Genomewide association analysis for average birth interval and stillbirth in swine

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 genomewide association study was undertaken. Samples of DNA were collected and tested using the Illumina Porcine SNP60 BeadChip from 798 females farrowing over a 4-yr period (all first parity). 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 born, 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 nonoverlapping SNP windows were identified by using a conservative approach requiring 1-Mb windows to have a genetic variance ≥1.0% of genomic variance and these were considered to be QTL. Quantitative trait loci were located for number of stillborn piglets ignoring the last piglet born (1 QTL), number of stillborns in the last birth position (1 QTL), and percent stillborn ignoring the last piglet (3 QTL). In addition, 2, 13, 3, and 6 suggestive 1-Mb nonoverlapping SNP windows were identified for litter average birth interval after deletion of the last piglet born, 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. Possible candidate genes affecting both birth interval and stillbirth included ADAMTS9 (ADAM metallopeptidase with thrombospondin type 1 motif, 9) and COL19A1 (collagen 19). Possible genes affecting only birth interval included TBC1D1 (TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1), and SEMA4C (Semaphorin 4C), and those affecting only stillbirth included NUBPL (nucleotide binding protein- like), LOC100518697 (a nostrin-like gene), and DPP10 (dipeptidyl-peptidase 10). The QTL and the suggestive 1-Mb nonoverlapping SNP windows may lead to genetic markers for marker assisted selection, marker assisted management, or genomic selection applications in commercial pig populations.