| Abstrakt: |
Simple Summary: Genome-wide association studies (GWAS) and run of homozygosity (ROH) analyses based on single nucleotide polymorphism (SNP) data were powerful tools for uncovering genetic factors associated with reproductive performance efficiency in various livestock breeds. The effectiveness of these studies may differ based on breed-specific characteristics, population genetics, and targeted production traits. In the present study, comparative analyses of the genetic profiles of pigs that exhibit diverse reproductive performance were conducted. This empowered us to identify genomic regions associated with the number of piglets born alive (NBA) and the total number of piglets born (TNB). The present finding greatly enhance its contributions to revisit breeding strategies in pigs by identifying significant genetic markers associated with reproductive performance traits. Background: Reproductive performance is critical in the pig industry, and improved sow performance could lead to increased economic benefits. GWAS and ROH analyses based on SNP array data were conducted to identify the breed-specific genetic architecture underlying the variation in NBA and TNB. Methods: A total of 7488 breeding pigs with phenotypic data from 1586 Duroc, 2256 Landrace, and 3646 Yorkshire breeds, along with 76,756 SNP markers from Korean grand-grand-parent (GGP) breeding farms, were used. Results: In the Duroc breeds, SNPs on SSC 9 and 17 were found to be associated with the SIDT2 and TGM2 genes, respectively. In the Landrace breed, PPP1R9A, LMTK2, and GTF2H3 on SSCs 9, 3, and 14, respectively, were associated with both TNB and NBA. With the Yorkshire breed genome, GRID1, DLGAP2, ZZEF1, PARG, RNF17, and NDUFAF5 in SSCs 14, 15, 12, 14, 11, and 17, respectively, were associated with NBA and TNB traits. These genes have distinct functions, ranging from synaptic transmission and cytoskeletal organization to DNA repair and cellular energy production. In the Duroc breed, six genes identified in the ROH islands were associated with various biological pathways, molecular functions, and cellular components. NT5DC1 was associated with metaphyseal chondrodysplasia, CRTAC1 with ion binding, CFAP43 with spermatogenic failure, CASC3 with intracellular mRNA localization, ERC2 with cellular component organization, and FOCAD with Focadhesin. In the Landrace and Yorkshire breeds, PDE6D was associated with GTPase inhibitor activity. Conclusions: Through GWAS and ROH analyses, we identified breed-specific SNP markers associated with NBA and TNB in three breed genotypes, providing insights for improving reproductive performance efficiency and contributing to future breeding strategies. [ABSTRACT FROM AUTHOR] |
