Integrated multi-population selection-signature scans identify putative functional genes influencing litter size in jishen black pigs

Background Reproduction traits constitute the primary objective of porcine genetic improvement programs, with litter size being the principal determinant of herd reproduction output. Relative to the intensively selected Large White line, as a breed derived from Large White (LW) and Beijing Black (BJB) pigs, Jishen Black (JSB) pigs exhibit markedly lower litter size, indicating substantial potential for genetic improvement. Results Whole-genome resequencing data were obtained from 110 individuals of six pig populations differed in litter size: a Large White line with high litter size (> 16, LWH), cryopreserved Large White samples from 1977 (LW1977), dam-selected (LWD) and sire-selected (LWS) lines derived from LW1977, Berkshire (BKS), and Jishen Black pigs (JSB). Principal component analysis (PCA) captured clear population genetic structure along PC2, with the observed distribution pattern descriptively coinciding with litter size variation across populations, though such an association was not statistically verified. A composite selection-signature scan that integrated Fst , π-ratio, and XP-EHH was performed between multiple population groups. Candidate signals were filtered by excluding those also detected in a control comparison (Jishen Black vs. Berkshire) that showed minimal litter‑size difference, to screen selection signatures with potential relevance to reproductive trait differentiation at the population level. Twelve genes were identified as putative candidate genes for litter size, including PEX14 , CDK15 , KCNQ1 , SPAG17 , TTF2 , CD101 , CASQ2 , VANGL1 , ARID5B , KLHL32 , EML1 , and NAV1 . Functional enrichment analysis indicated that these genes significantly over-represented in microtubule-related biological processes. Among them, KCNQ1 was consistently detected by all methods and comparison groups. Further analysis of KCNQ1 revealed multiple SNPs with significant allele-frequency differentiation among populations; notably, two intronic variants (chr2:A1,861,604G and chr2:A1,867,076G) showed population-specific allele frequency patterns that descriptively aligned with the stratification of litter size performance. Conclusions By comprehensively dissecting population genomic differentiation among multi-breed populations divergent in litter-size performance, this study implemented established a feasible framework for screening candidate loci associated with porcine prolificacy at the population level, expanded the gene list with suggestive selection signatures, and provided potential molecular markers requiring further independent cohort validation and functional verification to support future genetic improvement in swine reproduction efficiency.