Genome-wide association study identifies genetic variants associated with single-parity reproductive loss in three...

Reproductive performance is a critical aspect of livestock production and sustainability. The number of stillbirths (NS) and mummified (NM) piglets significantly affect reproductive efficiency in swine production. Identifying and understanding the genetic architecture and candidate genes influencing these reproductive loss traits are essential for genetic inheritance studies and selective breeding programs in the swine breeding industry. To elucidate the genetic architecture of these traits, we performed a genome-wide association study (GWAS) using porcine 70 K BeadChip arrays from 1,162 Duroc, 1,783 Landrace, and 2,366 Yorkshire pigs.

Single-parity breed-specific genome-wide association (GWA) analyses revealed that SIDT2 on Chr9 was associated with NM in Duroc pigs, whereas GTF2H3, PPP1R9A, and LMTK2 on Chr14, 9, and 3, respectively, were associated with both traits in Landrace pigs. Several genes have been linked to NS and NM in Yorkshire pigs, including GRID1 (chr14), DLGAP2 (chr15), ZZEF1 (chr12), RNF17 (chr11), SEL1L2 (chr17), ASCC3 (chr1), KCND2 (chr18), AP5B1(chr2), KAT5 (chr2), and SPATS2 (chr5). Across the breeds, five genes (DLGAP2, RNF17, SEL1L2, AP5B1, and KAT5) were exclusively associated with NS, whereas the other five (SIDT2, NDUFAF5, AKAP12, RCC1L, and BIRC6) were specific to NM. In addition, eight genes (GTF2H3, PPP1R9A, LMTK2, GRID1, ZZEF1, ASCC3, KCND2, and SPATS2) were associated with both traits, suggesting shared molecular pathways involved in piglet mortality.

This study showed genetic factors affecting reproductive performance loss in three commercial Korean pig breeds through first-parity GWA analysis and provided crucial genetic markers that breeders may use in marker-assisted breeding programs aimed at improving reproductive efficiency.