Identi®cation of porcine Lhx3 and SF1 as candidate genes for QTL affecting growth and reproduction traits in swine T. P. L. Smith*, A. D. Showalter ² , K. W. Sloop ² , G. A. Rohrer*, S. C. Fahrenkrug*, B. C. Meier ² and S. J. Rhodes ² *USDA, ARS, U.S. Meat Animal Research Center, PO Box 166, Clay Center, NE 68933, USA. ² Department of Biology, Indiana University-Purdue University, Indianapolis, IN 46202, USA. Summary The distal portion of the long arm of porcine chromosome 1 has been shown to harbour several quantitative trait loci affecting growth and reproductive traits in swine. In order to identify potential candidate genes that might underlie these effects, a comparative mapping analysis was undertaken to de®ne the extent of orthologous segments of human chromosome 9. A microsatellite associated with heat shock protein (HSP) A5 was used to de®ne the proximal boundary of the quantitative trait loci (QTL) region, which suggests the human orthologue of the gene(s) responsible for the observed effects lies between HSPA5 and the q arm telomere of human chromosome 9. Examination of this region revealed two candidate genes with known roles in production of hormones essential to growth and reproductive function. The steroidogenic factor 1 and Lhx3 LIM homeodomain transcription factor genes were mapped to 123 and 155 cM, respect- ively, of the Sus scrofa chromosome 1 (SSC1) linkage group, placing both genes within the con®dence interval for the observed QTL. To further evaluate Lhx3, we examined the expression pro®le during porcine embryonic development. Low levels were detected at early embryonic stages, when development of the nervous system is proceeding. A transient increase in expression level is observed during the time of pituitary orga- nogenesis and again at the time of differentiation of anterior pituitary cells, with rel- atively high levels of expression persisting in the adult pituitary gland. This ontology is consistent with Lhx3 being a candidate gene for the QTL. Keywords growth, reproduction, mapping, pituitary, QTL. Introduction Development of genetic maps of swine in the past decade has allowed identi®cation of quantitative trait loci (QTL) affecting a variety of traits of economic importance. While these results are promising with respect to potential improvement of pork production through marker-assisted selection procedures, it would be of signi®cant interest to identify the genes and speci®c allelic polymorphisms underlying the observed variation. This achievement would allow development of speci®c DNA-based genetic tests to evaluate individual animals for merit and genetic potential, as well as increase understanding of the genetic basis underlying non-disease producing variability among popu- lations. However, identi®cation of genes and DNA sequence differences that contribute to relatively minor (but still of substantial economic importance) variation in phenotype is a daunting task. The most promising avenue is the appli- cation of comparative mapping, making use of the wealth of knowledge and resources produced from the human genome project and biomedical research community. Genomic scans of a Meishan±White Composite reciprocal backcross resource population have identi®ed a number of QTL affecting traits of economic importance (Rohrer et al. Address for correspondence Timothy P. L. Smith, U.S. Meat Animal Research Center, PO Box 166, Clay Center, NE 68933±0166, USA. E-mail: smith@e-mail.marc.usda.gov Accepted for publication 3 July 2001 Ó 2001 International Society for Animal Genetics Animal Genetics, 32, 344±350