Analysis of candidate SNPs affecting milk and functional traits in the dual-purpose Italian Simmental cattle

A totalof113DNApolymorphismsin32candidategeneswerepre-screenedtoassesstheir variabilityin32ItalianSimmentalbulls.Atotalof64variantssuccessfullygenotypedand havingaminorallelefrequency(MAF)higherthan0.03werethenanalyzedin477Italian Simmentalbulls.Amongthese37hadaMAF Z0.05andwereinvestigatedforassociation withmilkproductionandfunctionaltraits.Daughteryielddeviations(DYD)wereavailable formilk,proteinandfatyield(MY,PYandFY,respectively),somaticcellcount(SCC),udder score(US),feetandlegsscore(FLS),whileforproteinpercent(PP),calvingeasedirecteffect (CED),fertility(FE)andmilkability(MA)associationswerecomputedusing(EBVs). TwelveSNPsweresignificantlyassociatedwithatleastonetrait(Pr0.05).The strongestassociation(P¼0.0009)wasfoundbetweenrs385640152inthegrowthhormone receptorgene(GHR) andPP.Alsomarkerrs42714483inthethyroidhormoneresponsive gene(THRSP) wasassociatedwithPP(P¼0.004).Pleiotropiceffectsweredetectedonlyfor β-lactoglobulin(LGB or PAEP progestagen-associatedendometrialprotein)polymorphisms on.SNPrs29004488intheleptingene(LEP) andrs41974998inmilkfatglobule-epidermal growthfactor8proteingene(MFGE8) wereassociatedwithMY(P¼0.043and P¼0.033, respectively).Suggestiveassociationswithfunctionaltraitswerealsodetected:rs43347906 in theleptinreceptorgene(LEPR) withUS(P¼0.029),rs29004485in LEP withFLS (P¼0.049),rs41703837inthev-srcsarcoma(Schmidt-RuppinA-2)viraloncogenehomolog (SRC) withCED(P¼0.021)andrs109019599intheoxidizedlowdensitylipoproteinreceptor 1 gene(OLR1) withMA(P¼0.024).Ourresultsbothprovide loci newlyassociatedwith functionaltraitsandconfirmassociationsalreadydetectedinItalianHolsteinandItalian Brownbreeds.