A whole genome scan for QTL affecting milk protein percentage in Italian Holstein cattle, applying selective milk DNA pooling and multiple marker mapping in a daughter design V. Russo*, L. Fontanesi*, M. Dolezal †,‡ , E. Lipkin § , E. Scotti*, P. Zambonelli*, S. Dall’Olio*, D. Bigi*, R. Davoli*, F. Canavesi ¶, **, I. Medugorac †† , M. Fo ¨ ster †† , J. So ¨ lkner ‡ , F. Schiavini**, A. Bagnato** and M. Soller § *Department of Agro-Food Science and Technology, Sezione di Allevamenti Zootecnici, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy. † Institut fu ¨ r Populationsgenetik Veterina ¨ rmedizinische, University of Wien, Josef Baumann Gasse 1, 1210, Wien, Austria. ‡ Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Applied Sciences (BOKU), Vienna, Austria. ¶ Associazione Nazionale Allevatori Frisona Italiana (ANAFI), Cremona, Italy. ** Department of VSA, Faculty of Veterinary Medicine, University of Milano, Milano, Italy. †† Faculty of Veterinary Medicine, Institute for Animal Breeding, The Ludwig-Maximilians-University Munich, Veterinaerstr. 13, 80539, Munich, Germany Summary We report on a complete genome scan for quantitative trait loci (QTL) affecting milk protein percentage (PP) in the Italian Holstein-Friesian cattle population, applying a selective DNA pooling strategy in a daughter design. Ten Holstein-Friesian sires were chosen, and for each sire, about 200 daughters, each from the high and low tails of estimated breeding value for PP, were used to construct milk DNA pools. Sires and pools were genotyped for 181 dinu- cleotide microsatellites covering all cattle autosomes. Sire marker allele frequencies in the pools were obtained by shadow correction of peak height in the electropherograms. After quality control, pool data from eight sires were used for all subsequent analyses. The QTL heterozygosity estimate was lower than that of similar studies in other cattle populations. Multiple marker mapping identified 19 QTL located on 14 chromosomes (BTA1, 2, 3, 4, 5, 6, 8, 9, 12, 14, 17, 20, 23 and 27). The sires were also genotyped for seven polymorphic sites in six candidate genes (ABCG2, SPP1, casein kappa, DGAT1, GHR and PRLR) located within QTL regions of BTA6, 14 and 20 found in this study. The results confirmed or excluded the involvement of some of the analysed markers as the causative polymorphic sites of the identified QTL. The QTL identified, combined with genotype data of these candi- date genes, will help to identify other quantitative trait genes and clarify the complex QTL patterns observed for a few chromosomes. Overall, the results are consistent with the Italian Holstein population having been under long-term selection for high PP. Keywords candidate genes, daughter design, genome scan, Italian Holstein cattle, milk protein percentage, multiple marker mapping, quantitative trait loci. Introduction A large number of studies have identified quantitative trait loci (QTL) for milk production and milk quality traits in dairy cattle. A variety of designs have been employed, depending on the availability of structured families, the number of animals per family, sources of DNA and pheno- typic records, and available budget. QTL databases for livestock species have been developed to summarise and group most of the QTL mapping studies (Khatkar et al. 2004; Polineni et al. 2006; Hu & Reecy 2007). The Holstein-Friesian is the most studied breed for QTL mapping owing to the large sire families that it provides. Until recently, the most common design for such studies was the granddaughter design, in which marker genotypes are determined on the half-sib sons (sires) of Address for correspondence L. Fontanesi, Department of Agro-Food Science and Technology, Sezione di Allevamenti Zootecnici, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy. E-mail: luca.fontanesi@unibo.it Accepted for publication 17 January 2012 doi: 10.1111/j.1365-2052.2012.02353.x 72 © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics. Animal Genetics 43 (Suppl. 1), 72–86