Validation of QTL in Commercial-Type Pigs at USMARC

The US Meat Animal Research Center’s commercial swine resource population was a closed population maintained for 10 generations and produced over 40,000 pigs with basic phenotypic measurements. Approximately 3,000 of the most heavily phenotyped pigs as well as all boars used were genotyped with the Illumina Porcine SNP60 BeadChip and QTL discovery has been quite successful. To expedite fine-mapping and discovery of functional genetic variation, a majority of the chromosomes contributing to this population were sequenced using next-generation sequencing technology (NGS). Interrogation of the NGS results permits selection of SNP markers with potential effects on function. These markers are then tested in the resource population. In addition, the females from the original population have been mated to commercial Landrace and Yorkshire boars, grading-up the population to current industry standards. These graded-up animals are being used to validate QTL discovered in the resource population. With these resources we have tested variation discovered by NGS in positional candidate genes for association with ovulation rate and immunocrit values.

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