Abstract
<title>Abstract</title> <p> Background N’Dama (West African taurine) cattle exemplify African breeds that evolved under distinct ecological and management regimes. The underlying genetic mechanisms behind these potentials are still not well defined. Understanding the genetic basis of milk and adaptive mechanism can guide in developing the effective breeding goals that both conserve the local breeds and improve the commercial cattle. In this study, we evaluated the genome-wide scans with runs of homozygosity (ROH), integrated haplotype scores (iHS) and Tajima’s D to unveil selection signatures for milk production and adaptive traits in N’Dama cattle using publicly available high density SNP chips. Results ROH islands, iHS and Tajima’s D hotspots overlapped milk and adaptation-related genes consistent with trypanotolerance in N’Dama. Manhattan plot and functional enrichment of these regions implicated milk production QTLs and disease resistance in N’Dama. Notably, ROH hotspots contained candidate genes associated with milk protein synthesis ( <italic>LEP, NCK1, IL6R, PDGFB, FGF23, CSNK1E, KIT, RPTOR, CSNK1D</italic> ), thermal adaptation ( <italic>DNAJB2, STRADB, OAZ3, SASH1, SOCS4, STRADA, MAPKAPK3</italic> ), adaptive immunity ( <italic>FCGR3A, IFIH1, IFI16, PDCD1, CTLA4, FCGR2A, CD1B, TLR6, ANXA1</italic> ) while iHS hotpot contained <italic>CDH2, TCN2, ITGA11, ITGA6</italic> for milk production and <italic>SMURF2, TNXB, CD47, THBS1</italic> for adaptation and Tajima’s D hot spot revealed <italic>IGF1, STAT5B, LPIN1, GALM</italic> and <italic>NREP, SMAD6, TLR9. TYRO3, SEL1, CAT, TNF, TXN, AP3B1</italic> as candidate genes associated with milk production and adaptive traits respectively. Some genes such as <italic>DCDC2, HECW1, CAPZB, FER, ANAPC4, HECTD2, RFFL, SLIT2</italic> were found to be overlapping between ROH and iHS. Among overlaps between ROH and Tajima’D were found to be <italic>ANXA1, GCG, GCK, SOCS7, ALOX15B</italic> and that between iHS and Tajima’s D were <italic>SDCCAG8</italic> and <italic>EPHB2</italic> . No overlap genes were intersected between the three selection signature methods. Conclusions The contrasting ROH, iHS and Tajima’s D landscapes of N’Dama reflected demographic history in selection and highlighted candidate loci for breeding milk productive and adaptive N’Dama cattle. The overlaps between ROH, iHS and Tajima’s D signals provides robust evidence of recent positive selection, highlighting high-confidence candidate genes likely contributing to adaptation and economically important traits such milk. </p>