Genome-wide association study for litter size and litter size variability in Large White pigs based on a whole-genome sequence data.

The objective of this study was to analyse the genomic basis of litter size variability. We used 172 644 observations on the total number born (TNB) from 40 518 Large White sows. First, the variance components and heritability for TNB were estimated using ASReml. Then, based on those results, the log-transformed variance of residuals for TNB (LnVarTNB) was used to quantify phenotypic variability and estimate its variance components. Finally, both LnVarTNB and meanTNB (i.e., the average TNB per sow) were used in a genome-wide association study (GWAS) with whole-genome sequence data comprising 27 035 402 SNPs across all chromosomes from 40 509 Large White sows. The GWAS was performed in GCTA using a mixed-model approach. We investigated the genomic regions associated with both the meanTNB and its variability. Heritability estimates were 0.125 for TNB and 0.003 for LnVarTNB. GWAS revealed a prominent QTL for meanTNB on SSC1 (164.8 Mbp), highlighting SMAD3, SMAD6, and MAP2K1 as key candidate genes. In contrast, LnVarTNB was associated with 20 significant SNPs across multiple Sus scrofa chromosomes (SSC 1, 4, 6, 7, 11, and 13). These variants were characterised by low minor allele frequencies (MAFs), with a major cluster on SSC13 near the TFF3 and UMODL1 candidate genes. Genotypic analysis showed that specific heterozygous genotypes significantly reduced litter size with a slight reduction in meanTNB compared to the homozygotes. The genetic control of litter size variability is driven by rare variants that are often missed in lower-density analyses. The identified loci on SSC13 and SSC1 suggest that selection for "robustness" alleles can improve production stability and farm efficiency. These findings provide valuable genomic markers for future breeding programmes aimed at balancing high prolificacy with phenotypic uniformity.