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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC AND GENOMIC APPROACHES TO IMPROVE EFFICIENCY OF SWINE PRODUCTION AND PRODUCT QUALITY Title: Genome wide association study of age at puberty in swine

Authors
item Schneider, James
item Nonneman, Danny
item Wiedmann, Ralph
item Rohrer, Gary

Submitted to: Journal of Animal Science Supplement
Publication Type: Abstract Only
Publication Acceptance Date: March 5, 2012
Publication Date: July 1, 2012
Citation: Schneider, J.F., Nonneman, D.J., Wiedmann, R.T., Rohrer, G.A. 2012. Genome-wide association study of age at puberty in swine [abstract]. Journal of Animal Science. 90 (Supplement 3):19 (Abstract #M41).

Technical Abstract: Age at puberty (AP) is an economically important trait in swine production. Reducing AP provides opportunities to lower the cost of gilt development, reduce age at first farrowing, increase litter size, and improve sow longevity. This analysis was designed to identify quantitative trait loci (QTL) associated with AP. Heat detection with boar contact began at 140 d of age and ended at 230 d of age. Seven hundred fifty seven gilts representing generations 5-8 of a Landrace-Duroc-Yorkshire cross reached puberty during 7 breeding seasons and were genotyped using a 60k chip. SNP were removed that met criteria including minor allele frequency < 0.05, call rates < 0.95, and unknown location. Five animals were removed with call rates < 0.95 or that failed a Mendelian test. Bayesian methods were used to analyze 41,848 SNP. Prior estimates of variances were taken from MTDFREML with heritability = 0.32. The genomic variance priors were estimated by a preliminary run of BayesC using estimates from MTDFREML as priors. A previous estimate of Pi = 0.99 was confirmed by BayesCPi. Final BayesC using a burnin of 1000 iterations and a total chain length of 51,000 produced an estimate of 0.16 for the proportion of phenotypic variances explained by genetic markers (genomic heritability). A total of 94 QTL (5 consecutive SNP) were selected for statistical testing based on QTL variance. Testing identified 72 significant QTL including 25 at P < 0.001, 32 at P < 0.005, and 15 at the P < 0.01 level. QTL were found on all chromosomes analyzed (SSC) except 17. Chromosome 2 (SSC2) contained the most QTL with 9, followed by SSC1, SSC3, and SSC7 with 6, and SSC6, SSC10, SSC12, and SSC15 with 5 QTL each. These regions correspond to previously identified QTL (http://www.animalgenome.org/cgi-bin/QTLdb/SS/index, accessed 2/6/2012). The results of this analysis demonstrate that opportunities exist to introduce QTL into genetic improvement programs designed to reduce AP.

Last Modified: 11/23/2014