackelford, S.D., King, D.A., Wheeler, T.L., Nonneman, D. 2013. Use of single nucleotide polymorphisms (SNP) to fine-map quantitative trait loci (QTL) in swine [abstract]. Plant and Animal Genome XXI Conference Proceedings. Abstract #W047.

Interpretive Summary:

Technical Abstract: Mapping quantitative trait loci (QTL) in swine at the US Meat Animal Research Center has relied heavily on linkage mapping in either F2 or Backcross families. QTL identified in the initial scans typically have very broad confidence intervals and further refinement of the QTL’s position is needed before the results can be applied in commercial production. The confidence interval is a function of marker density and number of meioses. The initial step in refining a QTL location is to genotype additional markers within the confidence interval. If a plethora of markers exists in the region, then the number of meioses will rapidly become the limiting factor. Therefore, the most effective method to fine-mapping QTL adds genetic markers as well as additional phenotyped animals. To demonstrate this approach, an example of fine-mapping a QTL for pork tenderness will be presented. The QTL was discovered in a Duroc-Landrace F2 population (n=370), fine-mapped by the inclusion of SNP markers in the F2 population and a composite research population (n=532), and finally validated in two industry populations (n=509 and 905). Initial SNP were selected from a pre-existing SNP linkage map or identified by sequencing fragments across the QTL region. Later, SNP markers were discovered by sequencing candidate gene segments of animals with divergent phenotypes. The study identified five potentially causative SNPs that were in high linkage disequilibrium with each other across all populations and were the most predictive of the phenotype in all populations. USDA is an equal opportunity provider and employer.