Genet. Sel. Evol. 35 (2003) 77-101
DOI: 10.1051/gse:2002037

Detection of genes influencing economic traits in three French dairy cattle breeds

Didier Boichard^a, Cécile Grohs^b, Florence Bourgeois^c, Frédérique Cerqueira^c, Rémi Faugeras^c, André Neau^d, Rachel Rupp^a, Yves Amigues^c, Marie Yvonne Boscher^c and Hubert Levéziel<sup>b

a</sup>  Station de génétique quantitative et appliquée, Institut national de la recherche agronomique, 78352 Jouy-en-Josas Cedex, France
^b  Laboratoire de génétique biochimique et de cytogénétique, Institut national de la recherche agronomique, 78352 Jouy-en-Josas Cedex, France
^c  GIE Labogena, 78352 Jouy-en-Josas Cedex, France
^d  Département de génétique animale, Institut national de la recherche agronomique, 78352 Jouy-en-Josas Cedex, France

(Received 25 February 2002; accepted 20 September 2002)

Abstract
A project of QTL detection was carried out in the French Holstein, Normande, and Montbéliarde dairy cattle breeds. This granddaughter design included 1 548 artificial insemination bulls distributed in 14 sire families and evaluated after a progeny-test for 24 traits (production, milk composition, persistency, type, fertility, mastitis resistance, and milking ease). These bulls were also genotyped for 169 genetic markers, mostly microsatellites. The QTL were analysed by within-sire linear regression of daughter yield deviations or deregressed proofs on the probability that the son receives one or the other paternal QTL allele, given the marker information. QTL were detected for all traits, including those with a low heritability. One hundred and twenty QTL with a chromosome-wise significance lower than 3% were tabulated. This threshold corresponded to a 15% false discovery rate. Amongst them, 32 were genome-wise significant. Estimates of their contribution to genetic variance ranged from 6 to 40%. Most substitution effects ranged from 0.6 to 1.0 genetic standard deviation. For a given QTL, only 1 to 5 families out of 14 were informative. The confidence intervals of the QTL locations were large and always greater than 20 cM. This experiment confirmed several already published QTL but most of them were original, particularly for non-production traits.

Key words: dairy cattle / QTL detection / genetic marker / granddaughter design

Correspondence and reprints: Didier Boichard
    e-mail: boichard@dga.jouy.inra.fr

© INRA, EDP Sciences 2003