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Reproductive performance is a complex quantitative trait, that is determined by multiple genes, regulatory pathways and environmental factors. A list of major genes with large effect have been detected, although multiple QTLs are identified. To identify candidate genes for pig prolificacy, whole genome variants from five high- and five low-prolificacy Yorkshire sows were collected using whole-genome resequencing. A total of 13,955,609 SNPs and 2,666,366 indels were detected across the genome. Common differential SNPs and indels were identified between the two groups of sows. Genes encoding components of the TGF-beta signaling pathway were enriched with the variations, including BMP5 , BMP6 , BMP7 , ACVR1 , INHBA , ZFYVE9 , TGFBR2 , DCN , ID4 , BAMBI , and ACVR2A. Several differential variants within these genes related to reproductive traits were identified to be associated with litter size. A comparison of selective regions and published QTL data suggests that NEDD9 , SLC39A11 , SNCA , and UNC5D are candidate genes for reproduction traits. • A total of 13,955,609 SNPs and 2,666,366 indels were identified across the genome. • 3293 common differential SNPs and 439 common differential indels were fixed between groups. • Genes encoding components of the TGF-beta signaling pathway were identified to be associated with sow reproductive traits. • Fourteen candidate genes were identified to contribute to sow prolificacy and merit further investigations. [ABSTRACT FROM AUTHOR]