Molecular Breeding 5: 33–42, 1999. © 1999 Kluwer Academic Publishers. Printed in the Netherlands. 33 Detection of linked QTL for soybean brown stem rot resistance in ‘BSR 101’ as expressed in a growth chamber environment ∗ K.S. Lewers 1 , E.H. Crane 2 , C.R. Bronson 2 , J.M. Schupp 3 , P. Keim 3 & R.C. Shoemaker 4,∗ 1 USDA-ARS-SARL, Bldg. 006, BARC-W, 10300 Baltimore Blvd., Beltsville, MD 20705-2350, USA; 2 Dept. of Plant Pathology, Iowa State University, Ames, IA 50011, USA; 3 Dept. of Biological Sciences, Northern Arizona Univer- sity, Flagstaff, AZ 86011-5640, USA; 4 USDA-ARS-CICGR and Dept. of Agronomy and Dept. of Zoology/Genetics, Iowa State University, Ames, IA 50011, USA ( ∗ author for correspondence; e-mail rcsshoe@iastate.edu) Received 12 March 1998; accepted in revised form 17 August 1998 Key words: brown stem rot, composite interval mapping, disease resistance QTL, Phialophora gregata, resistance gene analogue, soybean Abstract The objective of this study was to map the gene(s) conferring resistance to brown stem rot in the soybean cultivar BSR 101. A population of 320 recombinant inbred lines (RIL) was derived from a cross of BSR 101 and PI 437.654. Seedlings of each RIL and parent were inoculated by injecting stems with a suspension of spores and mycelia of Phialophora gregata, incubated in a growth chamber at 17 ◦ C, and assessed for resistance by monitoring the devel- opment of foliar and stem symptoms. The population also was evaluated with 146 RFLPs, 760 AFLPs, and 4 probes for resistance gene analogs (RGAs). Regression analysis identified a significant association between resistance and several markers on Linkage Group J of the USDA-ARS molecular marker linkage map. Interval analysis with Mapmaker QTL identified a major peak between marker RGA2V-1 and AFLP marker AAGATG152M on Linkage Group J. A second peak, associated only with stem symptoms, was identified between the RFLP B122I-1 and RGA2V-1, also on Linkage Group J. When composite interval mapping with QTL Cartographer was used, two linked QTL were identified with both foliar and stem disease assessment methods: a major QTL between AFLP markers AAGATG152E and ACAAGT260, and a minor QTL between RGA3I-3 and RGA3I-2. These results demonstrate that composite interval mapping gives increased precision over interval mapping and is capable of distinguishing two linked QTL. The minor QTL associated with the cluster of RGA3I loci is of special interest because it is the first example of a disease resistance QTL associated with a resistance gene analog. Introduction Brown stem rot (BSR) is one of the most fre- quently occurring and devastating diseases of soybean (Glycine max (L.) Merr.) in the North Central U.S. and in Canada [2]. It is caused by the soil-borne fungus Phialophora gregata (Allington and Chamberlain) W. Gams. Symptoms include interveinal chlorosis, necro- sis, premature leaf abscission, internal stem browning, ∗ Joint contribution of the USDA-ARS-CIGR, and Journal Paper J-17789 of the Iowa Agriculture and Home Economics Ex- periment Station, Ames, Iowa. Project No. 3236, and supported by Hatch Act and State of Iowa and the Iowa Soybean Promotion Board. and grain yield loss. Infected plants can exhibit re- duced photosynthate availability during seed filling that results in yield loss as high as 66% [9]. Resistance to BSR was first identified in PI 84946-2 [5]. Resistance is controlled by two dominant genes in PI 84946-2 and by a single dominant gene in L78-4094, derived from PI 84946-2 [27]. The single resistance gene in L78-4094 was designated Rbs 1 . Al- lelism tests with L78-4094 and PI 437833 were used to distinguish Rbs 1 from a second resistance gene, des- ignated Rbs 2 [14]. A third resistance gene, Rbs 3 , was identified in PI 437970 [38]. Other resistance sources have been identified, but their genetic control has not yet been determined [24, 36, 37, 39].