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 identified. A total 20 QTLs, which 18 them are novel, detected. QTL 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 ITCH ) that traits. provide insights into genetic basis SR Holstein breeds. a study aiming to identify Red (SR) cows, data on 3955 lactations 1164 1672 cows examined. dataset comprised (P4) levels n = 341,212) 14 herds, automatically collected analyzed DeLaval Herd Navigator™. Endocrine studied were: days from calving commencement luteal activity (C-LA), first phase length (LPL), inter-luteal interval, inter-ovulatory interval (IOI), during 60 DIM, proportion samples DIM. Classical based insemination also investigated, such as last interval. 180 312 genotyped low-density SNP chip imputed 50 K. Single-step genome-wide association (ssGWAS) was used explore mixed linear single-trait animal model fitted, considering season parity fixed effects permanent environment random effects. results revealed 990 415 SNPs above threshold (-log p -value) ≥4) for respectively. breeds shared only eight significantly Annotation analysis 281 located 241 genes. Functional enrichment DAVID tools reduced number 80 genes, mediated various biological processes KEGG pathways multiple functions, including folliculogenesis, embryogenesis, uterine growth development, immune response, ovarian cysts. Of 67 13 Holstein. Most LPL IOI but an trait C-LA. Twenty 40 both All QTLs detected, except at BTA2 BTA19 not reported previously. These include ITCH. may help improve progress female if selection decisions. challenge future research is determine why different seem relevant breeds, practical implications selection.