Genet. Sel. Evol. 35 (2003) 319-338
DOI: 10.1051/gse:2003011

Combined analysis of data from two granddaughter designs: A simple strategy for QTL confirmation and increasing experimental power in dairy cattle

Jörn Bennewitz^a, Norbert Reinsch^a, Cécile Grohs^b, Hubert Levéziel^b, Alain Malafosse^c, Hauke Thomsen^a, Ningying Xu^a, Christian Looft^a, Christa Kühn^d, Gudrun A. Brockmann^d, Manfred Schwerin^d, Christina Weimann^e, Stefan Hiendleder^e, Georg Erhardt^e, Ivica Medjugorac^f, Ingolf Russ^f, Martin Förster^f, Bertram Brenig^g, Fritz Reinhardt^h, Reinhard Reents^h, Gottfried Averdunkⁱ, Jürgen Blümel^a0, Didier Boichard^aa and Ernst Kalm<sup>a

a</sup>  Institut für Tierzucht und Tierhaltung, Christian-Albrechts-Universität, 24098 Kiel, Germany
^b  Laboratoire de génétique biochimique et de cytogénétique, Institut national de la recherche agronomique, 78352 Jouy-en-Josas Cedex, France
^c  Union nationale des coopératives d'élevage et d'insémination animale, 149 rue de Bercy, 75595 Paris Cedex 12, France
^d  Forschungsinstitut für die Biologie landwirtschaftlicher Nutztiere, 18196 Dummerstorf, Germany
^e  Institut für Tierzucht und Haustiergenetik der Justus-Liebig-Universität, 35390 Gießen, Germany
^f  Institut für Tierzucht der Ludwig-Maximilians-Universität, 80539 München, Germany
^g  Institut für Veterinärmedizin der Georg-August-Universität, 37073 Göttingen, Germany
^h  Vereinigte Informationssysteme Tierhaltung w.V., 27283 Verden, Germany
ⁱ  Bayerische Landesanstalt für Tierzucht, 85586 Grub, Germany
^a0  Institut für die Fortpflanzung landwirtschaftlicher Nutztiere, 16321 Schönow, Germany
^aa  Station de génétique quantitative et appliquée, Institut national de la recherche agronomique, 78352 Jouy-en-Josas Cedex, France

(Received 14 June 2002; accepted 5 December 2002)

Abstract
A joint analysis of five paternal half-sib Holstein families that were part of two different granddaughter designs (ADR- or Inra-design) was carried out for five milk production traits and somatic cell score in order to conduct a QTL confirmation study and to increase the experimental power. Data were exchanged in a coded and standardised form. The combined data set (JOINT-design) consisted of on average 231 sires per grandsire. Genetic maps were calculated for 133 markers distributed over nine chromosomes. QTL analyses were performed separately for each design and each trait. The results revealed QTL for milk production on chromosome 14, for milk yield on chromosome 5, and for fat content on chromosome 19 in both the ADR- and the Inra-design (confirmed within this study). Some QTL could only be mapped in either the ADR- or in the Inra-design (not confirmed within this study). Additional QTL previously undetected in the single designs were mapped in the JOINT-design for fat yield (chromosome 19 and 26), protein yield (chromosome 26), protein content (chromosome 5), and somatic cell score (chromosome 2 and 19) with genomewide significance. This study demonstrated the potential benefits of a combined analysis of data from different granddaughter designs.

Key words: QTL mapping / granddaughter design / combined analysis / QTL confirmation / dairy cattle

Correspondence and reprints: Jörn Bennewitz
    e-mail: jbennewitz@tierzucht.uni-kiel.de

© INRA, EDP Sciences 2003