Animal Science Department



Stephen D. Kachman

Date of this Version



Published in Animal Genetics 46:4 (August 2015), pp. 403–409; doi: 10.1111/age.12310


Copyright © 2015 Stichting International Foundation for Animal Genetics; published by John Wiley & Sons, Inc. Used by permission.


Genomic information could be used efficiently to improve traits that are expensive to measure, sex limited or expressed late in life. This study analyzed the phenotypic variation explained by major SNPs and windows for age at puberty in gilts, an indicator of reproductive longevity. A genome-wide association study using 56,424 SNPs explained 25.2% of the phenotypic variation in age at puberty in a training set (n = 820). All SNPs from the top 10% of 1-Mb windows explained 33.5% of the phenotypic variance compared to 47.1% explained by the most informative markers (n = 261). In an evaluation population, consisting of subsequent batches (n = 412), the predictive ability of all SNPs from the major 1-Mb windows was higher compared to the variance captured by the most informative SNP from each of these windows. The phenotypic variance explained in the evaluation population varied from 12.3% to 36.8% when all SNPs from major windows were used compared to 6.5–23.7% explained by most informative SNPs. The correlation between phenotype and genomic prediction values based on SNP effects estimated in the training population was marginal compared to their effects retrained in the evaluation population for all (0.46–0.81) or most informative SNPs (0.30–0.65) from major windows. An increase in genetic gain of 20.5% could be obtained if genomic selection included both sexes compared to females alone. The pleiotropic role of major genes such as AVPR1A could be exploited in selection of both age at puberty and reproductive longevity.

Two supplemental files are attached (below).

Lucot AG 2015 Evaluation of reduced SUPPL1.xlsx (321 kB)
Table S1. Genetic variance of age at puberty explained by 1-Mb genome windows.

Lucot AG 2015 Evaluation of reduced SUPPL2.xlsx (7546 kB)
Table S2. Genetic variance of age at puberty explained by 56,424 SNPs.