doi:10.1111/j.1365-2052.2011.02286.x Whole-genome analysis for backfat thickness in a tropically adapted, composite cattle breed from Brazil G. Veneroni-Gouveia*, S. L. Meirelles † , D. A. Grossi ‡ , A. C. Santiago § , T. S. Sonstegard ¶ , M. E. B. Yamagishi**, L. K. Matukumalli ¶ , L. L. Coutinho †† , M. M. Alencar ‡‡ , H. N. Oliveira §§ and L. C. A. Regitano ‡‡ *Graduate Program on Genetics and Evolution, Sa ˜ o Carlos Federal University, Sa ˜ o Carlos, SP 13565-905, Brazil. † Department of Animal Sciences, Lavras Federal University, Lavras, MG 37200-000, Brazil. ‡ Department of Exact Sciences, Sa ˜ o Paulo State University, Jaboticabal, SP 14884-900, Brazil. § Scholarship in Industrial Technology Development CNPq-Level 3, Sa ˜ o Carlos Federal University, Sa ˜ o Carlos, SP 13565-905, Brazil. ¶ USDA, Agricultural Research Service, Beltsville, MD 20705, USA. **Bioinformatics Applied Laboratory, National Center for Agricultural Research, Embrapa, Campinas, SP 13083-886, Brazil. †† CNPq Fellowship, Sa ˜ o Paulo University -ESALQ, Piracicaba, SP 13418-900, Brazil. ‡‡ CNPq Fellowship, Embrapa Southeast Stock Breeding Research Center, Sa ˜ o Carlos, SP 13560-970, Brazil. §§ CNPq Fellowship, Department of Animal Genetics and Improvement, Sa ˜ o Paulo State University, Jaboticabal, SP 14884-900, Brazil Summary Backfat thickness affects the preservation of the beef carcass after slaughter and confers organoleptic characteristics assessed by the consumer. One of the breeding goals for Can- chim, a tropically adapted breed, is to comprehensively increase fat thickness. Our goals were to identify genomic regions associated with backfat in Canchim populations and validate the association of single nucleotide polymorphisms (SNPs) overlapping previously identified QTL regions known to affect fat deposition. Fifteen animals with lower and 15 animals with higher residues for backfat, according to a linear model using the SAS GLM procedure, were selected from a population of 1171 animals and genotyped using the BovineSNP50 BeadChip. Initial analysis revealed more than 100 SNPs that discriminated the tails of phenotypic distribution. One extended region of association included the cen- tromeric region of chromosome (Chr) 14. Because this region overlapped with QTL from previous reports, we developed SNP assays to interrogate two linkage disequilibrium blocks, one in the centromeric region and another in the middle region of Chr 14 to confirm the association. The analysis validated the presence of specific haplotypes affecting fat thickness. Keywords fat deposition, single nucleotide polymorphism, tropically adapted cattle. Introduction Backfat thickness (BF), total fat and fat distribution have a strong impact on carcass and meat quality in beef cattle, while marbling and subcutaneous fat thickness remain as the most important features influencing palatability and consumer acceptability (Jeremiah 1996). Canchim is a composite breed of 5/8 Charolais and 3/8 Zebu; the Zebu most commonly used in this composition is Nellore and in the past also included Guzera and Indubrasil. Currently, there are two genetic groups in the Canchim breed: MA (offspring of Charolais bulls and 1/2 Canchim + 1/2 Zebu cows) and CA (offspring of MA · MA, MA · Canchim or Canchim · Canchim). Overall, this breed has good growth potential and tropical adaptation but suboptimal fat depo- sition. Several reports have described the presence of QTL for fat deposition on bovine chromosomes 2, 4, 5, 6, 14, 19, 21 and 23 (Taylor et al. 1998; Moore et al. 2003; Casas et al. 2004; Li et al. 2004; Mizoguchi et al. 2006), and the number of new genomic regions implicated in fat deposition is growing quickly due to the availability of genome-wide single nucleotide polymorphism (SNP) assays for cattle. The use of high-density SNP chips allows the incorporation of genomic selection into breeding schemes, especially to assist in predicting the breeding values of individuals. It may also contribute to identify major genes related to phenotypes of interest, which could be used in marker-assisted selection. In this study, we analysed the existence of genomic regions associated with BF in Canchim CA and MA Address for correspondence L. C. A. Regitano, Rodovia Washington Luiz, km 234 CP 339, CEP 13560-970, Sa ˜ o Carlos, SP, Brazil. E-mail: luciana@cppse.embrapa.br Accepted for publication 18 July 2011 Ó 2011 The Authors, Animal Genetics Ó 2011 Stichting International Foundation for Animal Genetics 1