Small Ruminant Research 70 (2007) 32–41 Integration of molecular and quantitative information in sheep and goat industry breeding programmes  K.G. Dodds ∗ , J.C. McEwan, G.H. Davis AgResearch, Invermay Agricultural Centre, Private Bag 50034, Mosgiel, New Zealand Available online 12 February 2007 Abstract Molecular information is finding increasing use in sheep and goat breeding programs, as systems become available to make use of this information and the cost of obtaining the information declines. Genetic markers have been used for parentage verification or determination, for product tracing or brand protection, and for assisting selection decisions for production or breeding stock. The predominant uses of markers in selection have been in selecting for scrapie resistance, high prolificacy and for increased size of higher value muscles. Most of these applications of selection have placed preferential emphasis on the favourable gene variant, and quantitative information is used to select within genotype. The sophisticated use of molecular and quantitative information on an industry-wide scale will require robust systems that can cope with imperfect data as well as development of selection indices to take full advantage of the information. The prospect for further increases in the use of molecular information looks bright. © 2007 Elsevier B.V. All rights reserved. Keywords: Genetic markers; Selection; Genotype 1. Introduction The use of quantitative information in livestock breeding programmes has become more sophisticated over time in order to allow breeders to make faster progress in a chosen set of traits. Quantitative infor- mation was initially used in mass selection, whereby individuals with better trait values were chosen to be parents of the next generation. This progressed to using information from relatives and multiple traits, by assum- ing an infinitesimal (and usually additive) model of inheritance. This models a trait as being influenced by a large (infinite) number of genes each with an infinitely  This paper is part of the special issue entitled “The Outlook of Quantitative and Molecular Genetics Applications in Improving Sheep and Goats” guest edited by David Notter, R. Leyden Baker and Noelle Cockett. ∗ Corresponding author. Tel.: +64 3489 9083; fax: +64 3489 9037. E-mail address: ken.dodds@agresearch.co.nz (K.G. Dodds). small effect. The proportion of total variance accounted for by these genes is the heritability. This model has worked remarkably well, and has allowed much progress in genetic merit. Even so, it has been recognised that the model is incorrect (there must be a finite set of genes having an influence) and that it is possible to detect and use genes with noticeable effects. Such genes could be detected as segregation in pedigrees, either by observation (in the case of extreme effects) or by sophisticated statistical analysis (Janss et al., 1995; Kerr and Kinghorn, 1996). The advent of easily scored genetic markers (i.e., molecular informa- tion) spaced across the genome of a species has allowed the inheritance of each position in the genome to be traced from parents to progeny, and consequently has allowed more powerful tests of segregation to be devel- oped. Genes that are detected with this methodology are known as quantitative trait loci (QTL). The identifica- tion and characterisation of QTL allows for their use in genetic improvement programmes, either through the 0921-4488/$ – see front matter © 2007 Elsevier B.V. All rights reserved. doi:10.1016/j.smallrumres.2007.01.010