Euphytica (2008) 162:231–239 DOI 10.1007/s10681-007-9558-4 123 Mapping QTL tolerance to Phytophthora root rot in soybean using microsatellite and RAPD/SCAR derived markers Yingpeng Han · Weili Teng · Kangfu Yu · Vaino Poysa · Terry Anderson · Lijuan Qiu · David A. Lightfoot · Wenbin Li Received: 8 July 2007 / Accepted: 22 August 2007 / Published online: 4 September 2007  Springer Science+Business Media B.V. 2007 Abstract Broad tolerance to phytophthora root rot (PRR) caused by Phytophthora sojae has become an important goal for the improvement of soybean (Glycine max) because of the rapid spread of races that defeat the available resistance genes. The aim of this research was to identify the location of quantita- tive trait loci (QTL) in ‘Conrad’, a soybean cultivar with broad tolerance to many races of P. sojae. A PRR susceptible breeding line ‘OX760-6-1’was crossed with Conrad. Through single-seed-descent, 112, F 2 derived, F 7 recombinant inbred lines (RILs) were advanced. A total of 39 random ampliWed polymorphic DNA bands (RAPDs) and 89 type 1 microsatellite (simple sequence repeat; SSR) markers were used to construct a genetic linkage map. In the greenhouse, RILs were inoculated with four P. sojae isolates (three from China and one from Canada). Disease was measured as the percent of dead plants 20 days after germination in P. sojae inoculated vermiculite in the greenhouse. Three QTLs (QGP1, QGP2, QGP3) for PRR tolerance in the greenhouse were detected using WinQTLCart 2.0 with a log-like- lihood (LOD) score 27.14 acquired through permuta- tions (1,000 at P · 0.05). QGP1 (near Satt509) was located at linkage group F and explained 13.2%, 5.9%, and 6.7% of the phenotypic variance for tolerance to the JiXi, JianSanJiang and ShuangYaShan isolates, respectively. QGP2 (near Satt334) was located in a diVerent interval on linkage group F and explained 5.1% and 2.4% of the phenotypic variance for JiXi and ShuangYaShan isolates, respectively. QGP3 was located on linkage group D1b + W (near OPL18 800 / SCL18 659 ) and explained 10.2% of the phenotypic variance for Woodslee isolate. QGP1 and QGP2 appeared to be associated with PRR tolerance across a range of isolates but QGP3 was active only against the Woodslee isolate. At Woodslee and Weaver (in Ontario) in 2000, the interval associated with QGP3 explained 21.6% and 16.7% of phenotypic variance in resistance to PRR, respectively and was referred as QFP1. The identiWed QTLs would be beneWcial for marker assistant selection of PRR tolerance varieties against both China and North America P. sojae races. Yingpeng Han and Weili Teng have equal contribution to the paper. Y. Han · W. Teng · W. Li (&) Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, China e-mail: wenbinli@neau.edu.cn K. Yu · V. Poysa · T. Anderson Greenhouse and Processing Crops Research Centre, Agriculture and Agri-Food Canada, Harrow, ON Canada, N0R 1G0 L. Qiu Institute of Crop Science, Chinese Academy of Agriculture, Beijing, 100081, China D. A. Lightfoot Centers for Excellence in Soybean Research, Southern Illinois University, Carbondale, IL 62901, USA