Effect of DNA Markers in Nebraska Selection Lines

1 Summary DNA from 57 generation-28 boars that had sired progeny in the NE selection and control lines was submitted to GeneSeek Inc., where genotypes for eight Single Nucleotide Polymorphic Markers (SNPs) affecting economic traits in pigs were determined. Three markers are reported to be associated with growth and composition of growth, three with meat quality, and two with number of live pigs per litter. Frequencies of marker alleles were estimated in two selection lines and in their respective controls to determine whether selection had increased the frequencies of alleles associated with increased performance. Relationships of boar marker genotype with growth, backfat, and loin eye area were studied by regressing both boar phenotype and progeny phenotype on the number of favorable alleles in the boar's genotype. Frequencies of markers affecting reproduction (ESR and EPOR) were inconsistent with the selection background of the lines. Frequencies of alleles of CCKAR and MC4R, markers that affect growth and composition of growth, in selection and control lines are consistent with observed selection responses, suggesting that the allele that decreased backfat was being selected for. Regression analyses were consistent with that result. There was little evidence there had been selection for meat quality markers in these lines. The study demonstrated that selection for markers in some populations may not produce desired responses.