SHORT COMMUNICATION Mapping and SNP analysis of bovine candidate genes for meat and carcass quality A. Haegeman*, J. L. Williams † , A. Law † , A. Van Zeveren* and L. J. Peelman* *Department of Animal Nutrition, Genetics, Breeding and Ethology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium. † Department of Genomics and Bioinformatics, Roslin Institute (Edinburgh), Roslin, Midlothian, UK Summary The chromosomal localization of 13 bovine genes was determined using radiation hybrid (RH) mapping. The RH mapping data were in agreement with published data using either linkage, somatic cell hybrids or in situ hybridization. Mutation analysis using single- stranded conformational polymorphism, restriction fragment length polymorphism (RFLP) and sequencing revealed 13 SNPs in four different genes, namely carboxypeptidase E (CPE), uncoupling protein 2 (UCP2), single-minded (Drosophila) homologue 1 (SIM1) and meth- allothionein IIa (MT2A). With the exception of one mutation in CPE, all other mutations are either silent or are situated in an intron. The polymerase chain reaction RFLP was used on unrelated animals from different cattle breeds for determing allelic distribution. Keywords radiation hybrid mapping, RFLP, SSCP, SNP. The increasing demand of the public for meat of higher quality which is more tender with less fat and the pressure to use more extensive management, endangers the cost- effectiveness of meat production and thereby the survival of the Ôbeef farmsÕ. A possible way for the farmers is to switch to a more focused breeding programme, with highly spe- cialized beef cattle. Selective breeding programmes have been in existence for a long time but they have relied upon selection on easily measured phenotypic characteristics and sometimes the results have been disappointing. Although environmental factors play a role in determining phenotypic properties, there is a clear genetic component underlying the phenotypic differences between different breeds. This genotypic diversity can be exploited to obtain more desirable phenotypes. However, to succeed the differences between the breeds need to be identified and characterized. For this purpose candidate genes were selected based upon their potential effects upon carcass and meat traits. The possible effects of these genes on carcass and meat traits, can be judged based upon the known involvement of the gene product in cellular or metabolic processes, such as: energy homeostasis e.g. uncoupling protein 1 and 2 (Argyropoulos & Harper 2002), beta pyruvate dehydrogenase (Calvani et al. 2000), lipolysis (hormone-sensitive lipase (Osuga et al. 2000) and developmental processes such as myogenesis [growth hormone (Florini et al. 1996), myocyte enhancer factor 2A (Black & Olson 1998) and adipogenesis (CCAAT/ enhancer binding protein alpha (Umek et al. 1991)]. Sig- nalling molecules and their receptors can also be considered as candidates for genes involved in meat traits, e.g. mel- anocortin receptors 1 and 5 (Yeo et al. 2000), dopamine receptor 4 (Contreras et al. 2002). Finally, genes whose effects in other species on carcass traits have been described in the literature can be considered, as candidates in cattle [e.g. carboxypeptidase E (Naggert et al. 1995), single- minded (Drosophila) homologue 1 (Holder et al. 2000), caveolin-3 (McNally et al. 1998), metallothionein 2A (Beattie et al. 1998)]. Primer pairs were designed for the candidate genes from bovine or human sequence data using the primer 3 pro- gramme (Rozen & Skaletsky 1998). Primer sequences, the annealing temperatures and the amplified fragment lengths are shown in Table 1. The polymerase chain reaction (PCR) amplifications were performed in 10 ll on a T3 Thermo- cycler (Biometra, Go ¨ttingen, Germany). The reaction mixes comprised 20–100 ng genomic DNA, 1.5 mM MgCl 2 , 20 mM Tris–HCl (pH 8.4), 50 mM KCl, 10 pmol of each primer, 200 lM dNTPs and 0.5 U Taq Platinum polymerase (Invitrogen, Merelbeke, Belgium). The thermal cycling profile was: 94 °C (10 min) one cycle, 94 °C (30 s), X °C (see Annealing temperature column; Table 1) (30 s), 72 °C (1 min) 40 cycles, 72 °C (10 min) one cycle. The PCR fragments were cloned in PCR TM II cloning vector (TA Address for correspondence Luc J. Peelman, Department of Animal Nutrition, Genetics, Breeding and Ethology, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium. E-mail: luc.peelman@rug.ac.be Accepted for publication 4 April 2003 Ó 2003 International Society for Animal Genetics, Animal Genetics, 34, 349–353 349