Genome Selection and Genome-Wide Association Analyses for Litter Size Traits in Large White Pigs.

(1) Background: Litter size traits are critical for pig breeding efficiency but pose challenges due to low heritability and sex-limited influences. This study aimed to elucidate the genetic architecture and identify candidate genes for these traits in Large White pigs using genomic selection (GS) and genome-wide association analyses (GWAS). (2) Methods: This study utilized phenotypic data from nine litter size traits in Large White sows. Genotyping-by-sequencing (GBS) was performed to obtain genotype data, retaining 153,782 high-quality SNPs after quality control. Genetic evaluation was conducted using single-step genomic best linear unbiased prediction (ssGBLUP), with genetic parameters (heritability and genetic correlations) estimated via an animal model (repeatability model). To assess prediction accuracy, 10-fold cross-validation was employed to compare traditional BLUP with ssGBLUP. Furthermore, a single-step genome-wide association study (ssGWAS) integrated genomic information and pedigree-based relationship matrices to screen for significant SNPs associated with litter size traits across the genome. Functional analysis of key candidate genes was subsequently conducted based on ssGWAS results. (3) Results: Heritabilities for litter traits ranged from 0.01 to 0.06. ssGBLUP improved genomic prediction accuracy by 6.38-13.33% over BLUP. Six genomic windows explaining 1.07-1.77% of genetic variance were identified via ssGWAS, highlighting