Single-step genome-wide association study uncovers known and novel candidate genomic regions for endocrine and classical fertility traits in Swedish Red and Holstein dairy cows

•In this study, the novel endocrine and classical fertility traits of Swedish dairy herds were evaluated using in-line milk progesterone profiles in ssGWAS approach.•The genomic regions associated with the endocrine and classical traits were identified.•A total of 20 QTLs, of which 18 of them are novel, were detected. The novel QTL regions embedded candidate genes (ATG7, GPI, GJA1, PPP3CA, ECT2, ARHGAP20, PHLDB1, CACNA1D, CCNE1, CDH13, PLD1, FBN2, KIF3A, FGF12, KCNMB2, MAN1A1, KCNN2, SMAD6, MAPK8IP1, PHF21A, LPXN, MMRN1, KCNIP4, NID2, PCDHGA8, GRIA1, PCDHGB4, PHLDB2, STXBP5L, PTPRR, SRGAP1, SNX27, SPTA1, S100A10, TBC1D20 and ITCH) that are associated with endocrine and classical fertility traits.•The candidate QTL regions provide insights into the genetic basis of endocrine and classical fertility in SR and Holstein dairy breeds.