Experimental population design for estimation of dominant molecular marker effect on egg-production traits M. G. Kaiser*, N. Lakshmanan*, J. A. Arthur † , N. P. O’Sullivan † and S. J. Lamont* *Department of Animal Science, Iowa State University, Ames, IA, USA. † Hy-Line International, Dallas Center, IA, USA Summary A potential limitation of the use of a dominant molecular marker system such as DNA fingerprinting (DFP) is the inability to distinguish homozygous from heterozygous allele state in an individual, and a resulting inaccuracy in estimating effects of the marker alleles. The objective of this study was to accurately estimate the effect of DFP markers on egg- production traits. A BC 1 population was produced from two distinct layer lines. Four DFP bands, each originating predominantly in one of the two parental lines, were evaluated for linkage with egg-production quantitative trait loci in the BC 1 population. The egg- production traits consisted of eight early period and seven late period measurements. Eight marker-trait linkages were identified out of 60 total statistical tests. By utilizing information on frequency of DFP bands in two parental lines, selecting F 1 sires with DFP bands present, and backcrossing to the line lacking these bands, the population design allowed definitive identification of the DFP zygosity in the BC 1 resource population hens. In this manner, accurate estimates of marker allele effects on egg-production traits were obtained from the dominant marker system of DNA fingerprinting. Keywords chicken, dominant marker system, DNA fingerprint, egg production traits, quantitative trait loci detection, resource population. Introduction Identification of genomic regions containing quantita- tive trait loci (QTL) can be accomplished by linkage- disequilibrium genome scans. The initial objective of a genome scan is to identify genetic linkage between a genomic marker and a QTL. The QTL-linked markers can then be applied in marker-assisted selection (MAS) and/or gene introgression (Soller & Andersson 1998). Further- more, the identification of marker-QTL linkage can also aid in the identification of the QTL (Milan et al. 2000). There are several genetic marker systems available to perform genome scans, including DNA fingerprinting (DFP), and polymerase chain reaction-based random amplified poly- morphic DNA (RAPD), amplified fragment length poly- morphism (AFLP), single nucleotide polymorphism (SNP) and microsatellites. Many marker-QTLs or genes have been identified for production traits in animals (Plotsky et al. 1993; Andersson et al. 1994; Georges et al. 1995; Lamont et al. 1996; Van Kaam et al. 1999a,b; Mosig et al. 2001; Tuiskula-Haavisto et al. 2002). The category of DFP markers, consisting of variable number of tandem repeats (VNTR) of a core sequence, was first described by Jeffreys et al. (1985). The use of DFP markers for genome scanning has several advantages as well as disadvantages. The DFP are non-species specific, highly polymorphic, and do not require pre-existing know- ledge of genomic sequence. The DFP markers provide a broad genome distribution with multiple non-cosegregating DNA bands identified per probe (Bruford & Burke 1994). Disadvantages of DFP markers are that they are unmapped, dominant markers, which can be technically difficult to convert into locus-specific markers (Bruford & Burke 1991). It is possible to overcome the difficulties of a dominant marker system in determining homozygositiy versus het- erozygosity by utilization of specialized population design. Generating a BC 1 population wherein the parental F 1 par- ents are selectively mated to a parental line based on complementary DFP band presence or absence can clarify progeny allele number. Previously, DNA fingerprint bands linked to early egg- production traits were identified in an F 2 population pro- duced by intermating a BC 1 chicken population that was derived from two commercial pure layer lines (Lamont et al. Address for correspondence Dr Susan J. Lamont, 2255 Kildee Hall, Iowa State University, Ames, IA 50011, USA. E-mail: sjlamont@iastate.edu Accepted for publication 26 April 2003 Ó 2003 International Society for Animal Genetics, Animal Genetics, 34, 334–338 334