Investigating the genetic imprint of long body length, high lean meat rate, high fertility and long gestation period in Danish Landrace pigs.

Abstract

Background: After long-term artificial selection and lineage mixing, the Danish Landrace pig (DLR), has developed characteristics such as a long body length, high lean meat rate, rapid growth rate, high litter size, and a longer gestation period, with an average gestation length of 117 days. However, the genes responsible for these desirable traits remain partly unknown. According to the breeding history of DLR pigs, it has undergone introgression from British Large White pigs (BLW), selection for high lean meat rate and long body length within the population, and a rapid improvement in reproductive performance since 1992. Research on Danish Duroc and Large White pigs has detected that the lineage of pigs in Taihu Lake region (TL) has introgressed into these two breeds. Therefore, we performed resequencing and chip scanning on 106 TL pigs and 557 DLR pigs, and downloaded 163 resequencing data from Eurasian pigs for shared haplotype analysis, selective sweep analysis, and GWAS.

Results: The results indicate that 12 important genes, including CREB3L2, PRKAB2, HIF1A, IGF1, have introgressed from BLW into DLR pigs. These genes enhance lean meat percentage by participating in thermogenesis, oxidative phosphorylation and HIF-1 signaling pathways. In the DLR pig population, 13 shared selected genes were identified across three selective sweep methods. These genes including HBM, RHBDF1, POLR3K, ZNF484, were found to be associated with growth rate, body length, lean meat percentage, and reproductive performance by pheWAS analysis. Interestingly, reproductive performance is primarily related to gestational trait. GWAS for gestational trait in DLR pig population revealed 13 significant genes which also under selection in selective sweeps. These genes include INSYN1, NPTN, NEO1, ZDHHC21. Our study clarifies that the lineage of TL pigs has also introgressed into DLR pigs, with NDUFS4 being an important introgressed gene influencing reproductive performance. Moreover, compared to the low-fertility American Landrace pigs, HTR7, RPP30, ANKRD1, ARHGAP42, and CNTN5 may be important genes selected for enhancing litter size within the DLR pigs.

Conclusions: Our research deepens the understanding of the breeding history of DLR pigs, preliminarily identifies genes associated with the characteristics of high lean meat percentage, long body length, and high fertility in DLR pigs, and also finds that the high litter size of DLR pigs may be related to gestation length.