title: Genome-wide association study of swine farrowing traits. Part I: genetic and genomic parameter estimates.
abstract: The primary objective of this study was to determine genetic and genomic parameters among swine (Sus scrofa) farrowing traits. Genetic parameters were obtained using MTDFREML. Genomic parameters were obtained using GENSEL. Genetic and residual variances obtained from MTDFREML were used as priors for the Bayes C analysis of GENSEL. Farrowing traits included total number born (TNB), number born alive (NBA), number born dead (NBD), number stillborn (NSB), number of mummies (MUM), litter birth weight (LBW), and average piglet birth weight (ABW). Statistically significant heritabilities included TNB (0.09, P = 0.048), NBA (0.09, P = 0.041), LBW (0.20, P = 0.002), and ABW (0.26, P < 0.0001). Statistically significant genetic correlations included TNB-NBA (0.97, P < 0.0001), TNB-LBW (0.74, P < 0.0001), NBA-LBW (0.56, P < 0.0017), NSB-LBW (0.87, P < 0.0395), and LBW-ABW (0.63, P < 0.0002). Genetic parameters are similar to others found in the literature. The proportion of phenotypic variance explained by genomic markers (GP) generated by GENSEL was TNB (0.04), NBA (0.06), NBD (0.00), NSB (0.01), MUM (0.00), LBW (0.11), and ABW (0.31). Limited information is available in the literature about genomic parameters. Only the GP estimate for NSB is significantly lower than what has been published. The GP estimate for ABW is greater than the estimate for heritability found in this study. Other traits with significant heritability had GP estimates half the value of heritability. This research indicates that significant genetic markers will be found for TNB, NBA, LBW, and ABW that will have either immediate use in industry or provide a roadmap to further research with fine mapping or sequencing of areas of significance. Furthermore, these results indicate that genomic selection implemented at an early age would have similar annual progress as traditional selection, and could be incorporated along with traditional selection procedures to improve genetic progress of litter traits.
authors.affiliation: U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE 68933, USA. Jim.Schneider@ARS.USDA.Gov
authors.forename: J F
authors.initials: JF
authors.lastname: Schneider
authors.forename: L A
authors.initials: LA
authors.lastname: Rempel
authors.forename: G A
authors.initials: GA
authors.lastname: Rohrer
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D001947:Breeding / Q000379:methods*; D005260:Female; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D010298:Parity; D036801:Parturition; D010641:Phenotype; D013552:Swine / Q000235:genetics / Q000502:physiology*