doi:10.1111/j.1365-2052.2006.01434.x Association of polymorphisms in the bovine FASN gene with milk-fat content R. Roy* 1 , L. Ordovas* 1 , P. Zaragoza*, A. Romero*, C. Moreno † , J. Altarriba † and C. Rodellar* *Laboratorio de Gene ´ tica Bioquı ´mica, Universidad de Zaragoza, Zaragoza 50013, Spain. † Grupo de Mejora Gene ´ tica, Universidad de Zaragoza, Zaragoza 50013, Spain Summary Fatty acid synthase (FASN) is a multifunctional protein that carries out the synthesis of fatty acids so it plays a central role in de novo lipogenesis in mammals. Previously, we defined the genetic structure and expression of the bovine FASN gene. Our mapping studies placed FASN on BTA19 (19q22) where several quantitative trait loci (QTL) affecting milk-fat content and related traits have been described. This study was conducted to identify polymorphisms in the bovine FASN gene and to study their association with milk-fat content. The bovine FASN gene was screened for polymorphisms in two cattle breeds. Sequence analysis revealed several single nucleotide polymorphisms (SNPs), and two of them were analysed: a G>C substitution in the untranslated exon 1 (g.763G>C), altering a potential Sp1 transcription factor-binding site, and an A>G substitution in exon 34 (g.16009A>G), which determines a non-conservative substitution of threonine by alanine. Allele-specific amplification of the SNPs in FASN revealed significant frequency differences for both polymorphisms in Holsteins with high and low breeding values for milk-fat content. The intragenic haplotypes comprising exon 1 (alleles G and C) and exon 34 (alleles A and G) polymorphisms were studied, and the existence of linkage disequilibrium between these SNPs was found (D CG ¼ 0.048, P < 0.001). Our results suggest that the FASN gene polymorphisms contribute to variation in milk-fat content. We propose that the bovine FASN gene is a candidate gene for a milk-fat content QTL. Keywords candidate gene, fatty acid synthase, linkage disequilibrium, single nucleotide polymorphisms. Introduction Fatty acid synthase (FASN) is a complex homodimeric en- zyme that regulates de novo biosynthesis of long-chain fatty acids. Mammalian FASN is not only an essential metabolic enzyme in fatty acid synthesis during the adult stage, but it also plays an important role during embryonic development (Chirala et al. 2003). This cytosolic enzyme catalyses the formation of palmitate from acetyl-coenzyme A and malo- nyl-coenzyme A in the presence of NADPH. Hence, because FASN plays a central role in de novo lip- ogenesis in mammals (Wakil et al. 1983), it is a candidate gene for fat content in milk animals. The FASN gene has been cloned in rat, human, goose, chicken and, recently, in bovine (Amy et al. 1992; Ja- yakumar et al. 1995; Kameda & Goodridge 1991; Chirala et al. 1997 and Roy et al. 2005 respectively). Furthermore, it has been mapped in human (HSC17), pig (SSC12) and mouse (MMU11). However, little is known about the FASN gene in ruminant species where fat production traits are very important. Our previous mapping studies placed the bovine FASN gene on BTA19 (Roy et al. 2001) where several quantita- tive trait loci (QTL) affecting milk-fat content and related traits have been described (Falaki et al. 1997; Taylor et al. 1998; Boichard et al. 2003). We have also studied the bo- vine FASN gene at the structural and functional levels (Roy et al. 2005). This study was designed to evaluate the poss- ible association of the FASN gene and milk-fat production. Address for correspondence Clementina Rodellar, Laboratorio de Gene ´tica Bioquı´mica, Facultad de Veterinaria, C/Miguel Servet 177, Zaragoza 50013, Spain. E-mail: rodellar@unizar.es 1 These authors contributed equally to this work. Accepted for publication 2 February 2006 Ó 2006 The Authors, Journal compilation Ó 2006 International Society for Animal Genetics, Animal Genetics, 37, 215–218 215