Genomewide association analysis for average birth interval and stillbirth in swine

Authors: Schneider, James; Miles, Jeremy; Brown-Brandl, Tami; Nienaber, John; Rohrer, Gary; Vallet, Jeff

Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/3/2014
Publication Date: 2/23/2015
Publication URL: http://handle.nal.usda.gov/10113/60858
Citation: Schneider, J.F., Miles, J.R., Brown-Brandl, T.M., Nienaber, J.A., Rohrer, G.A., Vallet, J.L. 2015. Genomewide association analysis for average birth interval and stillbirth in swine. Journal of Animal Science. 93(2):529-540.

Interpretive Summary: Reproductive efficiency has a great impact on the economic success of pork production. The number of pigs born alive in a litter has been shown to be one of the major components of reproduction efficiency. Stillborn pigs and average birth interval contribute to number born alive. It is the purpose of this study to better understand the underlying genetics of these traits. Significant groups of gene markers were found to be located for number of stillborn piglets ignoring the last piglet born (1), number of stillborns in the last birth position (1), and percent stillborn ignoring the last piglet (3). In addition, 13, 3, and 6 suggestive groups of gene markers were identified for number of stillborn piglets ignoring the last piglet born, number of stillborns in the last birth position, and percent stillborn ignoring the last piglet, respectively. These groups of gene markers have been shown to overlap genes known to affect these and other swine traits. Groups of genes found in the same regions provide useful information that could be used for marker-assisted selection, marker-assisted management, or genomic selection applications in commercial pig populations.

Technical Abstract: Reproductive efficiency has a great impact on the economic success of pork production. Stillborn pigs and average birth interval contribute to the number of pigs born alive in a litter. To better understand the underlying genetics of these traits, a genome-wide association study was undertaken. Samples of DNA were collected and tested using the Illumina Porcine SNP60 BeadChip from 798 parity 1 females farrowing over a 4-year period. Birth intervals and piglet birth status (stillborn or alive) were determined by videotaping each farrowing event. A total of 41,148 SNP were tested using the Bayes C option of GENSEL (version 4.61) and 1 Mb windows. These 1 Mb windows explained proportions of 0.017, 0.002, 0.032, 0.029, and 0.030 of the total variation, respectively for litter average birth interval after deletion of the last piglet in the litter, last birth interval in the litter, number of stillborn piglets ignoring the last piglet born, number of stillborns in the last birth position, and percent stillborn ignoring the last piglet. Significant 1 Mb non-overlapping SNP windows were identified by using a conservative approach requiring the 1 Mb windows to have a genetic variance >= 1.0% of the genomic variance and these were considered to be QTL. QTL were located for number of stillborn piglets ignoring the last piglet born (1), number of stillborns in the last birth position (1), and percent stillborn ignoring the last piglet (3). In addition, 2, 13, 3, and 6 suggestive 1 Mb non-overlapping SNP windows were identified for litter average birth interval after deletion of the last piglet in the litter, number of stillborn piglets ignoring the last piglet born, number of stillborns in the last birth position, and percent stillborn ignoring the last piglet, respectively. The QTL and the suggestive 1 Mb non-overlapping SNP windows when combined with information on genes found in the same regions provide useful information that could be used for marker assisted selection, marker assisted management, or genomic selection applications in commercial pig populations.