Analysis of candidate SNPs affecting milk and functional traits in the dual-purpose Italian Simmental cattle Stefania Chessa a,n , Ezequiel Luis Nicolazzi b , Letizia Nicoloso c , Riccardo Negrini d,e , Rosanna Marino d , Daniele Vicario f , Paolo Ajmone Marsan d , Alessio Valentini g , Bruno Stefanon h a Istituto di Biologia e Biotecnologia Agraria, CNR, via Einstein, 26900 Lodi, Italy b Fondazione Parco Tecnologico Padano, via Einstein, 26900 Lodi, Italy c Università degli Studi di Milano, Dipartimento di Scienze Veterinarie e Sanità Pubblica, via Celoria 10, 20133 Milano, Italy d Istituto di Zootecnica, Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29122 Piacenza, Italy e Associazione Italiana Allevatori, via G. Tomassetti 9, 00161 Roma, Italy f Associazione Nazionale Allevatori Bovini di Razza Pezzata Rossa Italiana, via Ippolito Nievo 19, 33100 Udine, Italy g Dipartimento per l’Innovazione nei sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, via Camillo de Lellis, 0100 Viterbo, Italy h Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Udine, via delle Scienze 208, 33100 Udine, Italy article info Article history: Received 2 July 2014 Received in revised form 17 December 2014 Accepted 19 December 2014 Keywords: SNP Candidate genes Milk traits Functional traits Italian Simmental abstract A total of 113 DNA polymorphisms in 32 candidate genes were pre-screened to assess their variability in 32 Italian Simmental bulls. A total of 64 variants successfully genotyped and having a minor allele frequency (MAF) higher than 0.03 were then analyzed in 477 Italian Simmental bulls. Among these 37 had a MAF Z0.05 and were investigated for association with milk production and functional traits. Daughter yield deviations (DYD) were available for milk, protein and fat yield (MY, PY and FY, respectively), somatic cell count (SCC), udder score (US), feet and legs score (FLS), while for protein percent (PP), calving ease direct effect (CED), fertility (FE) and milkability (MA) associations were computed using (EBVs). Twelve SNPs were significantly associated with at least one trait (P r0.05). The strongest association (P ¼0.0009) was found between rs385640152 in the growth hormone receptor gene (GHR) and PP. Also marker rs42714483 in the thyroid hormone responsive gene (THRSP) was associated with PP (P ¼0.004). Pleiotropic effects were detected only for β-lactoglobulin (LGB or PAEP progestagen-associated endometrial protein) polymorphisms on. SNP rs29004488 in the leptin gene (LEP) and rs41974998 in milk fat globule-epidermal growth factor 8 protein gene (MFGE8) were associated with MY (P ¼0.043 and P ¼0.033, respectively). Suggestive associations with functional traits were also detected: rs43347906 in the leptin receptor gene (LEPR) with US (P ¼0.029), rs29004485 in LEP with FLS (P ¼0.049), rs41703837 in the v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (SRC) with CED (P ¼0.021) and rs109019599 in the oxidized low density lipoprotein receptor 1 gene (OLR1) with MA (P ¼0.024). Our results both provide loci newly associated with functional traits and confirm associations already detected in Italian Holstein and Italian Brown breeds. & 2014 Elsevier B.V. All rights reserved. Contents lists available at ScienceDirect journal homepage: www.elsevier.com/locate/livsci Livestock Science http://dx.doi.org/10.1016/j.livsci.2014.12.015 1871-1413/& 2014 Elsevier B.V. All rights reserved. n Corresponding author. Tel.: þ39 0371 4662507; fax: þ39 0371 4662507. E-mail address: chessa@ibba.cnr.it (S. Chessa). Livestock Science 173 (2015) 1–8