Selective genotyping to identify late blight resistance genes in an accession of the tomato wild species Solanum pimpinellifolium Heather L. Merk • Hamid Ashrafi • Majid R. Foolad Received: 7 January 2012 / Accepted: 23 May 2012 Ó Springer Science+Business Media B.V. 2012 Abstract Late blight (LB), caused by the oomycete Phytophtohra infestans, is one of the most destructive diseases of tomato (Solanum lycopersicum) and other Solanaceae species. Current disease control and pre- vention strategies are not sufficient to control the disease in tomato. Recent germplasm screening experiments led to the identification of a new source of resistance (PI 270443) in the tomato wild species S. pimpinellifolium. This study was conducted to identify genomic regions associated with LB resistance in this accession. A large F 2 population (n = 986) derived from a cross between PI 270443 and a LB-susceptible tomato breeding line (NCEBR-2) was screened for LB resistance using a highly aggressive isolate of P. infestans. Twenty-five of the most resistant and 29 of the most susceptible, but surviving F 2 individuals were identified based on disease evaluations conducted in the F 2 and F 3 progeny populations. The selected individuals were genotyped with 153 DNA markers located across the 12 tomato chromosomes. A selective genotyping approach led to the identification of two genomic regions on tomato chromosomes 1 and 10 associated with LB resistance in PI 270443. Identification of two genomic regions associated with resistance was consistent with a previ- ous estimate of the number of LB resistance genes in this accession. Research is currently underway to fine map the two resistance genes and incorporate them into new tomato breeding lines and hybrid cultivars. Keywords Disease resistance  Phytophthora infestans  Qualitative resistance  Solanum pimpinellifolium  Trait-based analysis  Tomato  Resistance breeding  Vertical resistance Introduction Late blight (LB), an oomycete pathogen that gained notoriety as the causal agent of the Irish potato famine in the 1840s, has also greatly impacted tomato production worldwide (Foolad et al. 2008). Late blight can infect all above-ground plant parts, as well as potato tubers, with infection occurring at any time during the growing Electronic supplementary material The online version of this article (doi:10.1007/s10681-012-0729-6) contains supplementary material, which is available to authorized users. H. L. Merk  H. Ashrafi  M. R. Foolad (&) Department of Horticulture and the Intercollege Graduate Degree Program in Genetics, The Pennsylvania State University, University Park, PA 16802, USA e-mail: mrf5@psu.edu Present Address: H. L. Merk Department of Horticulture and Crop Sciences, OARDC, Ohio State University, 1680 Madison Avenue, Wooster, OH 44691, USA Present Address: H. Ashrafi Department of Plant Sciences, Seed Biotechnology Center, University of California, Davis, CA 95616, USA 123 Euphytica DOI 10.1007/s10681-012-0729-6