Genome-Wide Association Studies and Runs of Homozygosity Reveals Genetic Markers Associated with Reproductive Performance in Korean Duroc, Landrace, and Yorkshire Breeds.

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 9 and 17 were found to be associated with the and genes, respectively. In the Landrace breed, , , and on 9, 3, and 14, respectively, were associated with both TNB and NBA. With the Yorkshire breed genome, , , , , , and 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. was associated with metaphyseal chondrodysplasia, with ion binding, with spermatogenic failure, with intracellular mRNA localization, with cellular component organization, and with Focadhesin. In the Landrace and Yorkshire breeds, 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.